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Information on EC 2.7.13.3 - histidine kinase and Organism(s) Bacillus subtilis and UniProt Accession Q45614
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2.7.13.3 histidine kinaseIUBMB Comments
This entry has been included to accommodate those protein-histidine kinases for which the phosphorylation site has not been established (i.e. either the pros- or tele-nitrogen of histidine). A number of histones can act as acceptor.
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Word Map
- 2.7.13.3
- autophosphorylation
- photoreceptors
-
far-red
- seedling
-
phosphorelay
- chromophore
-
perception
-
regulons
- hypocotyls
-
quorum
-
perceived
- pfr
-
chemoreceptor
-
senses
-
light-induced
- chey
-
flagellar
- synechocystis
-
etiolated
- caulobacter
-
photomorphogenesis
-
transmitter
-
quorum-sensing
-
fluence
- biliverdin
-
cryptochrome
- crescentus
-
methyl-accepting
-
dark-grown
- radiodurans
-
transphosphorylation
-
autoinducer
-
histidine-containing
-
chemosensory
-
photomorphogenic
-
extracytoplasmic
- arca
- deinococcus
- phototropins
- tetrapyrrole
- ompc
- c-di-gmp
-
diguanylate
- spo0a
-
four-helix
-
gravitropism
-
photoresponses
-
non-cognate
- xanthus
-
photoisomerization
- synthesis
- medicine
The taxonomic range for the selected organisms is: Bacillus subtilis
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
histidine kinase, sensor kinase, sensor protein, phytochrome a, ethylene receptor, sensor histidine kinase, bacteriophytochrome, ornithine decarboxylase antizyme, chemotaxis protein, hybrid histidine kinase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
alkaline phosphatase synthesis sensor protein phoR
-
KINA
sensor histidine kinase
sporulation kinase A (stage II sporulation protein J)
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
phospho group transfer
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
ATP:protein-L-histidine N-phosphotransferase
This entry has been included to accommodate those protein-histidine kinases for which the phosphorylation site has not been established (i.e. either the pros- or tele-nitrogen of histidine). A number of histones can act as acceptor.
CAS REGISTRY NUMBER
COMMENTARY
99283-67-7
protein-histidine kinases, EC 2.7.13.1, EC 2.7.13.2, and EC 2.7.13.3 are not distinguished in Chemical Abstracts
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
ATP + a protein
ADP + a phosphoprotein
kinase of the alternate pathway for phosphorylating the SpoOF protein
-
-
?
ATP + Spo0F protein L-histidine
ADP + Spo0F protein N-phospho-L-histidine
-
-
-
-
?
ATP + a protein
ADP + a phosphoprotein
the essential two-component regulatory system yycF/yycG modulates expression of the ftsAZ operon in Bacillus subtilis
-
-
?
ATP + a protein
ADP + a phosphoprotein
the two-component signal transduction system yycF/yycG is essential for growth of Bacillus subtilis
-
-
?
ATP + YycF
ADP + phospho-YycF
the formation of the division septum is necessary for YycG phosphorylation of YycF
-
-
?
ATP + YycF
ADP + phospho-YycF
a response regulator/transcription factor
-
-
?
ATP + protein L-histidine
ADP + protein N-phospho-L-histidine
-
-
-
?
ATP + protein L-histidine
ADP + protein N-phospho-L-histidine
-
-
-
?
additional information
?
-
The sensor histidine kinase YycG acts in a two-component system with response regulator/transcription factor YycF in Bacillus subtilis controling the synthesis of autolysins and autolysin inhibitors, that function in cell wall remodelling and cell separation, YycG sensor histidine kinase is a component of and perceives infirmation at the division septum in growing cells constituting a positive feedback loop, that serves to co-ordinate cell division with cell wall homeostasis, overview
-
-
?
additional information
?
