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Information on EC 3.1.4.52 - cyclic-guanylate-specific phosphodiesterase
for references in articles please use BRENDA:EC3.1.4.52
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EC Tree 3 Hydrolases
3.1 Acting on ester bonds
3.1.4 Phosphoric-diester hydrolases
3.1.4.52 cyclic-guanylate-specific phosphodiesterase
IUBMB Comments
Requires Mg2+ or Mn2+ for activity and is inhibited by Ca2+ and Zn2+. Contains a heme unit. This enzyme linearizes cyclic di-3′,5′-guanylate, the product of EC 2.7.7.65, diguanylate cyclase and an allosteric activator of EC 2.4.1.12, cellulose synthase (UDP-forming), rendering it inactive . It is the balance between these two enzymes that determines the cellular level of c-di-GMP .
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
showSynonyms
hd-gyp, c-di-gmp phosphodiesterase, phosphodiesterase a, blrp1, putative uncharacterized protein, pa4781, cyclic di-gmp phosphodiesterase, c-di-gmp-specific phosphodiesterase, pde-a, pa4108, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
BifA
BlrP1
-
also known as KPN 01598, BlrP1 consists of a BLUF sensor domain and a phosphodiesterase EAL output domain which hydrolyses cyclic dimeric GMP, so BlrP1 possesses c-di-GMP-phosphodiesterase activity
c-di-GMP hydrolysis protein 1
c-di-GMP PDE
c-di-GMP phosphodiesterase
c-di-GMP-hydrolyzing-phosphodiesterase
c-di-GMP-specific PDE
c-di-GMP-specific phosphodiesterase
c-di-GMP/cGAMP degrading phosphodiesterase VcEAL
CdpA
chp1
cyclic di-GMP phosphodiesterase
cyclic di-GMP-specific phosphodiesterase
cyclic-di-GMP phosphodiesterase
GAF/HD-GYP protein
HD-GYP
HD-GYP domain cyclic-di-GMP phosphodiesterase
HD-GYP phosphodiesterase
NbdA
PA3947
PAS-GGDEF-EAL domain-containing protein
PdcB
PDE
PdeA
PdeB
PdeH
perma_0986
PmGH
Putative uncharacterized protein
RapA
RavR
RbdA
RocR
SO0437
Tlr0485
TM0186
TM_0186
VC1710
HD-GYP
Vibrio cholerae serotype O1 El Tor C6706
-
-
-
PdeA
-
containing HD-GYP or EAL domains (associated with cyclic di-3',5'-guanylate degradation), RavR (Xcc1958, originally named PdeA) encodes a response regulator with an GGDEF-EAL fusion domain, RavS (regulation of adaptation and virulence, sensor) encoded by Xcc1960, in the genome of Xanthomonas campestris pv. campestris strain ATCC33913
PdeA
containing HD-GYP or EAL domains (associated with c-di-GMP degradation), RavR (Xcc1958, originally named RdeA) encodes a response regulator with an GGDEFEAL fusion domain, RavS (regulation of adaptation and virulence, sensor) encoded by Xcc1960. ravS and ravR belong to the same operon in strain XC1
PdeA
-
containing HD-GYP or EAL domains (associated with cyclic di-3',5'-guanylate degradation), RavR (Xcc1958, originally named PdeA) encodes a response regulator with an GGDEF-EAL fusion domain, RavS (regulation of adaptation and virulence, sensor) encoded by Xcc1960, in the genome of Xanthomonas campestris pv. campestris strain ATCC33913
-
PdeA
containing HD-GYP or EAL domains (associated with c-di-GMP degradation), RavR (Xcc1958, originally named RdeA) encodes a response regulator with an GGDEFEAL fusion domain, RavS (regulation of adaptation and virulence, sensor) encoded by Xcc1960. ravS and ravR belong to the same operon in strain XC1
-
RocR
the EAL domain of RocR is catalytically active with cyclic di-GMP-specific phosphodiesterase activity
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cyclic di-3',5'-guanylate + H2O = 5'-phosphoguanylyl(3'->5')guanosine
-
-
-
-
cyclic di-3',5'-guanylate + H2O = 5'-phosphoguanylyl(3'->5')guanosine
hydrolysis of cyclic di-GMP by a general base-catalyzed mechanism with the assistance of a Mg2+ ion, the essential residue E352 functions as a general base catalyst assisting the deprotonation of Mg2+-coordinated water to generate the nucleophilic hydroxide ion, reaction mechanism, residue positioning, and substrate binding, overview
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric diester
hydrolysis of phosphoric diester
Vibrio cholerae serotype O1 El Tor C6706
-
-
-
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SYSTEMATIC NAME
IUBMB Comments
cyclic bis(3->5')diguanylate 3-guanylylhydrolase
Requires Mg2+ or Mn2+ for activity and is inhibited by Ca2+ and Zn2+. Contains a heme unit. This enzyme linearizes cyclic di-3',5'-guanylate, the product of EC 2.7.7.65, diguanylate cyclase and an allosteric activator of EC 2.4.1.12, cellulose synthase (UDP-forming), rendering it inactive [1]. It is the balance between these two enzymes that determines the cellular level of c-di-GMP [1].
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CAS REGISTRY NUMBER
COMMENTARY
338732-46-0
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
5'-phosphoguanylyl(3'-5')guanosine + H2O
guanosine 5'-monophosphate + guanosine
-
Substrates: -
Products: -
Products: -
?
5'-phosphoguanylyl(3'->5')guanosine + H2O
GMP + guanosine
Substrates: the isozyme hydrolyses c-di-GMP in a two-step reaction via the linear intermediate 5'-phosphoguanylyl(3'->5')guanosine, it produces GMP in vitro at a low rate, reaction of EC 3.1.4.1
Products: -
Products: -
?
3',5'-di-cGMP + H2O
5'-phosphoguanylyl-(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
3',5'-di-cGMP + H2O
5'-phosphoguanylyl-(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
3',5'-di-cGMP + H2O
5'-phosphoguanylyl-(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
3'3'-cyclic GMP-AMP + H2O
?
Substrates: -
Products: -
Products: -
?
3'3'-cyclic GMP-AMP + H2O
?
Substrates: -
Products: -
Products: -
?
5'-phosphoguanylyl-(3'->5')guanosine + H2O
2 5'-GMP
Substrates: -
Products: -
Products: -
?
5'-phosphoguanylyl-(3'->5')guanosine + H2O
2 5'-GMP
Substrates: -
Products: -
Products: -
?
5'-phosphoguanylyl-(3'->5')guanosine + H2O
2 5'-GMP
Substrates: -
Products: -
Products: -
?
c-di-GMP + H2O
?
Substrates: -
Products: -
Products: -
?
c-di-GMP + H2O
?
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: BB0374/PdeB specifically hydrolyzed cyclic di-GMP
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: specific substrate
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: enzyme has no diguanylate cyclase activity
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: degradation
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
Substrates: RocR, an EAL domain protein that regulates the expression of virulence genes and biofilm formation in Pseudomonas aeruginosa PAO1, catalyzes the hydrolysis of cyclic di-GMP by using a general base-catalyzed mechanism with the assistance of Mg2+ ion
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
-
Substrates: -
Products: final product is GMP
Products: final product is GMP
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
-
Substrates: -
Products: final product is GMP
Products: final product is GMP
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: the isozyme hydrolyses c-di-GMP in a two-step reaction via the linear intermediate 5'-phosphoguanylyl(3'->5')guanosine, it produces GMP in vitro at a low rate
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Pseudomonas aeruginosa KT1115
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Shewanella oneidensis MR-1 / ATCC 700550
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: no activity with cAMP and cGMP
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Thermosynechococcus vestitus NIES-2133
Substrates: no activity with cAMP and cGMP
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'phosphoguanylyl(3'-5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'phosphoguanylyl(3'-5')guanosine
Vibrio cholerae serotype O1 El Tor C6706
-
Substrates: -
Products: -
Products: -
?
additional information
?
-
-
Substrates: CD0522 has dual enzymatic activity, as cyclic di-GMP phosphodiestrase and as diguanylate cyclase
Products: -
Products: -
?
additional information
?
-
-
Substrates: enzyme plays a protective role in response to oxidative stress
Products: -
Products: -
?
additional information
?
-
-
Substrates: enzyme and cyclic guanylate cyclase YvvD a may be part of a fine-tuning mechanism for regulating the intracellular levels of cyclic diguanylate
Products: -
Products: -
?
additional information
?
-
-
Substrates: no substrates: cyclic guanosine monophosphate, cyclic adenosine monophosphate
Products: -
Products: -
?
additional information
?
-
-
Substrates: purified YfgF GGDEF-EAL (YfgFGE) and EAL (YfgFE) domains possess cyclic di-GMP-specific phosphodiesterase activity, but lack diguanylate cyclase activity
Products: -
Products: -
?
additional information
?
-
-
Substrates: Protein Rv 1357c, named as MtbPDE, is an EAL domain protein and degrades cyclic di-GMP to pGpG in vitro. MtbDGC is a bifunctional protein, which can synthesize and degrade cyclic di-GMP in vitro
Products: -
Products: -
?
additional information
?
-
-
Substrates: substrate and product binding structures, overview
Products: -
Products: -
?
additional information
?
-
-
Substrates: substrate and product binding structures, overview
Products: -
Products: -
?
additional information
?
-
-
Substrates: purified enzyme shows phosphodiesterase activity, but no diguanylate cyclase activity
Products: -
Products: -
?
additional information
?
-
-
Substrates: Arr is required for induction of biofilms under DNA replication stress by a mechanism of stimulated adhesion of planktonic filaments having impaired DNA replication, the induction is suppressed by either inhibition or mutation of the c-di-GMP phosphodiesterase, overview
Products: -
Products: -
?
additional information
?
-
-
Substrates: no hydrolysis of cyclic AMP and cyclic GMP
Products: -
Products: -
?
additional information
?
-
Substrates: no hydrolysis of cyclic AMP and cyclic GMP
Products: -
Products: -
?
additional information
?
-
-
Substrates: phosphodiesterase RapA is an inhibitor of biofilm formation in response to limiting phosphate supply. Enzyme lowers the levels of cyclic diguanylate which in turn inhibits the secretion of protein LapA required fro biofilm formation
Products: -
Products: -
?
additional information
?
-
-
Substrates: phosphodiesterase RapA is an inhibitor of biofilm formation in response to limiting phosphate supply. Enzyme lowers the levels of cyclic diguanylate which in turn inhibits the secretion of protein LapA required fro biofilm formation
Products: -
Products: -
?
additional information
?
