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Enzyme Nomenclature
Information on EC 3.1.4.60 - pApA phosphodiesterase
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3.1.4.60 pApA phosphodiesteraseIUBMB Comments
The enzyme, characterized from the Gram-positive bacterium Staphylococcus aureus, is a cytoplasmic protein that contains a DHH/DHHA1 domain. It can act on cyclic di-3',5'-adenylate with a much lower activity (cf. EC 3.1.4.59, cyclic-di-AMP phosphodiesterase). Activity requires Mn2+ and is inhibited by ppGpp.
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The enzyme appears in viruses and cellular organisms
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
BB0619
Dhhp
MSMEG_2630
pApA hydrolase
-
-
-
-
PDE
PDE2
SAUSA300_1650
PDE2
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
5'-O-phosphonoadenylyl-(3'->5')-adenosine + H2O = 2 AMP
-
-
-
-
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SYSTEMATIC NAME
IUBMB Comments
5'-O-phosphonoadenylyl-(3'->5')-adenosine phosphohydrolase
The enzyme, characterized from the Gram-positive bacterium Staphylococcus aureus, is a cytoplasmic protein that contains a DHH/DHHA1 domain. It can act on cyclic di-3',5'-adenylate with a much lower activity (cf. EC 3.1.4.59, cyclic-di-AMP phosphodiesterase). Activity requires Mn2+ and is inhibited by ppGpp.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
5'-O-phosphonoadenylyl-(3'->5')-adenosine + H2O
2 AMP
-
-
-
?
5'-O-phosphonoadenylyl-(3'->5')-adenosine + H2O
2 AMP
-
-
-
?
5'-O-phosphonoadenylyl-(3'->5')-adenosine + H2O
2 AMP
-
-
-
?
5'-O-phosphonoadenylyl-(3'->5')-adenosine + H2O
2 AMP
-
-
-
?
cyclic di-3',5'-adenylate + H2O
5'-O-phosphonoadenylyl-(3'->5')-adenosine
-
-
-
?
cyclic di-3',5'-adenylate + H2O
5'-O-phosphonoadenylyl-(3'->5')-adenosine
-
-
-
?
cyclic di-3',5'-adenylate + H2O
5'-O-phosphonoadenylyl-(3'->5')-adenosine
-
-
-
?
additional information
?
-
Pde2 is capable of hydrolyzing c-di-AMP, but5 preferentially converts linear 5'-phosphadenylyl-adenosine (pApA) to AMP. No substrate: ATP
-
-
?
additional information
?
-
-
Pde2 is capable of hydrolyzing c-di-AMP, but5 preferentially converts linear 5'-phosphadenylyl-adenosine (pApA) to AMP. No substrate: ATP
-
-
?
additional information
?
-
Pde2 directly hydrolyzes c-di-AMP into AMP. Additionally, Pde2 degrades 5'-O-phosphonoadenylyl-(3'->5')-adenosine into AMP. Pde2 prefers substrate 5'-O-phosphonoadenylyl-(3'->5')-adenosine
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
5'-O-phosphonoadenylyl-(3'->5')-adenosine + H2O
2 AMP
-
-
-
?
5'-O-phosphonoadenylyl-(3'->5')-adenosine + H2O
2 AMP
-
-
-
?
5'-O-phosphonoadenylyl-(3'->5')-adenosine + H2O
2 AMP
-
-
-
?
cyclic di-3',5'-adenylate + H2O
5'-O-phosphonoadenylyl-(3'->5')-adenosine
-
-
-
?