-
-
The sensor histidine kinase YycG acts in a two-component system with response regulator/transcription factor YycF in Bacillus subtilis controling the synthesis of autolysins and autolysin inhibitors, that function in cell wall remodelling and cell separation, YycG sensor histidine kinase is a component of and perceives infirmation at the division septum in growing cells constituting a positive feedback loop, that serves to co-ordinate cell division with cell wall homeostasis, overview
-
-
?
additional information
?
-
YycG interacts with the latter stage cell division proteins DivIB, Pbp2B and FtsL
-
-
?
additional information
?
-
-
YycG interacts with the latter stage cell division proteins DivIB, Pbp2B and FtsL
-
-
?
additional information
?
-
mediates the transfer of phosphate to the Spo0A and Spo0F sporulation regulatory proteins. Spo0F protein is a much better phosphoreceptor for this kinase than Spo0A protein in vitro
-
-
?
additional information
?
-
two-component regulatory system CssR-CssS, is required for the cell to survive the severe secretion stress caused by a combination of high-level production of the alpha-amylase AmyQ and reduced levels of the extracytoplasmic folding factor PrsA. The Css system is required to degrade misfolded exported proteins at the membrane-cell wall interface. CssS represents the first identified sensor for extracytoplasmic protein misfolding in a Gram-positive eubacterium
-
-
?
additional information
?
-
the CitST two-component system regulates the expression of the Mg-citrate transporter in Bacillus subtilis
-
-
?
additional information
?
-
mediates the transfer of phosphate to the Spo0A and Spo0F sporulation regulatory proteins
-
-
?
additional information
?
-
the enzyme is a regulator of chemotaxis
-
-
?
additional information
?
-
enzyme is responsible for regulation of subtilin biosynthesis
-
-
?
additional information
?
-
enzyme is responsible for regulation of subtilin biosynthesis
-
-
?
additional information
?
-
activation role for ResD, and to a lesser extent ResE, in global regulation of aerobic and anaerobic respiration in Bacillus subtilis
-
-
?
additional information
?
-
the N-terminal Per-ARNT-Sim domain plays a critical role in the catalytic activity of this enzyme, a significant decrease occurs of the autophosphorylation rate of a KinA protein lacking this domain
-
-
?
additional information
?
-
-
the N-terminal Per-ARNT-Sim domain plays a critical role in the catalytic activity of this enzyme, a significant decrease occurs of the autophosphorylation rate of a KinA protein lacking this domain
-
-
?
additional information
?
-
the enzyme performs catalytic autophosphorylation, mechanism and kinetics, overview. DesK displays a compact structure at the ATP-binding pocket: the ATP lid loop is short with no secondary structural organization and becomes ordered upon ATP loading. Sequence conservation mapping onto the molecular surface, semi-flexible protein-protein docking simulations, and structure-based point mutagenesis present a specific domain-domain geometry during autophosphorylation catalysis. In vitro, DesKC catalyzes three different reactions depending on the phosphorylation states of the partners: its own phosphorylation, phosphotransfer to DesR, and dephosphorylation of phospho-DesR. Protein-protein docking and modelling of the enzyme in autophosphorylation state, residues involved in domain-domain interaction modulate catalysis, overview
-
-
?
additional information
?
-
-
the enzyme performs catalytic autophosphorylation, mechanism and kinetics, overview. DesK displays a compact structure at the ATP-binding pocket: the ATP lid loop is short with no secondary structural organization and becomes ordered upon ATP loading. Sequence conservation mapping onto the molecular surface, semi-flexible protein-protein docking simulations, and structure-based point mutagenesis present a specific domain-domain geometry during autophosphorylation catalysis. In vitro, DesKC catalyzes three different reactions depending on the phosphorylation states of the partners: its own phosphorylation, phosphotransfer to DesR, and dephosphorylation of phospho-DesR. Protein-protein docking and modelling of the enzyme in autophosphorylation state, residues involved in domain-domain interaction modulate catalysis, overview
-
-
?