-
-
Substrates: CdgC regulates expression of genes required for Vibrio cholerae polysaccharide synthesis and the transcriptional regulator genes vpsR, vpsT, and hapR. CdgC also regulates expression of genes involved in extracellular protein secretion, flagellar biosynthesis, and virulence factor production. The regulons of CdgC and MbaA overlap, but with different timing
Products: -
Products: -
?
additional information
?
-
-
Substrates: no substrate: cyclic guanosine monophosphate
Products: -
Products: -
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
3',5'-di-cGMP + H2O
5'-phosphoguanylyl-(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
3',5'-di-cGMP + H2O
5'-phosphoguanylyl-(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
3',5'-di-cGMP + H2O
5'-phosphoguanylyl-(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
5'-phosphoguanylyl-(3'->5')guanosine + H2O
2 5'-GMP
Substrates: -
Products: -
Products: -
?
5'-phosphoguanylyl-(3'->5')guanosine + H2O
2 5'-GMP
Substrates: -
Products: -
Products: -
?
5'-phosphoguanylyl-(3'->5')guanosine + H2O
2 5'-GMP
Substrates: -
Products: -
Products: -
?
c-di-GMP + H2O
?
Substrates: -
Products: -
Products: -
?
c-di-GMP + H2O
?
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: BB0374/PdeB specifically hydrolyzed cyclic di-GMP
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: degradation
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
Substrates: RocR, an EAL domain protein that regulates the expression of virulence genes and biofilm formation in Pseudomonas aeruginosa PAO1, catalyzes the hydrolysis of cyclic di-GMP by using a general base-catalyzed mechanism with the assistance of Mg2+ ion
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'-5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
-
Substrates: -
Products: final product is GMP
Products: final product is GMP
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
-
Substrates: -
Products: final product is GMP
Products: final product is GMP
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Shewanella oneidensis MR-1 / ATCC 700550
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'-phosphoguanylyl(3'->5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'phosphoguanylyl(3'-5')guanosine
-
Substrates: -
Products: -
Products: -
?
cyclic di-3',5'-guanylate + H2O
5'phosphoguanylyl(3'-5')guanosine
Vibrio cholerae serotype O1 El Tor C6706
-
Substrates: -
Products: -
Products: -
?
additional information
?
-
-
Substrates: enzyme plays a protective role in response to oxidative stress
Products: -
Products: -
?
additional information
?
-
-
Substrates: enzyme and cyclic guanylate cyclase YvvD a may be part of a fine-tuning mechanism for regulating the intracellular levels of cyclic diguanylate
Products: -
Products: -
?
additional information
?
-
-
Substrates: purified YfgF GGDEF-EAL (YfgFGE) and EAL (YfgFE) domains possess cyclic di-GMP-specific phosphodiesterase activity, but lack diguanylate cyclase activity
Products: -
Products: -
?
additional information
?
-
-
Substrates: Protein Rv 1357c, named as MtbPDE, is an EAL domain protein and degrades cyclic di-GMP to pGpG in vitro. MtbDGC is a bifunctional protein, which can synthesize and degrade cyclic di-GMP in vitro
Products: -
Products: -
?
additional information
?
-
-
Substrates: Arr is required for induction of biofilms under DNA replication stress by a mechanism of stimulated adhesion of planktonic filaments having impaired DNA replication, the induction is suppressed by either inhibition or mutation of the c-di-GMP phosphodiesterase, overview
Products: -
Products: -
?
additional information
?
-
-
Substrates: phosphodiesterase RapA is an inhibitor of biofilm formation in response to limiting phosphate supply. Enzyme lowers the levels of cyclic diguanylate which in turn inhibits the secretion of protein LapA required fro biofilm formation
Products: -
Products: -
?
additional information
?
-
-
Substrates: phosphodiesterase RapA is an inhibitor of biofilm formation in response to limiting phosphate supply. Enzyme lowers the levels of cyclic diguanylate which in turn inhibits the secretion of protein LapA required fro biofilm formation
Products: -
Products: -
?
additional information
?
-
-
Substrates: CdgC regulates expression of genes required for Vibrio cholerae polysaccharide synthesis and the transcriptional regulator genes vpsR, vpsT, and hapR. CdgC also regulates expression of genes involved in extracellular protein secretion, flagellar biosynthesis, and virulence factor production. The regulons of CdgC and MbaA overlap, but with different timing
Products: -
Products: -
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
heme
-
enzyme is regulated via reversible binding of O2 to the heme. Apo-enzyme has less than 2% of phosphodiesterase activity of holo-enzyme. The rate of enzyme autoxidation is the slowest observed so far for this type of heme protein with half-life above 12 h
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
Fe2+
-
trinuclear Fe binding site located at the bottom of the HD-GYP domain cavity formed by the two claws of the open chela. Residues E185, H189, H221, D222, H250, H276, H277, and D305 are involved in metal binding
Iron
Mg2+
Mn2+
additional information
Co2+
activity of is highest in the presence of Co2+ which is a bout 1.5 times higher than that of Mn2+ or twice than that of Mg2+, respectively. Ca2+, Fe2+, Ni2+, Zn2+ do not support activity
Iron
-
heme protein with remarkable stability against electron transfer to O2. Oxy-enzyme is only 30% oxidized to the ferric form after 8 h in airsaturated Tris buffer pH 8.0, 23°C
Mg2+
-
or Mn2+, absolutely required, with Mn2+ being slightly more efficient
Mg2+
-
required, best at 10 mM for both YfgF GGDEF-EAL (YfgFGE) and EAL (YfgFE) domains
Mg2+
-
or Mn2+, required, with Mg2+ being more efficient. Enzyme activity increases with with increasing Mg2+ concentration up to 25 mM MgCl2
Mg2+
activity of is highest in the presence of Co2+ which is a bout 1.5 times higher than that of Mn2+ or twice than that of Mg2+, respectively. Ca2+, Fe2+, Ni2+, Zn2+ do not support activity
Mn2+
-
or Mg2+, absolutely required, with Mn2+ being slightly more efficient
Mn2+
-
required, best at 10 mM for both YfgF GGDEF-EAL (YfgFGE) and EAL (YfgFE) domains
Mn2+
activity of is highest in the presence of Co2+ which is a bout 1.5 times higher than that of Mn2+ or twice than that of Mg2+, respectively. Ca2+, Fe2+, Ni2+, Zn2+ do not support activity
additional information
the enzyme can accommodate both di- and trimetal active sites. An as-isolated iron-containing TM0186 has an oxo/carboxylato-bridged diferric site, and the reduced diferrous form is necessary and sufficient to catalyze conversion of cyclic di-GMP to 5'-phosphoguanylyl(3',5')guanosine. Similar cyclic di-GMP phosphodiesterase activities are obtained with divalent iron or manganese. A Glu residue conserved in a subset of homologous enzymes is required for formation of the trimetal site and can also serve as a labile ligand to the dimetal site
additional information
-
the enzyme can accommodate both di- and trimetal active sites. An as-isolated iron-containing TM0186 has an oxo/carboxylato-bridged diferric site, and the reduced diferrous form is necessary and sufficient to catalyze conversion of cyclic di-GMP to 5'-phosphoguanylyl(3',5')guanosine. Similar cyclic di-GMP phosphodiesterase activities are obtained with divalent iron or manganese. A Glu residue conserved in a subset of homologous enzymes is required for formation of the trimetal site and can also serve as a labile ligand to the dimetal site
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
5'-phosphoguanylyl-(3'-5')-guanosine
-
the cyclic di-GMP phosphodiesterase activity of YfgFGE and YfgFE is inhibited by the reaction product
GTP
-
inhibition of the phosphodiesterase, reduction of tobramycin biofilm stimulation, and suppression of biofilm response, overview
N-(4-hydroxyphenyl)-4-(3-oxo-1,2-benzothiazol-2(3H)-yl)butanamide
compound inhibits Pseudomonas. aeruginosa (PAO1) swarming but not swimming or biofilm formation, it does not inhibit other Pseudomonas aeruginosa phosphodiesterases, such as DipA, PvrR and PA4108
Nalidixic acid
-
reduction of tobramycin biofilm stimulation and suppression of biofilm response, overview
additional information
-
inhibition of the enzyme leads to suppression of induction of biofilm formation
-
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
cyclic-di-GMP phosphodiesterase activity of CdpA is regulated by its inactive degenerate GGDEF domain
-
GTP
-
specifically activates phosphodiesterase activity by binding to GGDEF domain. Activation occurs via lowering the Km value for cyclic diguanylate, under physiological conditions enzyme activity is fully induced. KD value 0.004 mM
GTP
-
binds to the GGDEF domain which in turn activates the EAL domain
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Bacterial Infections
Cyclic di-GMP signalling in the virulence and environmental adaptation of Xanthomonas campestris.
Cholera
Role of cyclic Di-GMP during el tor biotype Vibrio cholerae infection: characterization of the in vivo-induced cyclic Di-GMP phosphodiesterase CdpA.
Confusion
Serum Proteomics of Older Patients Undergoing Major Cardiac Surgery: Identification of Biomarkers Associated With Postoperative Delirium.
Diabetes Mellitus, Type 2
Proteomic characterization of a second-generation version of the BCG?BCG1419c vaccine candidate by means of electrospray-ionization quadrupole time-of-flight mass spectrometry.
Infections
A systematic analysis of the in vitro and in vivo functions of the HD-GYP domain proteins of Vibrio cholerae.
Infections
Host cell contact induces expression of virulence factors and VieA, a cyclic di-GMP phosphodiesterase in Vibrio cholerae.
Infections
Proteomic characterization of a second-generation version of the BCG?BCG1419c vaccine candidate by means of electrospray-ionization quadrupole time-of-flight mass spectrometry.
Infections
Role of cyclic Di-GMP during el tor biotype Vibrio cholerae infection: characterization of the in vivo-induced cyclic Di-GMP phosphodiesterase CdpA.
Neoplasms
Abnormal regulation of cyclic AMP phosphodiesterase: a hypothesis for the development of cancer of nerve cells.
Pneumonia
Azithromycin Modulates 3',5'-cyclic Diguanylic Acid Signaling in Pseudomonas aeruginosa.
Salmonella Infections
The EAL domain containing protein STM2215 (rtn) is needed during Salmonella infection and has cyclic di-GMP phosphodiesterase activity.