cyclic di-3',5'-adenylate + H2O
5'-O-phosphonoadenylyl-(3'->5')-adenosine
-
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
Pde is strictly dependent on Co2+, Mn2+, Mg2+ or Fe2+, with maximum activity with Mn2+ as a cofactor
Fe2+
Pde is strictly dependent on Co2+, Mn2+, Mg2+ or Fe2+, with maximum activity with Mn2+ as a cofactor
Mg2+
Pde is strictly dependent on Co2+, Mn2+, Mg2+ or Fe2+, with maximum activity with Mn2+ as a cofactor
Mn2+
Mn2+
Pde is strictly dependent on Co2+, Mn2+, Mg2+ or Fe2+, with maximum activity with Mn2+ as a cofactor
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0239
5'-O-phosphonoadenylyl-(3'->5')-adenosine
pH 7.5, 37°C
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
protein contains a DHH-DHHAI domain
UniProt
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
protein possesses two transmembrane helices
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
physiological function
a Pde2 mutant strain displays a growth defect in the early growth phase. The mutant displays an increase in cellular c-di-AMP and 5'-O-phosphonoadenylyl-(3'->5')-adenosine levels and increased oxacillin resistance. A strain producing a high level of c-di-AMP has increased and a stain producing low levels has decreased acid resistance
physiological function
deficiency of Pde significantly enhances intracellular C12-C20 fatty acid accumulation. Superfluous c-di-AMP in Mycobacterium smegmatis may lead to abnormal colonial morphology
physiological function
deletion of either isoform Pde1 or Pde2 results in a moderate increase of the c-di-AMP levels compared with the parental strain. Deletion of both genes results in an up to 4fold increase in c-di-AMP levels compared to that of the parental strain. Both Pde1 and Pde2 play a role in pneumococcal growth. Deletion of either isoform Pde1 or Pde2 reduces the growth rate slightly, and the double mutant synergizes the reduction
physiological function
DhhP is essential for Borrelia burgdorferi growth both in vitro and in the mammalian host. The conditional DhhP mutant has a dramatic increase in intracellular c-di-AMP level in comparison to the isogenic wild-type strain. Elevated cellular c-di-AMP in Borrelia burgdorferi does not result in an increased resistance to beta-lactamase antibiotics. The DhhP mutant is defective in induction of the sigmaS factor, RpoS, and the RpoS-dependent outer membrane virulence factor OspC
physiological function
-
a Pde2 mutant strain displays a growth defect in the early growth phase. The mutant displays an increase in cellular c-di-AMP and 5'-O-phosphonoadenylyl-(3'->5')-adenosine levels and increased oxacillin resistance. A strain producing a high level of c-di-AMP has increased and a stain producing low levels has decreased acid resistance
-
physiological function
-
deficiency of Pde significantly enhances intracellular C12-C20 fatty acid accumulation. Superfluous c-di-AMP in Mycobacterium smegmatis may lead to abnormal colonial morphology
-
physiological function
-
DhhP is essential for Borrelia burgdorferi growth both in vitro and in the mammalian host. The conditional DhhP mutant has a dramatic increase in intracellular c-di-AMP level in comparison to the isogenic wild-type strain. Elevated cellular c-di-AMP in Borrelia burgdorferi does not result in an increased resistance to beta-lactamase antibiotics. The DhhP mutant is defective in induction of the sigmaS factor, RpoS, and the RpoS-dependent outer membrane virulence factor OspC
-
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). A0A0H2XFX6_STAA3
Staphylococcus aureus (strain USA300)
313
0
35097
TrEMBL
-
A0A0H2ZNP2_STRP2
Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)
311
0
34967
TrEMBL
-
A0QVM9_MYCS2
Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
340
0
35536
TrEMBL
-
O51564_BORBU
Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680)
320
0
36190
TrEMBL
-
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
protein possesses two transmembrane helices, a PAS domain, an atypical GGDEF domain, a DHH domain, and a DHHA1 domain
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D134a/H135A/H136A
mutation in DHH domain, complete loss of catalytic activity
G313A/G314A/G315A/H316A
mutation in DHHA1 domain, mutant displays residual activity
D134a/H135A/H136A
-
mutation in DHH domain, complete loss of catalytic activity
-
G313A/G314A/G315A/H316A
-
mutation in DHHA1 domain, mutant displays residual activity
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ye, M.; Zhang, J.J.; Fang, X.; Lawlis, G.B.; Troxell, B.; Zhou, Y.; Gomelsky, M.; Lou, Y.; Yang, X.F.
DhhP, a cyclic di-AMP phosphodiesterase of Borrelia burgdorferi, is essential for cell growth and virulence
Infect. Immun.
82
1840-1849
2014
Borreliella burgdorferi (O51564), Borreliella burgdorferi DSM 4680 (O51564)
brenda
Tang, Q.; Luo, Y.; Zheng, C.; Yin, K.; Ali, M.; Li, X.; He, J.
Functional analysis of a c-di-AMP-specific phosphodiesterase MsPDE from Mycobacterium smegmatis
Int. J. Biol. Sci.
11
813-824
2015
Mycolicibacterium smegmatis (A0QVM9), Mycolicibacterium smegmatis ATCC 700084 (A0QVM9)
brenda
Bai, Y.; Yang, J.; Eisele, L.E.; Underwood, A.J.; Koestler, B.J.; Waters, C.M.; Metzger, D.W.; Bai, G.
Two DHH subfamily 1 proteins in Streptococcus pneumoniae possess cyclic di-AMP phosphodiesterase activity and affect bacterial growth and virulence
J. Bacteriol.
195
5123-5132
2013
Streptococcus pneumoniae D39 (A0A0H2ZNP2)
brenda
Bowman, L.; Zeden, M.S.; Schuster, C.F.; Kaever, V.; Gruendling, A.
New insights into the cyclic di-adenosine monophosphate (c-di-AMP) degradation pathway and the requirement of the cyclic dinucleotide for acid stress resistance in Staphylococcus aureus
J. Biol. Chem.
291
26970-26986
2016
Staphylococcus aureus (A0A0H2XFX6)
brenda
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