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
ATP + YycF
ADP + phospho-YycF
the formation of the division septum is necessary for YycG phosphorylation of YycF
-
-
?
ATP + a protein
ADP + a phosphoprotein
kinase of the alternate pathway for phosphorylating the SpoOF protein
-
-
?
ATP + a protein
ADP + a phosphoprotein
the essential two-component regulatory system yycF/yycG modulates expression of the ftsAZ operon in Bacillus subtilis
-
-
?
ATP + a protein
ADP + a phosphoprotein
the two-component signal transduction system yycF/yycG is essential for growth of Bacillus subtilis
-
-
?
ATP + protein L-histidine
ADP + protein N-phospho-L-histidine
-
-
-
?
ATP + protein L-histidine
ADP + protein N-phospho-L-histidine
-
-
-
?
additional information
?
-
The sensor histidine kinase YycG acts in a two-component system with response regulator/transcription factor YycF in Bacillus subtilis controling the synthesis of autolysins and autolysin inhibitors, that function in cell wall remodelling and cell separation, YycG sensor histidine kinase is a component of and perceives infirmation at the division septum in growing cells constituting a positive feedback loop, that serves to co-ordinate cell division with cell wall homeostasis, overview
-
-
?
additional information
?
-
-
The sensor histidine kinase YycG acts in a two-component system with response regulator/transcription factor YycF in Bacillus subtilis controling the synthesis of autolysins and autolysin inhibitors, that function in cell wall remodelling and cell separation, YycG sensor histidine kinase is a component of and perceives infirmation at the division septum in growing cells constituting a positive feedback loop, that serves to co-ordinate cell division with cell wall homeostasis, overview
-
-
?
additional information
?
-
two-component regulatory system CssR-CssS, is required for the cell to survive the severe secretion stress caused by a combination of high-level production of the alpha-amylase AmyQ and reduced levels of the extracytoplasmic folding factor PrsA. The Css system is required to degrade misfolded exported proteins at the membrane-cell wall interface. CssS represents the first identified sensor for extracytoplasmic protein misfolding in a Gram-positive eubacterium
-
-
?
additional information
?
-
the CitST two-component system regulates the expression of the Mg-citrate transporter in Bacillus subtilis
-
-
?
additional information
?
-
mediates the transfer of phosphate to the Spo0A and Spo0F sporulation regulatory proteins
-
-
?
additional information
?
-
the enzyme is a regulator of chemotaxis
-
-
?
additional information
?
-
enzyme is responsible for regulation of subtilin biosynthesis
-
-
?
additional information
?
-
enzyme is responsible for regulation of subtilin biosynthesis
-
-
?
additional information
?
-
activation role for ResD, and to a lesser extent ResE, in global regulation of aerobic and anaerobic respiration in Bacillus subtilis
-
-
?
additional information
?
-
the N-terminal Per-ARNT-Sim domain plays a critical role in the catalytic activity of this enzyme, a significant decrease occurs of the autophosphorylation rate of a KinA protein lacking this domain
-
-
?
additional information
?