Tuberculosis
Identification, activity and disulfide connectivity of C-di-GMP regulating proteins in Mycobacterium tuberculosis.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.017
5'-phosphoguanylyl(3'->5')guanosine
pH 8.0, 30°C, recombinant wild-type enzyme
0.027
5'-phosphoguanylyl(3'->5')guanosine
pH 8.0, 30°C, recombinant wild-type enzyme
0.03
5'-phosphoguanylyl(3'->5')guanosine
pH 8.0, 30°C, recombinant enzyme
0.0000029
cyclic di-3',5'-guanylate
-
pH and temperature not specified in the publication
0.0002
cyclic di-3',5'-guanylate
-
mutant RocR enzyme D56N, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
0.0003
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutant E268Q
0.0003
cyclic di-3',5'-guanylate
-
mutant RocR enzyme E268Q, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
0.00042
cyclic di-3',5'-guanylate
-
presence of 0.004 mM GTP, pH 8.0, 30°C
0.0007
cyclic di-3',5'-guanylate
-
mutant RocR enzyme F297A, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
0.0013
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutant Q372A
0.0022
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutants E352D and T267A
0.0026
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutant E355A
0.0032
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant wild-type RocR
0.0032
cyclic di-3',5'-guanylate
-
wild type RocR enzyme, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
0.0038
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutant E352Q
0.00458
cyclic di-3',5'-guanylate
pH and temperature not specified in the publication
0.0052
cyclic di-3',5'-guanylate
-
wild type PA2567 enzyme, in 100 mM Tris buffer (pH 8.0) (23°C), 50 mM KCl, and 10 mM MgCl2
0.0055
cyclic di-3',5'-guanylate
-
mutant RocR enzyme S302A, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
0.0059
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutant D318A
0.0063
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutant Q161A
0.00676
cyclic di-3',5'-guanylate
pH and temperature not specified in the publication, in the presence of the activator cAMP (0.002 mM)
0.0068
cyclic di-3',5'-guanylate
pH 8.0, 30°C, recombinant mutant enzyme E314A
0.008
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutant R179A
0.0086
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutant D296A
0.0086
cyclic di-3',5'-guanylate
-
mutant RocR enzyme D296A, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
0.0094
cyclic di-3',5'-guanylate
-
mutant RocR enzyme D56N/D296A, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
0.013
cyclic di-3',5'-guanylate
-
mutant PA2567 enzyme E464A, in 100 mM Tris buffer (pH 8.0) (23°C), 50 mM KCl, and 10 mM MgCl2
0.02
cyclic di-3',5'-guanylate
pH 8.0, 30°C, recombinant enzyme
0.119
cyclic di-3',5'-guanylate
pH 8.0, 30°C, recombinant wild-type enzyme
0.0003
cyclic-di-GMP
mutant enzyme E268Q, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.0013
cyclic-di-GMP
mutant enzyme Q372A, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.0022
cyclic-di-GMP
mutant enzyme T267A, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.0022
cyclic-di-GMP
mutant enzyme E352D, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.0026
cyclic-di-GMP
mutant enzyme E355A, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.0032
cyclic-di-GMP
wild type enzyme, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.0038
cyclic-di-GMP
mutant enzyme E352Q, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.0059
cyclic-di-GMP
mutant enzyme D318A, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.0063
cyclic-di-GMP
mutant enzyme Q161A, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.008
cyclic-di-GMP
mutant enzyme R179A, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.0086
cyclic-di-GMP
mutant enzyme D296A, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
additional information
additional information
-
steady-state kinetics of wild-type and mutant RocRs, overview
-
additional information
additional information
steady-state kinetics of wild-type and mutant RocRs, overview
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.00012
5'-phosphoguanylyl(3'->5')guanosine
pH 8.0, 30°C, recombinant enzyme
0.0002
5'-phosphoguanylyl(3'->5')guanosine
pH 8.0, 30°C, recombinant wild-type enzyme
0.00077
5'-phosphoguanylyl(3'->5')guanosine
pH 8.0, 30°C, recombinant wild-type enzyme
0.000011
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutant E352Q
0.000022
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutant E352D
0.00015
cyclic di-3',5'-guanylate
pH 8.0, 30°C, recombinant enzyme
0.0002
cyclic di-3',5'-guanylate
pH 8.0, 30°C, recombinant wild-type enzyme
0.0006
cyclic di-3',5'-guanylate
pH 8.0, 30°C, recombinant mutant enzyme E314A
0.0015
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutant E268Q
0.0015
cyclic di-3',5'-guanylate
-
mutant RocR enzyme E268Q, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
0.012
cyclic di-3',5'-guanylate
-
mutant RocR enzyme D56N/D296A, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
0.02
cyclic di-3',5'-guanylate
-
mutant RocR enzyme F297A, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
0.021
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutant D296A
0.021
cyclic di-3',5'-guanylate
-
mutant RocR enzyme D296A, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
0.023
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutant R179A
0.049
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutant T267A
0.08
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutants Q372A and D318A
0.13
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutant Q161A
0.13
cyclic di-3',5'-guanylate
-
mutant RocR enzyme D56N, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
0.13
cyclic di-3',5'-guanylate
-
wild type enzyme, at pH 7.5, 20°C, under dark conditions
0.14
cyclic di-3',5'-guanylate
-
mutant RocR enzyme S302A, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
0.27
cyclic di-3',5'-guanylate
-
mutant enzyme R93S, at pH 7.5, 20°C, under dark conditions
0.28
cyclic di-3',5'-guanylate
pH and temperature not specified in the publication, in the presence of the activator cAMP (0.002 mM)
0.39
cyclic di-3',5'-guanylate
-
wild type PA2567 enzyme, in 100 mM Tris buffer (pH 8.0) (23°C), 50 mM KCl, and 10 mM MgCl2
0.51
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant mutant E355A
0.54
cyclic di-3',5'-guanylate
-
wild type enzyme, at pH 7.5, 20°C, under light conditions
0.64
cyclic di-3',5'-guanylate
-
wild type enzyme, in the presence of 10 mM Mn2+, at pH 7.5, 20°C, under dark conditions
0.67
cyclic di-3',5'-guanylate
pH 8.0, 23°C, recombinant wild-type RocR
0.67
cyclic di-3',5'-guanylate
-
wild type RocR enzyme, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
1.1
cyclic di-3',5'-guanylate
-
mutant PA2567 enzyme E464A, in 100 mM Tris buffer (pH 8.0) (23°C), 50 mM KCl, and 10 mM MgCl2
1.17
cyclic di-3',5'-guanylate
-
wild type enzyme, in the presence of 10 mM Mn2+, at pH 7.5, 20°C, under light conditions
1.42
cyclic di-3',5'-guanylate
-
mutant enzyme R93S, at pH 7.5, 20°C, under light conditions
1.84
cyclic di-3',5'-guanylate
-
wild type enzyme, at pH 8.0, 20°C, under dark conditions
2.06
cyclic di-3',5'-guanylate
-
mutant enzyme L128C/G353C, at pH 7.5, 20°C, under dark conditions
2.54
cyclic di-3',5'-guanylate
-
wild type enzyme, at pH 8.0, 20°C, under light conditions
3.48
cyclic di-3',5'-guanylate
-
mutant enzyme L128C/G353C, at pH 7.5, 20°C, under light conditions
6.17
cyclic di-3',5'-guanylate
-
wild type enzyme, at pH 9.3, 20°C, under light conditions
6.7
cyclic di-3',5'-guanylate
-
wild type enzyme, at pH 9.3, 20°C, under dark conditions
0.000011
cyclic-di-GMP
mutant enzyme E352Q, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.000022
cyclic-di-GMP
mutant enzyme E352D, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.0015
cyclic-di-GMP
mutant enzyme E268Q, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.021
cyclic-di-GMP
mutant enzyme D296A, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.023
cyclic-di-GMP
mutant enzyme R179A, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.049
cyclic-di-GMP
mutant enzyme T267A, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.08
cyclic-di-GMP
mutant enzyme D318A, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.08
cyclic-di-GMP
mutant enzyme Q372A, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.13
cyclic-di-GMP
mutant enzyme Q161A, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.51
cyclic-di-GMP
mutant enzyme E355A, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
0.67
cyclic-di-GMP
wild type enzyme, in 100 mM Tris buffer (pH 8.0) with 20 mM KCl and 25 mM MgCl2
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2.1
cyclic di-3',5'-guanylate
-
mutant RocR enzyme D56N/D296A, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
2.7
cyclic di-3',5'-guanylate
-
mutant RocR enzyme D296A, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
4.8
cyclic di-3',5'-guanylate
-
mutant RocR enzyme E268Q, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
25
cyclic di-3',5'-guanylate
-
mutant RocR enzyme S302A, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
28
cyclic di-3',5'-guanylate
-
mutant RocR enzyme F297A, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
75
cyclic di-3',5'-guanylate
-
wild type PA2567 enzyme, in 100 mM Tris buffer (pH 8.0) (23°C), 50 mM KCl, and 10 mM MgCl2
84
cyclic di-3',5'-guanylate
-
mutant PA2567 enzyme E464A, in 100 mM Tris buffer (pH 8.0) (23°C), 50 mM KCl, and 10 mM MgCl2
210
cyclic di-3',5'-guanylate
-
wild type RocR enzyme, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
650
cyclic di-3',5'-guanylate
-
mutant RocR enzyme D56N, in 100 mM Tris buffer (pH 8.0) (23°C), 20 mM KCl, and 25 mM MgCl2
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.12
-
hydrolysis of 5-phosphoguanylyl(3-5)guanosine, recombinant enzyme, pH 8.0, 30°C
2.42
-
synthesis of 5-phosphoguanylyl(3-5)guanosine, recombinant enzyme, pH 8.0, 30°C
additional information
additional information
-
Xanthomonas campestris XC1 wild-type activity 100%, Xanthomonas campestris XC1 mutant lacking ravR 62%, Xanthomonas campestris XC1 mutant lacking ravR transformed with GGDEFEAL fusion domain almost 100%, Xanthomonas campestris XC1 mutant lacking ravR transformed with GGDEF domain 62%, Xanthomonas campestris XC1 mutant lacking ravR transformed with EAL domain almost 100%, Xanthomonas campestris XC1 mutant lacking ravR transformed with mutated EAL domain (DAA): 62%
additional information
Xanthomonas campestris XC1 wild-type activity 100%, Xanthomonas campestris XC1 mutant lacking ravR 62%, Xanthomonas campestris XC1 mutant lacking ravR transformed with GGDEFEAL fusion domain almost 100%, Xanthomonas campestris XC1 mutant lacking ravR transformed with GGDEF domain 62%, Xanthomonas campestris XC1 mutant lacking ravR transformed with EAL domain almost 100%, Xanthomonas campestris XC1 mutant lacking ravR transformed with mutated EAL domain (DAA): 62%
additional information
Xanthomonas campestris XC1 wild-type activity 100%, Xanthomonas campestris XC1 mutant lacking ravR 62%, Xanthomonas campestris XC1 mutant lacking ravR transformed with GGDEFEAL fusion domain almost 100%, Xanthomonas campestris XC1 mutant lacking ravR transformed with GGDEF domain 62%, Xanthomonas campestris XC1 mutant lacking ravR transformed with EAL domain almost 100%, Xanthomonas campestris XC1 mutant lacking ravR transformed with mutated EAL domain (DAA): 62%
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
7.6
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5 - 9
-
no significant changes in reaction rates within this range
6.2 - 9.5
pH profiles of recombinant wild-type and mutant E352Q enzymes
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
37
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
conditional expression of phosphodiesterase RapA upon exposure to phosphate. Expression is mediated by the Pho regulon
-
-
brenda
conditional expression of phosphodiesterase RapA upon exposure to phosphate. Expression is mediated by the Pho regulon
-
-
brenda
enzyme Blrp undergoes a reversible photocycle upon exposure to light
-
-
brenda
protein FimX with both GGDEF and EAL domains. FimX is involved in assembly of type IV pili
-
-
brenda
strain PA14, gene PA4367 encodes a protein with an EAL domain associated with cyclic di-3'5'-guanylate phosphodiesterase activity, and a DDGEF domain associated with cyclic di-di-3'5'-guanylate cyclase activity
-
-
brenda
expression of genes cdgC and mbaA harboring both EAL and GGDEF motifs is higher in the rugose phase variant than in the smooth variant. CdgC regulates expression of genes required for Vibrio cholerae polysaccharide synthesis and the transcriptional regulator genes vpsR, vpsT, and hapR. CdgC also regulates expression of genes involved in extracellular protein secretion, flagellar biosynthesis, and virulence factor production. The regulons of CdgC and MbaA overlap, but with different timing
-
-
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
-
anaerobic expression of yfgF is greatest in stationary phase, and in cultures grown at 28°C
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
restriction of protein to a single pole requires intact GGDEF and EAL domains
brenda
the transmembrane protein contains two transmembrane segments, positions 7 to 29 and 230 to 252
brenda
Shewanella oneidensis MR-1 / ATCC 700550
-
the transmembrane protein contains two transmembrane segments, positions 7 to 29 and 230 to 252
-
brenda
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
PipA is highly conserved across 83 Pseudomonas aeruginosa strains
malfunction
metabolism
physiological function
additional information
malfunction
-
deletion of bpdA results in a dramatic decrease in flagellar promoter activities, and a flagellar mutant shows similar phenotypes to the bpdA and bpdB mutant strains in mouse models of infection. Genes bpdA and bpdB mutants exhibit decreased dissemination within immunocompetent mice
malfunction
-
mutation of rbdA, which encodes a fusion protein consisting of PAS-PAC-GGDEF-EAL multidomains, results in decreased biofilm dispersal
malfunction
-
overexpression of BinA enhances motility. Disruption or deletion of binA increased biofilm formation in culture and leads to increased cellulose production. The phenotypes of the DELTAbinA mutant strain can be disrupted by insertions in genes in the bacterial cellulose biosynthesis cluster, suggesting that cellulose production is negatively regulated by Bin A
malfunction
-
mutation of yfgF results in altered cell surface properties and enhanced sensitivity when anaerobic cultures are exposed to peroxides
malfunction
a pdeB deletion mutant exhibits decreased swimming motility and increased biofilm formation under rich growth medium conditions, which is consistent with an increase in intracellular c-di-GMP. A mutation inactivating the EAL domain also produces similar swimming and biofilm phenotypes, indicating that the increase in c-di-GMP is likely due to a loss in phosphodiesterase activity. Transcriptional profiling by DNA microarray analysis of biofilms of pdeB (in-frame deletion and EAL) mutant cells reveals that expression of genes involved in sulfate uptake and assimilation are repressed. Addition of sulfate recovers cell mobility of the mutants
malfunction
inability of the recombinant Escherichia coli-expressed protein to bind c-di-GMP with high affinity might be due to the nonphosphorylated REC domain which traps the protein in an inactive state, which hampers c-di-GMP binding. Phosphorylation of the REC domain may trigger the conformational change necessary to unmask the active site, thus allowing PA4781 to bind c-di-GMP and enter a catalytic cycle
malfunction
deletion of the pipA gene significantly increases the intracellular c-di-GMP level and promotes the formation of aggregates both on surfaces and in planktonic cultures
malfunction
deletion of proE significantly increased the transcriptional expression of the genes encoding EPS production in Pseudomonas aeruginosa PAO1 and changed the bacterial colony morphology
malfunction
deletion of Chp1 results in increased intracellular c-di-GMP level, decreased motility, increased aggregation, and increased EPS (extracellular polysaccharide) production
malfunction
Shewanella oneidensis MR-1 / ATCC 700550
-
a pdeB deletion mutant exhibits decreased swimming motility and increased biofilm formation under rich growth medium conditions, which is consistent with an increase in intracellular c-di-GMP. A mutation inactivating the EAL domain also produces similar swimming and biofilm phenotypes, indicating that the increase in c-di-GMP is likely due to a loss in phosphodiesterase activity. Transcriptional profiling by DNA microarray analysis of biofilms of pdeB (in-frame deletion and EAL) mutant cells reveals that expression of genes involved in sulfate uptake and assimilation are repressed. Addition of sulfate recovers cell mobility of the mutants
-
malfunction
-
deletion of Chp1 results in increased intracellular c-di-GMP level, decreased motility, increased aggregation, and increased EPS (extracellular polysaccharide) production
-
metabolism
disulfide bond formation in the periplasmic CSS domain by the DsbA/DsbB system reduces phosphodiesterase activity. The free thiol form is enzymatically highly active, and the transmembrane region TM2 promotes dimerization. This form is processed by periplasmic proteases DegP and DegQ, yielding a highly active TM2 + cytoplasmic domain EAL fragment that is slowly removed by further proteolysis
metabolism
EIIA(Glc) interacts with and modulates the activity of a cdi-GMP phosphodiesterase depending on its phosphorylation state and thereby regulates biofilm formation in the aquatic and host environment
metabolism
-
the enzyme NbdA regulates the levels of intracellular c-di-GMP in a fermentation-dependent manner and therefore controls the shift from the biofilm stage to the rhamnolipids stage in rugose small colony variant (RSCV) strains during the fermentation process
metabolism
-
EIIA(Glc) interacts with and modulates the activity of a cdi-GMP phosphodiesterase depending on its phosphorylation state and thereby regulates biofilm formation in the aquatic and host environment
-
metabolism
Pseudomonas aeruginosa KT1115
-
the enzyme NbdA regulates the levels of intracellular c-di-GMP in a fermentation-dependent manner and therefore controls the shift from the biofilm stage to the rhamnolipids stage in rugose small colony variant (RSCV) strains during the fermentation process
-
physiological function
-
CdpA from Burkholderia pseudomallei is involved in autoaggregation, flagellum synthesis, motility, biofilm formation, cell invasion, and cytotoxicity
physiological function
-
CdpA inhibits biofilm formation but has no effect on colonization of the infant mouse small intestine
physiological function
-
Brucella melitensis cyclic di-GMP phosphodiesterase BpdA controls expression of flagellar genes, regulation of flagella in Brucella melitensis via cyclic-di-GMP
physiological function
the fold and active site of the HD-GYP domain are different from those of EAL proteins, and restricted access to the active-site cleft is indicative of a different mode of activity regulation. The region encompassing the GYP motif has a novel conformation and is surface exposed and available for complexation with binding partners, including GGDEF proteins. Structure of the GYP motif and structure-function relationship. Mechanistic implications for HD-GYP family proteins
physiological function
-
RbdA is involved in positive regulation of bacterial motility and production of rhamnolipids, which are associated with biofilm dispersal, and in negative regulation of production of exopolysaccharides, which are required for biofilm formation. The cyclic di-GMP-degrading regulatory protein RbdA promotes biofilm dispersal through its two-pronged effects on biofilm development, i.e., downregulating biofilm formation and upregulating production of the factors associated with biofilm dispersal.. RbdA contains a highly conserved GGDEF domain and EAL domain, which are involved in the synthesis and degradation of cyclic di-GMP, respectively. The full-length RbdA protein only displays phosphodiesterase activity, causing cyclic di-GMP degradation
physiological function
-
PdeB is a functional cyclic di-GMP PDE, and PdeA and PdeB are the only active PDEs in Borrelia burgdorferi
physiological function
-
a key regulator of biofilm formation in bacteria is the intracellular signaling molecule cyclic diguanylate. Cyclic-di-GMP phosphodiesterase BinA negatively regulates cellulose-containing biofilms in Vibrio fischeri, BinA functions as a phosphodiesterase, its activity depends on the EAL domain, and cyclic di-GMP activates cellulose biosynthesis
physiological function
-
anaerobic cyclic di-GMP phosphodiesterase is involved in remodelling the cell surface of Escherichia coli K-12 and in the response to peroxide shock, with implications for integrating three global regulatory networks, i.e. oxygen regulation, cyclic di-GMP signalling and the oxidative stress response. YfgF does possess diguanylatecyclase and/or phosphodiesterase activities, while purified YfgF GGDEF-EAL (YfgFGE) and EAL (YfgFE) domains possess cyclic di-GMP-specific phosphodiesterase activity, but lack diguanylate cyclase activity
physiological function
-
Clostridium difficile encodes a large assortment of functional DGCs and PDEs, revealing that cyclic di-GMP signalling is an important and well-conserved signal transduction system in the human pathogen. The second messenger cyclic di-3',5'-guanylate is degraded by phosphodiesterases that contain either an EAL or an HD-GYP conserved domain
physiological function
-