-
-
the N-terminal Per-ARNT-Sim domain plays a critical role in the catalytic activity of this enzyme, a significant decrease occurs of the autophosphorylation rate of a KinA protein lacking this domain
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ATP
DesK displays a compact structure at the ATP-binding pocket: the ATP lid loop is short with no secondary structural organization and becomes ordered upon ATP loading. Sequence conservation mapping onto the molecular surface, semi-flexible protein-protein docking simulations, and structure-based point mutagenesis present a specific domain-domain geometry during autophosphorylation catalysis
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
YycH
an extracytoplasmic membrane anchored protein. Enzyme YycG activity in non-dividing cells is suppressed by its interaction with YycH and YycI. YycG regulation is accomplished through its transmembrane and extra-membrane domains interacting with the membrane associated YycH and YycI proteins that do not localize to the divisome
-
YycI
an extracytoplasmic membrane anchored protein. Enzyme YycG activity in non-dividing cells is suppressed by its interaction with YycH and YycI. YycG regulation is accomplished through its transmembrane and extra-membrane domains interacting with the membrane associated YycH and YycI proteins that do not localize to the divisome
-
kinase inhibitor protein
-
the kinase inhibitor protein KipI prevents sporulation by binding KinA and inhibiting the autophosphorylation reaction
-
suppressor of dnaA
-
Sda, inhibits KinA by directly binding to the autokinase domain
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
subtilin
subtilin activates the two-component system SpaRK of Bacillus subtilis to autoinduce its biosynthesis. Amino acid position 20 is crucial for SpaK activation by subtilin. An engineered nisin molecule with phenylalanine at position 20 (nisin N20F) is able to activate SpaK in a specific manner. In combination with the N-terminal tryptophan of subtilin (nisin I1W/N20F), SpaK autoinduction reaches almost the level of subtilin-mediated autoinduction. The overall structure of subtilin is also important for its association with the histidine kinase. The destruction of the second lanthionine ring (subtilin C11A, ring B), as well as mutations that interfere with the flexibility of the hinge region located between lanthionine rings C and D (subtilin L21P/Q22P), abolish SpaK autoinduction. The C-terminal part of subtilin is needed for efficient SpaK autoinduction, but the destruction of lanthionine rings D and E has no measurable impact
-
additional information
-
KinC becomes active by forming a homotetramer via the N-terminal PAS domain, but its activity is independent of both the lipid raft and the potassium leakage
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
Michaelis-Menten kinetics
-
additional information
additional information
-
Michaelis-Menten kinetics
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
wild-type strain JH642 and conditional ftsZ expression strain KP444, gene yycG
SwissProt
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
division septum, a cytoplasmic domain of YycG is sufficient for septum localization. All recombinant truncated YycG constructs including the shortest one that featured only the cytoplasmic PAS and the two catalytic HisKA and HATPase domains retain the ability to localize to the septum
the YycG kinase is associated in the membrane as a complex with YycH and YycI through interaction of their transmembrane domains
-
KinC localizes as puncta along the cell membrane in a manner independent of FloTA proteins, localization pattern of GFP-tagged KinC, overview. KinC does not localize at specific sites on membrane under the conditions tested
-
additional information
the enzyme structure displays an N-terminal sensor domain (about 150 residues) with almost no extracellular region, other than the loops that connect the four or five transmembrane segments
additional information
YycG is located at the division septum in growing cells, YycG localization is dependent upon FtsZ, but independent of YycH and YycI
-
additional information
-
YycG is located at the division septum in growing cells, YycG localization is dependent upon FtsZ, but independent of YycH and YycI
-
additional information
the enzyme has a C-terminal cytoplasmic catalytic core of about 220 residues
-
additional information
-
the enzyme has a C-terminal cytoplasmic catalytic core of about 220 residues
-
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