cyclic di-GMP, a bacterial second messenger plays a key role in survival and adaptation of bacteria under different environmental conditions. The level of cyclic di-GMP is regulated by two opposing activities, namely diguanylate cyclase, DGC, and phosphodiesterase, PDE-A, exhibited by GGDEF and EAL domain, respectively, in the same protein. Mycobacterium tuberculosis possesses a bifunctional GGDEF-EAL domain protein, i.e. MtbDGC, showing both these activities, while protein Rv 1357c, named as MtbPDE, is an EAL domain protein and degrades cyclic di-GMP to pGpG in vitro
physiological function
the organism forms biofilms on mineral surfaces through a process controlled by the cyclic dinucleotide messenger c-di-GMP. Cellular concentrations of c-di-GMP are maintained by proteins containing GGDEF and EAL domains, which encode diguanylate cyclases for c-di-GMP synthesis and phosphodiesterases for c-di-GMP hydrolysis, respectively. The enzyme PdeB contains a GGDEF-EAL multidomain and an additional Per-Arnt-Sim (PAS) sensor domain. The purified enzyme PdeB exhibits phosphodiesterase activity via the EAL domain, but no diguanylate cyclase activity
physiological function
cyclic di-3',5'-guanylate is a ubiquitous intracellular second messenger, which is crucial for the physiology and pathogenesis of a variety of bacteria, including those of clinical relevance. C-di-GMP regulates complex prokaryotic processes such as virulence, motility and biofilm formation
physiological function
-
the dual-functioning diguanylate cyclase/phosphodiesterase enzyme is responsible for regulating the intracellular concentrations of cyclic-di-GMP, a secondary signaling molecule essential to biofilm formation in bacteria
physiological function
-
a bifA mutant displays increased biofilm and pellicle formation, cell aggregation in liquid medium and decreased starvation-induced biofilm dispersal relative to the wild type. The mutation does not affect swarming motility. The hyperadherent phenotype of the mutant correlates with a general increase in cyclic diguanylate levels, Congo Red-binding exopolysaccharide production and transcription of the adhesin-encoding lapA gene. Integrity of the EAL motif and a modified GGDEF motif are crucial for BifA activity. c-Di-GMP depletion by overexpression of a heterologous cyclic di-GMP phosphodiesterase in the mutant restores wild-type biofilm dispersal and lapA expression
physiological function
deletion or overexpression of phosphodiesterase leads to changes in pellicle production, cellular protein profiles, lipid production, resistance to nitrosative stress and maintenance in lungs and spleens of infected immunocompetent BALB/mice
physiological function
-
mutation of RpfR causes a reduction in growth on CPG agar and swimming motility as well as a rough colony morphology on Congo red agar. The mutant strain displays reduced secretion of N-acyl homoserine lactones and produces significantly more biofilm than the parent strain. The overproduced biofilm contains a filamentous structure
physiological function
-
deletion of the BifA gene results in decreased swimming motility. Overexpression of BifA has a positive impact on swimming motility and negatively affects biofilm formation. Deletion of BifA results in reduced fitness and virulence of the microbes in olive plants. Olive plants infected with green fluorescent protein (GFP-)tagged Pseudomonas savastanoi cells display an altered spatial distribution of mutant cells inside olive knots compared with the wild-type strain
physiological function
-
deletion of the BifA gene results in decreased swimming motility and inhibits swarming motility. Deletion of BifA results in reduced fitness and virulence of the microbes in tomato plants
physiological function
the enzyme regulates auto-aggregation and Pf4 bacteriophage production in Pseudomonas aeruginosa PAO1
physiological function
ProE, together with other three key phosphodiesterase, i.e., RbdA, BifA, and DipA regulates the exopolysaccharide production in Pseudomonas aeruginosa PAO1
physiological function
deL represses the transcription of the class II flagellar operon fliFGHIJK, activates sslE, and regulates additional loci. Transcription repression of the fliFGHIJK operon results in inhibition of motility by reducing the number of assembled flagella, independent of the phosphodiesterase activity of PdeL
physiological function
-
phase variation of PdcB enables Clostrdidium difficile to coordinately regulate the production multiple factors by generating heterogeneity in intracellular c-di-GMP levels among bacteria in the population
physiological function
the enzyme is involved in motility, extracellular polysaccharide production, and nodulation of the host plant
physiological function
the three c-di-GMP specific phosphodiesterases, DipA, NbdA, and RbdA, act through MapZ to control flagellar motor switching
physiological function
-
deletion of the BifA gene results in decreased swimming motility and inhibits swarming motility. Deletion of BifA results in reduced fitness and virulence of the microbes in tomato plants
-
physiological function
-
CdpA from Burkholderia pseudomallei is involved in autoaggregation, flagellum synthesis, motility, biofilm formation, cell invasion, and cytotoxicity
-
physiological function
Shewanella oneidensis MR-1 / ATCC 700550
-
the organism forms biofilms on mineral surfaces through a process controlled by the cyclic dinucleotide messenger c-di-GMP. Cellular concentrations of c-di-GMP are maintained by proteins containing GGDEF and EAL domains, which encode diguanylate cyclases for c-di-GMP synthesis and phosphodiesterases for c-di-GMP hydrolysis, respectively. The enzyme PdeB contains a GGDEF-EAL multidomain and an additional Per-Arnt-Sim (PAS) sensor domain. The purified enzyme PdeB exhibits phosphodiesterase activity via the EAL domain, but no diguanylate cyclase activity
-
physiological function
-
phase variation of PdcB enables Clostrdidium difficile to coordinately regulate the production multiple factors by generating heterogeneity in intracellular c-di-GMP levels among bacteria in the population
-
physiological function
-
a bifA mutant displays increased biofilm and pellicle formation, cell aggregation in liquid medium and decreased starvation-induced biofilm dispersal relative to the wild type. The mutation does not affect swarming motility. The hyperadherent phenotype of the mutant correlates with a general increase in cyclic diguanylate levels, Congo Red-binding exopolysaccharide production and transcription of the adhesin-encoding lapA gene. Integrity of the EAL motif and a modified GGDEF motif are crucial for BifA activity. c-Di-GMP depletion by overexpression of a heterologous cyclic di-GMP phosphodiesterase in the mutant restores wild-type biofilm dispersal and lapA expression
-
physiological function
-
the enzyme is involved in motility, extracellular polysaccharide production, and nodulation of the host plant
-
additional information
Bd1817 lacks the active-site tyrosine present in most HD-GYP family members
additional information
-
Bd1817 lacks the active-site tyrosine present in most HD-GYP family members
additional information
-
mutation of PA0861 encoding a multidomain regulatory protein implicated in cyclic di-GMP metabolism resulted in a hyperbiofilm phenotype
additional information
-
the catalytically inactive GGDEF domain is required for YfgFGE dimerization and enhanced cyclic di-GMP phosphodiesterase activity in the presence of physiological concentrations of Mg2+
additional information
the enzyme contains a HD-GYP type catalytic domain responsible for
additional information
the enzyme contains a HD-GYP type catalytic domain responsible for
additional information
-
the enzyme contains a HD-GYP type catalytic domain responsible for
additional information
the enzyme contains a HD-GYP type catalytic domain
additional information
the enzyme contains a HD-GYP type catalytic domain
additional information
-
the enzyme contains a HD-GYP type catalytic domain
additional information
-
an heme-nitric oxide/oxygen binding protein, H-NOX , in the biofilm-dwelling bacterium Shewanella woodyi mediates NO-induced biofilm dispersal. SwH-NOX is cocistronic with a gene encoding a dual-functioning diguanylate cyclase/phosphodiesterase enzyme, designated here as H-NOX-associated cyclic-di-GMP processing enzyme, HaCE. Interaction analysis of recombinant enzyme with recombinnat wild-type SwH-NOX and mutants E16K, F17A, and E20K, the mutants show a weaker binding of the enzyme HaCE compared to the wild-type, overview
additional information
-
the enzyme comprises a HD-GYP domain fused to a GAF domain. D183 and K225 are catalytic residues, GYP domain residues R314, K317, G284, Y285 and P286 are involved in substrate binding, substrate and product binding structures, overview
additional information
the enzyme is expressed constitutively throughout the Bdellovibrio life cycle
additional information
direct repression of c-di-GMP signaling by cAMP signal may be generally crucial for cyanobacteria
additional information
induction of the Pseudomonas aeruginosa c-di-GMP phosphodiesterases PA2133 and BifA results in the dispersal of Pseudomonas aeruginosa biofilms in both a microtiter tray biofilm assay and a flow cell biofilm system
additional information
-
TriP is a regulator that is epistatic to PdeR in positively regulating virulence expression in Xanthomonas oryzae pv. oryzae. TriP promotes the PDE activity of PdeR to degrade c-di-GMP in the presence of PdeK
additional information
-
the enzyme comprises a HD-GYP domain fused to a GAF domain. D183 and K225 are catalytic residues, GYP domain residues R314, K317, G284, Y285 and P286 are involved in substrate binding, substrate and product binding structures, overview
-
additional information
Thermosynechococcus vestitus NIES-2133
-
direct repression of c-di-GMP signaling by cAMP signal may be generally crucial for cyanobacteria
-
additional information
-
the enzyme is expressed constitutively throughout the Bdellovibrio life cycle
-
Show AA Sequence and Transmembrane Helices (21415 entries)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
197200
-
tetrameric heterotetramer of dual-functioning diguanylate cyclase/phosphodiesterase enzyme complex, sedimentation equilibrium analysis
23000
-
2 * 74500 + 2 * 23000, about, sedimentation equilibrium analysis, the dual-functioning diguanylate cyclase/phosphodiesterase enzyme, formed by heme-nitric oxide/oxygen binding protein and cyclic-di-GMP processing enzyme, builds a tetrameric structure
42837
4 * 42837, calculated from amino acid sequence, RocR is mainly a tetramer in solution
74500
74500
-
2 * 74500 + 2 * 23000, about, sedimentation equilibrium analysis, the dual-functioning diguanylate cyclase/phosphodiesterase enzyme, formed by heme-nitric oxide/oxygen binding protein and cyclic-di-GMP processing enzyme, builds a tetrameric structure
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
monomer
tetramer
additional information
?
x * 90000, His6- and maltose binding protein-tagged enzyme, SDS-PAGE
?
-
x * 90000, His6- and maltose binding protein-tagged enzyme, SDS-PAGE
-
?
-
x * 90000, His6- and maltose binding protein-tagged enzyme, SDS-PAGE
-
?
Xcc1959 encodes a GGDEF and EAL fusion domain protein with two PAS domains
?
-
Xcc1959 encodes a GGDEF and EAL fusion domain protein with two PAS domains
-
dimer
-
the enzyme forms a dimer with each monomer consisting of an N-terminal GAF domain connected to a C-terminal HD-GYP domain by an approximately 42 residue-long helix. Assembly of the head-to-head dimer relies exclusively on the GAF domain and the long alpha5 helix with the HD-GYP domain playing no role in the dimeric interface, crstal structure analysis, overview
dimer
-
the enzyme forms a dimer with each monomer consisting of an N-terminal GAF domain connected to a C-terminal HD-GYP domain by an approximately 42 residue-long helix. Assembly of the head-to-head dimer relies exclusively on the GAF domain and the long alpha5 helix with the HD-GYP domain playing no role in the dimeric interface, crstal structure analysis, overview
-
dimer
phosphorylated and non-phosphorylated proteins are both dimeric
monomer
-
YfgFE, the monomeric EAL domain can be active as phosphodiesterases
monomer
truncated mutant PA4781HD-GYP protein is mainly a monomer, determined by gel filtration
tetramer
4 * 42837, calculated from amino acid sequence, RocR is mainly a tetramer in solution
tetramer
-
2 * 74500 + 2 * 23000, about, sedimentation equilibrium analysis, the dual-functioning diguanylate cyclase/phosphodiesterase enzyme, formed by heme-nitric oxide/oxygen binding protein and cyclic-di-GMP processing enzyme, builds a tetrameric structure
additional information
-
catalytic activity is confined to the C-terminal EAL domain. The GGDEF domain lacks diguanylate cyclase activity but is able to bind GTP which results in activation of the phosphodiresterase activity in the neighbouring EAL domain
additional information
-
MtbDGC contains cysteine pairs Cys94-Cys584, Cys2-Cys479 and Cys429-Cys614, and one unbound Cys406. Structure-function relationship, homology modeling, minimization and model validation, overview
additional information
-
primary sequence and three-dimensional structure comparisons, overview
additional information
-
primary sequence and three-dimensional structure comparisons, overview
-
additional information
-
structure modeling and computational docking, overview
additional information
structure modeling and computational docking, overview
additional information
enzyme domain structure analysis, overview
additional information
Shewanella oneidensis MR-1 / ATCC 700550
-
enzyme domain structure analysis, overview
-
additional information
-
wild-type heme-nitric oxide/oxygen binding protein , SwH-NOX, alone exists as a monomer and the cyclic-di-GMP phosphodiesterase, SwHaCE, as a dimer
additional information
-
the HD-GYP phosphodiesterase domain of RpfG, which is part of a system necessary for the diffusible signalling factor dependent production of extracellular pathogenicity, interacts directly with diguanylate cyclase GGDEF domain-containing proteins. Physical linkage between quorum-sensing and cyclic diguanylate signalling pathways
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POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
phosphoprotein
the REC domain of PA4781 cannot be allosterically activated by phosphorylation in the Escherichia coli background, the REC domain at the N-terminus of the protein is responsible for the phosphodiesterase activity of the enzyme. Phosphorylated and non-phosphorylated proteins are both dimeric
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystals are grown by hanging-drop method at 18°C using 0.001 ml of protein solution mixed with an equal volume of reservoir solution, varying conditions using 0.1 M bis-Tris, pH 5.5, 0.2-0.4 M ammonium acetate, 25% w/v PEG 3350, with or without 20% v/v DMSO or 2.1 M DL-malic acid, pH 7.0, X-ray diffraction structure determination and analysis at 2.5 A resolution
enzyme does not undergo global changes upon exposure to light. The chromophore environment of full-length enzyme is asymmetric
-
BlrP1 is crystallized at 4°C in the dark using polyethyleneglycol in the presence of cyclic-di-GMP and Ca2+
-
purified recombinant detagged enzyme in complex with Fe2+, substrate cyclic di-3',5'-guanylate or final product GMP, hanging drop vapour diffusion method, mixing of equal volumes of 10 mg/ml protein with a precipitant solution made up of 0.1 M MES pH 6.5, 0.9 M succinic acid, and 2% PEG 2000, anomalous X-ray diffraction structure determination and analysis at 2.03-2.8 A resolution
-
hanging drop vapour diffusion method, high-resolution crystal structures of the enzyme with Ca2+, cyclic di-3',5'-guanylate-Ca2+, 5'-pGpG-Ca2+ and 3'3'-cyclic GMP-AMP-Ca2+
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E323Q
-
mutation in EAL motif, both catalytic activity and induction by GTP are not affected
L128C/G353C
-
the mutant shows higher catalytic efficiency at pH 7.5 and 20°C compared to the wild type enzyme under light and dark conditions
R93S
-
the mutant shows higher catalytic efficiency at pH 7.5 and 20°C compared to the wild type enzyme under light and dark conditions
S309C/S312C
-
inactive at pH 7.5 and 20°C under dark and light conditions
C406S
-
site-directed mutagenesis of enzyme MtbDGC, the mutant is catalytically inactive
D183A
-
site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme
D222A
-
site-directed mutagenesis, the mutant shows highly reduced catalytic activity compared to the wild-type enzyme
D305A
-
site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme
E185A
-
site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme
G284A
-
site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme
H189A
-
site-directed mutagenesis, the mutant shows highly reduced catalytic activity compared to the wild-type enzyme
H221A
-
site-directed mutagenesis, the mutant shows highly reduced catalytic activity compared to the wild-type enzyme
H250A
-
site-directed mutagenesis, the mutant shows highly reduced catalytic activity compared to the wild-type enzyme
H276A
-
site-directed mutagenesis, the mutant shows highly reduced catalytic activity compared to the wild-type enzyme
H277A
-
site-directed mutagenesis, the mutant shows highly reduced catalytic activity compared to the wild-type enzyme
K225A
-
site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme
K317A
-
site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme
P286A
-
site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme
R314 A
-
site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme
Y285 A
-
site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme
D222A
-
site-directed mutagenesis, the mutant shows highly reduced catalytic activity compared to the wild-type enzyme
-
E185A
-
site-directed mutagenesis, the mutant shows reduced catalytic activity compared to the wild-type enzyme
-
H189A
-
site-directed mutagenesis, the mutant shows highly reduced catalytic activity compared to the wild-type enzyme
-
H221A
-
site-directed mutagenesis, the mutant shows highly reduced catalytic activity compared to the wild-type enzyme
-
H250A
-
site-directed mutagenesis, the mutant shows highly reduced catalytic activity compared to the wild-type enzyme
-
D295A
D296A
D318A
D347A
-
mutant is indistinguishable from enzyme null mutant. Loss of twitching activity and PO4 phage sensitivity, mutant fails to assemble surface pili
D56N
-
the RocR mutant exhibits a significantly smaller Km value than that of the wild type enzyme
E175A
E265A
E268A
E268Q
E352A
E352C
E352D
E352Q
E355A
E464A
-
the PA2567 mutant shows increased kcat and Km compared to the wild type enzyme
E475A
-
mutant is indistinguishable from enzyme null mutant. Loss of twitching activity and PO4 phage sensitivity, mutant fails to assemble surface pili
F297A
-
the RocR mutant shows decreased kcat and Km compared to the wild type RocR enzyme
F498A
-
the PA2567 mutation reduces the enzyme activity to below the measurable level
G346A
-
mutant is indistinguishable from enzyme null mutant. Loss of twitching activity and PO4 phage sensitivity, mutant fails to assemble surface pili
K316A
L477A
-
mutant is indistinguishable from enzyme null mutant. Loss of twitching activity and PO4 phage sensitivity, mutant fails to assemble surface pili
N233A
Q161A
Q372A
R179A
S302A
-
the RocR mutant shows decreased kcat and increased Km compared to the wild type RocR enzyme
S493A
-
the PA2567 mutation reduces the enzyme activity to below the measurable level
T267A
V476A
-
mutant is indistinguishable from enzyme null mutant. Loss of twitching activity and PO4 phage sensitivity, mutant fails to assemble surface pili
E634A
D289A
-
VCA0681, mutation in active site, eliminated VCA0681 repression of vpsL-lux, biofilm formation not repressed by mutant contrary to wild-type. Expression of the active-site mutant (D289A) in a luxO D47E strain has little effect on cyclic di-3',5'-guanylate levels
E215D
mutant has 25% higher activity than the wild-type
K179M
mutant enzyme shows reduced activity. Biofilm formation is significantly higher mutant as compared with control BL21 strain
R49K/D159E
mutant enzyme shows reduced activity. Biofilm formation is significantly higher mutant as compared with control BL21 strain
D289A
Vibrio cholerae serotype O1 El Tor C6706
-
VCA0681, mutation in active site, eliminated VCA0681 repression of vpsL-lux, biofilm formation not repressed by mutant contrary to wild-type. Expression of the active-site mutant (D289A) in a luxO D47E strain has little effect on cyclic di-3',5'-guanylate levels
-
K179M
-
mutant enzyme shows reduced activity. Biofilm formation is significantly higher mutant as compared with control BL21 strain
-
R49K/D159E
-
mutant enzyme shows reduced activity. Biofilm formation is significantly higher mutant as compared with control BL21 strain
-
DAA
additional information
D296A
site-directed mutagenesis, the mutant shows a 33.5fold reduced kcat and increased Km compared to the wild-type enzyme
D296A
-
the RocR mutant shows decreased kcat and increased Km compared to the wild type RocR enzyme
D318A
site-directed mutagenesis, the mutant shows a reduced kcat and altered Km compared to the wild-type enzyme
E268A
-
the RocR mutation reduces the enzyme activity to below the measurable level
E268Q
site-directed mutagenesis, the mutant shows a reduced kcat and altered Km compared to the wild-type enzyme
E352D
site-directed mutagenesis, the mutant shows a reduced kcat and altered Km compared to the wild-type enzyme
E352Q
site-directed mutagenesis, the mutant shows a reduced kcat and altered Km compared to the wild-type enzyme
E355A
site-directed mutagenesis, the mutant shows a 1.3fold reduced kcat and increased Km compared to the wild-type enzyme
Q161A
site-directed mutagenesis, the mutant shows increased Km compared to the wild-type enzyme
Q372A
site-directed mutagenesis, the mutant shows a reduced kcat and altered Km compared to the wild-type enzyme
R179A
site-directed mutagenesis, the mutant shows a 29.1fold reduced kcat and increased Km compared to the wild-type enzyme
T267A
site-directed mutagenesis, the mutant shows a reduced kcat and altered Km compared to the wild-type enzyme
DAA
EAL domain of ravR mutated (DAA): key residues E and L are substituted by D and A
DAA
-
EAL domain of ravR mutated (DAA): key residues E and L are substituted by D and A
-
additional information
-
disruption or deletion of binA increased biofilm formation in culture and leads to increased cellulose production. The phenotypes of the DELTAbinA mutant strain can be disrupted by insertions in genes in the bacterial cellulose biosynthesis cluster
additional information
-
construction of a pdeA pdeB double mutant and a pdeB single mutant. pdeB single mutant cells exhibit significantly increased flexing, indicating a role for cyclic di-GMP in motility. While virulence in needle-inoculated C3H/HeN mice does not appear to be altered significantly in pdeB mutant cells, these cells exhibit a reduced ability to survive in Ixodes scapularis ticks. All phenotypes are restored when the mutant is complemented
additional information
-
deletion of bpdA results in a dramatic decrease in flagellar promoter activities, and a flagellar mutant shows similar phenotypes to the bpdA and bpdB mutant strains in mouse models of infection. Genes bpdA and bpdB mutants exhibit decreased dissemination within immunocompetent mice. Flagellar transcription is strongly downregulated in the bpdA mutant
additional information
-
enzyme deletion mutant shows 80% reduction in catalytic activity. Isolated C-terminal EAL domain shows no significant reduxtion in catalytic activity
additional information
-