N-terminal truncations of YycG lose negative regulation of their activity, phenotypes, overview. Truncated YycG constructs fail to co-immunoprecipitate with the regulatory proteins YycH and YycI. Deletion or depletion of later stage cell division proteins does not perturb YycG localization
physiological function
The enzyme YycG is part of the two-component signal transduction system YycFG or WalRK. The YycG (WalK) sensor histidine kinase coordinates cell wall remodeling with cell division in Gram-positive bacteria by controlling the transcription of genes for autolysins and their inhibitors. The essential enzyme YycG senses cell division and is enzymatically activated by associating with the divisome at the division septum. The cytoplasmic PAS domain of this multidomain trans-membrane kinase is a determining factor translocating the kinase to the division septum. YycG activity in non-dividing cells is suppressed by its interaction with YycH and YycI and its activation is coordinated to cell division in dividing cells by specific interactions that occur within the divisome. This regulation is accomplished through its transmembrane and extra-membrane domains interacting with the membrane associated YycH and YycI proteins that do not localize to the divisome. Signaling by YycG involves later stage cell division proteins, overview
evolution
malfunction
the DELTAkinD mutant (and less significantly the DELTAkinC mutant) has the most defective phenotype, while all other kin kinase mutants are able to respond to the addition of GM by forming robust biofilm
metabolism
physiological function
additional information
evolution
glycerol and manganese have a similar biofilm-promoting effect in two related Bacillus species, Bacillus licheniformis and Bacillus cereus, indicating that the biofilm-promoting effect of GM is conserved in Bacillus species
evolution
the class I enzyme DesK belongs to the HK family HPK7, which includes the nitrogen metabolism regulators NarX/Q and the antibiotic sensor LiaS among other important sensor kinases
metabolism
biofilm formation depends on the synthesis of an extracellular matrix, which is indirectly regulated by the transcriptional regulator Spo0A. The activity of Spo0A depends on its phosphorylation state. Low and intermediate levels of phosphorylated Spo0A lead to induction of the epsA-O and tapA operons, which results in production of the extracellular matrix and thus biofilm formation, while at high levels, the matrix genes are repressed. The level of phosphorylated Spo0A is controlled by a network of kinases and phosphatases, which respond to environmental and physiological signals. Biofilm formation of Bacillus subtilis in LB medium is triggered by a combination of glycerol and manganese via KinD sensoring. The kinase KinD contains an extracellular domain, so called CACHE domain, for sensing small chemical molecules released from plant host during colonization. The glpK-encoded glycerol kinase and glpF encoded glycerol transport facilitator are critical in utilization of glycerol as a carbon source
metabolism
five distinct sensor kinases (KinA, KinB, KinC, KinD, and KinE) have the capability of transferring a phosphoryl group into the phosphorelay to control the level of phosphorylated transcriptional regulator Spo0A present at any moment in the cell
metabolism
-
in response to starvation, Bacillus subtilis cells differentiate into different subsets, undergoing cannibalism, biofilm formation or sporulation. These processes require a multiple component phosphorelay, wherein the master regulator Spo0A is activated upon phosphorylation by one or a combination of five histidine kinases (KinA-KinE) via two intermediate phosphotransferases, Spo0F and Spo0B. KinC controls the expression of cannibalism genes in a manner independent of surfactin andthe bacterial flotillin-like proteins FloT and FloA
physiological function
-
histidine kinase KinA promotes the initiation of sporulation when nutrients are limiting
physiological function
DesK is a sensor histidine kinase that allows Bacillus subtilis to respond to cold shock, triggering the adaptation of membrane fluidity via transcriptional control of a fatty acid desaturase. The transmembrane region can sense temperature-modulated fluidity changes of lipid bilayers, transmitting the signal toward the C-terminal cytoplasmic catalytic core of about 220 residues. The cold thermal stimulus is detected by DesK, which then interacts with its cognate response regulator, DesR, constituting a canonical two-component system, TCS
physiological function
-
enzyme KinC regulates cannibalism and biofilm formation, and activates the expression of cannibalism genes in response to starvation in a manner dependent on phosphorelay. KinC activity and the membrane localization are independent of both the lipid raft marker proteins FloTA and cytoplasmic potassium concentration. KinC becomes active by forming a homotetramer via the N-terminal PAS domain