system development to survey the activity of putative c-di-GMP metabolic enzymes, method design and evaluation, overview. Generation of 19 inducible translational fusion constructs for genes encoding putative c-di-GMP phosphodiesterases from Clostridium difficile 630 in engineered Clostridium difficile strain NPS235. To construct a c-di-GMP-responsive biosensor, a chimeric ribo switch is engineered upstream of the coding sequence for green fluorescent protein with nucleotides -564 to-86 of Bacillus cereus gene bc_4140 of strain ATCC 14579, containing an M-box riboswitch promoter, aptamer, transcriptional terminator, and flanking sequences, as a scaffold, construction of c-di-GMP riboswitch reporter strains using main parts of the sequence from Bacillus cereus strain ATCC 14579, gene bc_4140, UniProt ID Q818V1 and the aptamer sequence from a c-di-GMP-responsive riboswitch (GEMM motif), of Bacillus cereus gene bce_0489, strain ATCC 10987
additional information
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system development to survey the activity of putative c-di-GMP metabolic enzymes, method design and evaluation, overview. Generation of 19 inducible translational fusion constructs for genes encoding putative c-di-GMP phosphodiesterases from Clostridium difficile 630 in engineered Clostridium difficile strain NPS235. To construct a c-di-GMP-responsive biosensor, a chimeric ribo switch is engineered upstream of the coding sequence for green fluorescent protein with nucleotides -564 to-86 of Bacillus cereus gene bc_4140 of strain ATCC 14579, containing an M-box riboswitch promoter, aptamer, transcriptional terminator, and flanking sequences, as a scaffold, construction of c-di-GMP riboswitch reporter strains using main parts of the sequence from Bacillus cereus strain ATCC 14579, gene bc_4140, UniProt ID Q818V1 and the aptamer sequence from a c-di-GMP-responsive riboswitch (GEMM motif), of Bacillus cereus gene bce_0489, strain ATCC 10987
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additional information
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enzyme disruption mutant renders the cells unable to divide properly. Enzyme gene is co-transcribed with cyclic guanylate cyclase YvvD
additional information
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both full-length enzyme and the isolated EAL domain hydrolyze cyclic diguanylate. Hydrolysis of 5-phosphoguanylyl(3-5)guanosine to guanosine monophosphate by isolated domain EAL is very poor
additional information
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disruption in the yfgF gene by linear transformation, phenotype, overview. The mutant is more sensitive to stress than the parent strain
additional information
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expression of Mtbdgc in Mycobacterium smegmatis complements the MSDGC-1 knock out strain by restoring the long term survival of Mycobacterium smegmatis
additional information
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deletion of gene PA4367 results in severe defect in swarming motility and a hyperbiofilm phenotype. Mutant exhibits increased cellular pools of cyclic di-3,5-guanylate, increased synthesis of a polysaccharide produced by the pel locus and decreased flagellar reversals. GGDQF and EAL domains of BifA are both required for complementation of the mutant
additional information
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deletion of either the GGDEF or the EAL domain results in a phenotype indistinguishable from enzyme deletion mutant. Deletion of the amino-terminal REC domain containing a putative polar localization signal results in a protein that still supports intermediate levels of pilus assembly and function, but is no longer localized to the bacterial pole. Enzyme deletion mutant is as virulent as wild-type in a murine model of acute pneumonia
additional information
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mutation of Arr leads to suppression of induction of biofilm formation
additional information
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deletion of the PAS domain or substitution of the key residues implicated in sensing low-oxygen stress abrogates the functionality of RbdA
additional information
construction of a truncated enzyme version PA4781HD-GYP lacking the REC domain, the recombinant mutant shows highly reduced activity compared to thw wild-type enzyme
additional information
construction of a truncated enzyme version PA4781HD-GYP lacking the REC domain, the recombinant mutant shows highly reduced activity compared to thw wild-type enzyme
additional information
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construction of a truncated enzyme version PA4781HD-GYP lacking the REC domain, the recombinant mutant shows highly reduced activity compared to thw wild-type enzyme
additional information
generation of GFP-tagged or untagged markerless in-frame deletion mutants and chromosomal gene replacement
additional information
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generation of GFP-tagged or untagged markerless in-frame deletion mutants and chromosomal gene replacement
additional information
Shewanella oneidensis MR-1 / ATCC 700550
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generation of GFP-tagged or untagged markerless in-frame deletion mutants and chromosomal gene replacement
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additional information
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removal of the EAL domain reverses enzyme activity, converting it to an inhibitor of swarming and activator of cps gene expression
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
GGDEF domain and GGDEF-EAL fusion domains: GST-affinity chromatography
recombinant C- and N-terminally His-tagged enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
recombinant GST-tagged enzyme from Escherichia coli by glutathione affinity chromatography
-
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3)pLysS cell-free supernatant by nickel affinity chromatography
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recombinant His-tagged MtbDGC and MtbPDE by nickel affinity chromatography from inclusion bodies
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recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
recombinant N-terminally His6-tagged enzyme from Escherichiia coli strain BL21(DE3) by nickel affinity chromatography and cleavage of the the His-tag by HRV 3C protease
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recombinant N-terminally maltose-binding protein tagged and C-terminally His6 tagged truncated wild-type enzyme and mutant E364A from Escherichia coli strain Tuner(DE3)pLysS by nicel affinity and amylose affinity chromatography
recombinant wild-type and mutant C- and N-terminally His-tagged enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
autoinducer-deficient Vibrio cholerae strain transformed with library of random Vibrio cholerae genomic fragments fused to a promoterless luciferase cassette. Verification of Quorum sensing (QS) regulation: wild-type Vibrio cholerae El and QS mutants are transformed with each candidate reporter plasmid, each candidate exhibits similar expression pattern in a luxO D47E strain (response regulator luxO) and a hapR strain (QS transcription factor HapR) that both simulate low cell density, indicating expression of each target gene is dependent on LuxO-P as well as HapR. VCA0681 is overexpressed in Vibrio cholerae luxO D47Eel: reduction of reporter expression. Deletion of either VCA0681 from the Vibrio cholerae El genome does not alter biofilm formation (transcriptional activator vps expression). Absolute level of vps expression in the (HapR minus) Vibrio cholerae El strain 100 times higher than that of wild-type (HapR minus) Vibrio cholerae C1 strain
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commercial synthetic gene PA4108, DNA and amino acid sequence determination and analysis, recombinant overexpression of C- and N-terminally His-tagged enzyme in an endogenous PDE yhjH-lacking Escherichia coli strain and in strain BL21(DE3)
commercial synthetic gene PA4781, DNA and amino acid sequence determination and analysis, recombinant overexpression of wild-type and mutant C- and N-terminally His-tagged enzymes in an endogenous PDE yhjH-lacking Escherichia coli strain and in strain BL21(DE3), the REC domain of PA4781 cannot be allosterically activated by phosphorylation in the Escherichia coli background
DNA fragments encoding GGDEF (1-172 aa) and GGDEF-EAL domain (10-426 aa) amplified separately and fused to the GST coding region in pGEX-6p-1, transformation of Escherichia coli BL21. Deletion of Xcc1959 in Xcc strain XC1 or 8004 had no significant effect on virulence factor production in vitro
ectopic expression of 31 of the conserved genes from 20 genomes of Clostridium difficile for comparison of their effect on motility and biofilm formation. Most of the PDEs are active in a Vibrio cholerae model
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expression in Escherichia coli
Flagellar promoter analysis in the bpdA, bpdB, and cgsB mutants using a luminescent reporter system. Expression in Vibrio parahaemolyticus strain LM5984
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gene PA3947, expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
gene pdeB, gene expression profiling and quantitative PCR in wild-type and mutant cells, expression of GFP-tagged mutant enzymes, expression of N-terminally maltose-binding protein tagged and C-terminally His6 tagged truncated wild-type enzyme and mutant E364A in Escherichia coli strain Tuner(DE3)pLysS
gene perma_0986, expression of N-terminally His6-tagged enzyme in Escherichiia coli strain BL21 (DE3)
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gene yfgF is expressed under anaerobic conditions from a class II FNR, i.e. regulator of fumarate and nitrate reduction-dependent promoter
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genes 1357c and Rv 1354c, expression of enzymes MtbDGC and MtbPDE as His-tagged proteins in inculsion bodies
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mutated DAA domain cloned in expression vector pLAFR3 (lac promoter) for complementation analysis in a Xanthomonas campestris XC1 mutant lacking ravR. Deletion of ravR results in decreased virulence factor production. RavS and RavR constitute a two-component regulatory system (ravS gene deleted inframe in Xanthomonas campestris strains XC1 and 8004): no effect on bacterial growth in YEB and LB medium, similar phenotype changes compared to Xanthomonas campestris XC1 mutant lacking ravR. RavR is a c-di-GMP phosphodiesterase: fusionated domains GGDEF and EAL (cloned separately into the expression vector pLAFR3 for in trans expression in the mutant deltaravR). RavS/RavR 2-component system regulates diverse functions in Xanthomonas campestris XC1
overexpression is sufficient to induce lateral flagellar gene expression in liquid, decrease biofilm formation, decrease cps gene expression, and suppress the DeltascrABC phenotype
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overexpression of BinA in Vibrio fischeri enhancing motility. Expression of wild-type and mutant enzymes in Escherichia coli
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recombinant expression of genetic constructs in Bacillus subtilis strain DS2569 to generate phage lysates for transduction
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recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)pLysS
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sequence comparisons, comparative transcriptional profiling of Bd1817 expression
VCA0895 is overexpressed in Vibrio cholerae luxO D47Eel: growth inhibition, deletion of vca0895 from the Vibrio cholerae El genome does not alter biofilm formation (transcriptional activator vps expression)
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
cdpA is expressed during in vitro growth in a biofilm but is not expressed in vivo until the late stage of infection, after colonization has occurred
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cdpA is expressed during in vitro growth in a biofilm but is not expressed in vivo until the late stage of infection, after colonization has occurred, cdpA expression is not regulated by cyclic-di-GMP concentration
-
expression is downregulated in cells grown over a solid surface
the product of the VP1881 gene promotes its own expression when the levels of c-di-GMP are low or when the phosphodiesterase is catalytically inactive
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RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
refolding of recombinant His-tagged MtbDGC and MtbPDE after purification from inclusion bodies via stepwise dialysis
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REF.
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The HD-GYP domain of RpfG mediates a direct linkage between the Rpf quorum-sensing pathway and a subset of diguanylate cyclase proteins in the phytopathogen Xanthomonas axonopodis pv citri
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62
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Xanthomonas axonopodis
brenda
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Phosphate-dependent modulation of c-di-GMP levels regulates Pseudomonas fluorescens Pf0-1 biofilm formation by controlling secretion of the adhesin LapA
Mol. Microbiol.
63
656-679
2007
Pseudomonas fluorescens, Pseudomonas fluorescens Pf0-1
brenda
Rajagopal, S.; Key, J.M.; Purcell, E.B.; Boerema, D.J.; Moffat, K.
Purification and initial characterization of a putative blue light-regulated phosphodiesterase from Escherichia coli
Photochem. Photobiol.
80
542-547
2004
Escherichia coli
brenda
Rao, F.; Yang, Y.; Qi, Y.; Liang, Z.X.
Catalytic Mechanism of c-di-GMP specific phosphodiesterase: a study of the EAL domain-containing RocR from Pseudomonas aeruginosa
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190
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2008
Pseudomonas aeruginosa, Pseudomonas aeruginosa (Q9HX69)
brenda
Gotoh, H.; Zhang, Y.; Dallo, S.F.; Hong, S.; Kasaraneni, N.; Weitao, T.
Pseudomonas aeruginosa, under DNA replication inhibition, tends to form biofilms via Arr
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159
294-302
2008
Pseudomonas aeruginosa
brenda
Hammer, B.K.; Bassler, B.L.
Distinct sensory pathways in Vibrio cholerae El Tor and classical biotypes modulate cyclic dimeric GMP levels to control biofilm formation
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191
169-177
2009
Vibrio cholerae serotype O1, Vibrio cholerae serotype O1 El Tor C6706
brenda
He, Y.W.; Boon, C.; Zhou, L.; Zhang, L.H.
Co-regulation of Xanthomonas campestris virulence by quorum sensing and a novel two-component regulatory system RavS/RavR
Mol. Microbiol.
71
1464-1476
2009
Xanthomonas campestris pv. campestris, Xanthomonas campestris pv. campestris (Q8P947), Xanthomonas campestris pv. campestris (Q8P9A5), Xanthomonas campestris pv. campestris X1 (Q8P9A5), Xanthomonas campestris pv. campestris ATCC 33913, Xanthomonas campestris pv. campestris XC1 (Q8P947)
brenda
Tamayo, R.; Schild, S.; Pratt, J.T.; Camilli, A.
Role of cyclic di-GMP during el tor biotype Vibrio cholerae infection: characterization of the in vivo-induced cyclic di-GMP phosphodiesterase CdpA
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76
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2008
Vibrio cholerae serotype O1
brenda
Lee, H.S.; Gu, F.; Ching, S.M.; Lam, Y.; Chua, K.L.
CdpA is a Burkholderia pseudomallei cyclic di-GMP phosphodiesterase involved in autoaggregation, flagellum synthesis, motility, biofilm formation, cell invasion, and cytotoxicity
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78
1832-1840
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Burkholderia pseudomallei, Burkholderia pseudomallei KHW
brenda
Rao, F.; Qi, Y.; Chong, H.S.; Kotaka, M.; Li, B.; Li, J.; Lescar, J.; Tang, K.; Liang, Z.X.
The functional role of a conserved loop in EAL domain-based cyclic di-GMP-specific phosphodiesterase
J. Bacteriol.
191
4722-4731
2009
Pseudomonas aeruginosa
brenda
Barends, T.R.; Hartmann, E.; Griese, J.J.; Beitlich, T.; Kirienko, N.V.; Ryjenkov, D.A.; Reinstein, J.; Shoeman, R.L.; Gomelsky, M.; Schlichting, I.
Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase
Nature
459
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Klebsiella pneumoniae
brenda
An, S.; Wu, J.; Zhang, L.H.
Modulation of Pseudomonas aeruginosa biofilm dispersal by a cyclic-di-GMP phosphodiesterase with a putative hypoxia-sensing domain
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76
8160-8173
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Pseudomonas aeruginosa
brenda
Sultan, S.Z.; Pitzer, J.E.; Boquoi, T.; Hobbs, G.; Miller, M.R.; Motaleb, M.A.
Analysis of the HD-GYP domain cyclic dimeric GMP phosphodiesterase reveals a role in motility and the enzootic life cycle of Borrelia burgdorferi
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79
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Borreliella burgdorferi
brenda
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Aliivibrio fischeri
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Brucella melitensis
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The structure of an unconventional HD-GYP protein from Bdellovibrio reveals the roles of conserved residues in this class of cyclic-di-GMP phosphodiesterases
mBio
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Bdellovibrio bacteriovorus (Q6MM30), Bdellovibrio bacteriovorus
brenda
Lacey, M.M.; Partridge, J.D.; Green, J.
Escherichia coli K-12 YfgF is an anaerobic cyclic di-GMP phosphodiesterase with roles in cell surface remodelling and the oxidative stress response
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156
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Escherichia coli
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Shewanella woodyi
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Shewanella oneidensis (Q8EJM6), Shewanella oneidensis, Shewanella oneidensis MR-1 / ATCC 700550 (Q8EJM6)
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brenda
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PLoS ONE
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Pseudomonas aeruginosa (Q9HV27), Pseudomonas aeruginosa (Q9HWS0), Pseudomonas aeruginosa
brenda
Miner, K.D.; Kurtz, D.M.
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Thermotoga maritima (Q9WY30), Thermotoga maritima, Thermotoga maritima ATCC 43589 (Q9WY30), Thermotoga maritima DSM 3109 (Q9WY30)
brenda
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Pseudomonas aeruginosa (Q9HX69), Pseudomonas aeruginosa, Pseudomonas aeruginosa ATCC 15692 (Q9HX69)
brenda
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Escherichia coli (P32701)
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The c-di-GMP phosphodiesterase BifA regulates biofilm development in Pseudomonas putida
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78-84
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Pseudomonas putida, Pseudomonas putida KT2442
brenda
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Mycobacterium tuberculosis variant bovis (A0A0H3M3N9)
brenda
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16
604-615
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Pseudomonas savastanoi pv. savastanoi, Pseudomonas syringae pv. tomato, Pseudomonas syringae pv. tomato DC3000
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Induction of native c-di-GMP phosphodiesterases leads to dispersal of Pseudomonas aeruginosa biofilms
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Pseudomonas aeruginosa (Q9I1Y2)
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Cai, Y.M.; Yu, K.W.; Liu, J.H.; Cai, Z.; Zhou, Z.H.; Liu, Y.; Wang, T.F.; Yang, L.
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Pseudomonas aeruginosa (Q9I6K5)
brenda
Sun, Y.; Liu, Y.; Liu, X.; Dang, X.; Dong, X.; Xie, Z.
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104
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Azorhizobium caulinodans (A8IJI0), Azorhizobium caulinodans ATCC 43989 (A8IJI0)
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529
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Vibrio cholerae serotype O1 (Q9KVL2), Vibrio cholerae serotype O1 ATCC 39315 (Q9KVL2)
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476
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Vibrio cholerae serotype O1 (A0A0H3AJ04), Vibrio cholerae serotype O1 O395 (A0A0H3AJ04)
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1226
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Pseudomonas aeruginosa (Q9HTQ9)
brenda
Liu, S.; Xu, A.; Xie, B.; Xin, F.; Dong, W.; Zhou, J.; Jiang, M.
Priority changes between biofilm exopolysaccharides synthesis and rhamnolipids production are mediated by ac-di-GMP-specific phosphodiesterase NbdA inPseudomonas aeruginosa
iScience
25
105531
2022
Pseudomonas aeruginosa, Pseudomonas aeruginosa KT1115
brenda
Martinez-Mendez, R.; Camacho-Hernandez, D.A.; Sulvaran-Guel, E.; Zamorano-Sanchez, D.
A trigger phosphodiesterase modulates the global c-di-GMP pool, motility, and biofilm formation in Vibrio parahaemolyticus
J. Bacteriol.
203
e0004621
2021
Vibrio parahaemolyticus (Q87NI7)
brenda
Yilmaz, C.; Rangarajan, A.A.; Schnetz, K.
The transcription regulator and c-di-GMP phosphodiesterase PdeL represses motility in Escherichia coli
J. Bacteriol.
203
e00427-20
2020
Escherichia coli (P21514)
brenda
Xin, L.; Zeng, Y.; Sheng, S.; Chea, R.; Liu, Q.; Li, H.; Yang, L.; Xu, L.; Chiam, K.; Liang, Z.
Regulation of flagellar motor switching by c-di-GMP phosphodiesterases in Pseudomonas aeruginosa
J. Biol. Chem.
294
13789-13799
2019
Pseudomonas aeruginosa (A0A0F6RW04)
brenda
Enomoto, G.; Kamiya, A.; Okuda, Y.; Narikawa, R.; Ikeuchi, M.
Tlr0485 is a cAMP-activated c-di-GMP phosphodiesterase in a cyanobacterium Thermosynechococcus
J. Gen. Appl. Microbiol.
66
147-152
2020
Thermosynechococcus vestitus (Q8DLK6), Thermosynechococcus vestitus NIES-2133 (Q8DLK6)
brenda
Li, H.; Xue, D.; Tian, F.; Yuan, X.; Yang, F.; Chen, H.; Hutchins, W.; Yang, C.; He, C.
Xanthomonas oryzae pv. oryzae response regulator TriP regulates virulence and exopolysaccharide production via interacting with c-di-GMP phosphodiesterase PdeR
Mol. Plant Microbe Interact.
32
729-739
2019
Xanthomonas oryzae pv. oryzae
brenda
Heo, K.; Park, Y.H.; Lee, K.A.; Kim, J.; Ham, H.I.; Kim, B.G.; Lee, W.J.; Seok, Y.J.
Sugar-mediated regulation of a c-di-GMP phosphodiesterase in Vibrio cholerae
Nat. Commun.
10
5358
2019
Vibrio cholerae serotype O1 (Q9KRD2), Vibrio cholerae serotype O1 ATCC 39315 (Q9KRD2)
brenda
Reyes Ruiz, L.M.; King, K.A.; Agosto-Burgos, C.; Gamez, I.S.; Gadda, N.C.; Garrett, E.M.; Tamayo, R.
Coordinated modulation of multiple processes through phase variation of a c-di-GMP phosphodiesterase in Clostridioides difficile
PLoS Pathog.
18
e1010677
2022
Clostridioides difficile, Clostridioides difficile R20291
brenda
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