physiological function
KinD is a principal histidine kinase for sensing the presence of GM, exclusively by its extracellular CACHE domain. A combination of glycerol and manganese promotes multicellular development by Bacillus subtilis. The strong biofilm-stimulating activity in response to the addition of a combination of glycerol and manganese is indeed due to upregulation of the matrix genes mediated mainly by the histidine kinase KinD
physiological function
the activity of transcriptional regulator Spo0A depends on its phosphorylation state. The level of phosphorylated Spo0A is controlled by a network of kinases and phosphatases, which respond to environmental and physiological signals. KinD is a principal histidine kinase responsible for sensing the presence of glycerol and manganese, which trigger biofilm formation of Bacillus subtilis in LB medium, exclusively by its extracellular CACHE sensor domain. The biofilm-promoting effect of glycerol and manganese is mediated mainly by the histidine kinase KinD
physiological function
a helix linking the transmembrane region with the cytoplasmic catalytic domain is involved in DesK pH sensing. This helix contains several glutamate, lysine, and arginine residues At neutral pH, the linker forms an alpha helix that is stabilized by hydrogen bonds in the i, i + 4 register and favors the kinase state. At low pH, protonation of glutamate residues breaks salt bridges, which results in helix destabilization and interruption of signaling. This mechanism inhibits unsaturated fatty acid synthesis and rigidifies the membrane when Bacillus subtilis grows in acidic conditions
additional information
KinD is located upstream of Spo0A and AbrB in the pathway. CACHE is present in many bacterial sensory histidine kinases and is capable of sensing small molecules, often in the presence of cofactors, such as metal ions
additional information
-
KinD is located upstream of Spo0A and AbrB in the pathway. CACHE is present in many bacterial sensory histidine kinases and is capable of sensing small molecules, often in the presence of cofactors, such as metal ions
additional information
protein-protein docking analysis of the catalytic domain with the dimerization DHp domain of DesK, the C-terminal part of the ATP lid interacts with helix alpha1 of the DHp, through hydrogen bonds between His335 and Asp289 as well as Gly199 with Lys333, overview
additional information
-
protein-protein docking analysis of the catalytic domain with the dimerization DHp domain of DesK, the C-terminal part of the ATP lid interacts with helix alpha1 of the DHp, through hydrogen bonds between His335 and Asp289 as well as Gly199 with Lys333, overview
additional information
-
the N-terminal transmembrane domain is dispensable but the PAS domain is needed for the kinase activity
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
46000
-
YbdK-transmembrane domain dodecyl-phosphocholine complex, solution state NMR T1/T2 relaxation analysis
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homodimer
homotetramer
-
KinC becomes active by forming a homotetramer via the N-terminal PAS domain
additional information
homodimer
-
YbdK-transmembrane domain forms homodimers in dodecyl-phosphocholine micelles, cross-linking assay and analytical ultracentrifugation analysis
additional information
determination of the importance of several residues at the dimer interface for KinA enzymatic activity in vitro and in vivo, KinA architecture and domain structure, and PAS-A domain organization and secondary structure, overview
additional information
-
determination of the importance of several residues at the dimer interface for KinA enzymatic activity in vitro and in vivo, KinA architecture and domain structure, and PAS-A domain organization and secondary structure, overview
additional information
analysis of the structure of enzyme catalytic and ATP-binding domain using the crystal structure, overview
additional information
-
analysis of the structure of enzyme catalytic and ATP-binding domain using the crystal structure, overview
additional information
-
the N-terminal transmembrane domain is dispensable but the PAS domain is needed for the kinase activity
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
phosphoprotein
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant DesK mutant H188V catalytic and ATP-binding domain in complex with ATP, by hanging drop vapour diffusion method, mixing of 0.002 ml of 10 mg/ml protein in 50 mM Tris-HCl, pH 8.0, 300 mM NaCl, 0.5 mM DTT, 10 mM MgCl2, 5 mM ATP, and 5 mM BeF3, with 0.002 ml of reservoir solution containing 20% PEG 3350, 0.2 M NH4ClX-ray diffraction structure determination and analysis at 1.8 A resolution
purified recombinant residues 10-117 of KinA, fused to an N-terminal His6Gbeta1-tag and a TEV protease site in the tag-protein linker, free or as selenomethionine-tagged variant, hanging-drop vapor-diffusion method, 20°C, mixing of 0.001 ml 7 mg/mL protein solution containing 25 mM Tris pH 8.0, 100 mM NaCl, with 0.001 ml well solution containing 13-15% w/v PEG 10000, 0.1 M ammonium acetate, and 0.1 M bis-Tris, pH 5.5, and with 20 mM DTT in case of the selenomethionine-labeled protein, 4 days, cryoprotetion using 25% v/v glycerol, X-ray diffraction structure determination and analysis at 1.7-2.0 A resolution
the phosphorylated cytoplasmic domain of DesK is crystallized by hanging drop vapor diffusion, using 10% (w/v) PEG 3000, 0.1 M CHES, pH 9.5, and 10 mM MgCl2, at 18°C
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
F436S
-
the mutation increases the efficiency of sporulation in cells overexpressing KinA inhibitor Sda by about 10fold while actually reducing the efficiency of sporulation in cells that lack sda
G192C/G334C
site-directed mutagenesis, the Cys-engineered mutant is used for interdomain disulfide covalent bonding studies
H188V
I108A
the point mutation does not affect KinA autophosphorylation activity, but interfers with KinA PAS-A dimerization
I95A
the point mutation slightly reduces the KinA autophosphorylation activity and interfers with KinA PAS-A dimerization
I95E
the point mutation reduces the KinA autophosphorylation activity and interfers with KinA PAS-A dimerization
K32E/E36K
mutations in linker region, mutant shows higher activity at higher pH and maintains pH regulation
P410L
-
the mutation increases the efficiency of sporulation in cells overexpressing KinA inhibitor Sda by about 10fold while actually reducing the efficiency of sporulation in cells that lack sda
Q193C/G334C
site-directed mutagenesis, the Cys-engineered mutant is used for interdomain disulfide covalent bonding studies
R34E/ E36K/ R37E
mutations in linker region, mutant is inactive and insensitive to pH
S196C/G334C
site-directed mutagenesis, the Cys-engineered mutant is used for interdomain disulfide covalent bonding studies
Y29A
the point mutation is an activating mutation in full-length KinA, but interfers with KinA PAS-A dimerization shifting the PAS-A monomer/dimer equilibrium significantly toward the monomeric form
additional information
H188V
the mutant retains the phosphatase activity of the wild type protein, the mutation triggers formation of an N-terminal 2-helical coiled-coil and extensive dimerization and histidine phosphotransfer domain-ATP-binding domain association
additional information
YycG depletion does not interfere with FtsZ localization, YycG is less active as a kinase of YycF in the absence of a division septum
additional information
-
YycG depletion does not interfere with FtsZ localization, YycG is less active as a kinase of YycF in the absence of a division septum
additional information
generation of several truncation mutant of enzyme YycG. All truncated YycG constructs including the shortest one that featured only the cytoplasmic PAS and the two catalytic HisKA and HATPase domains retain the ability to localize to the septum. N-terminal truncations of YycG lose negative regulation of their activity, truncated YycG constructs fail to co-immunoprecipitate with the regulatory proteins YycH and YycI
additional information
-
generation of several truncation mutant of enzyme YycG. All truncated YycG constructs including the shortest one that featured only the cytoplasmic PAS and the two catalytic HisKA and HATPase domains retain the ability to localize to the septum. N-terminal truncations of YycG lose negative regulation of their activity, truncated YycG constructs fail to co-immunoprecipitate with the regulatory proteins YycH and YycI
additional information
a significant decrease occurs of the autophosphorylation rate of a KinA protein lacking the N-terminal Per-ARNT-Sim domain, which plays a critical role in the catalytic activity of this enzyme
additional information
-
a significant decrease occurs of the autophosphorylation rate of a KinA protein lacking the N-terminal Per-ARNT-Sim domain, which plays a critical role in the catalytic activity of this enzyme
additional information
deletion in the abrB gene suppresses the DELTAkinD mutation
additional information
-
deletion in the abrB gene suppresses the DELTAkinD mutation
additional information
generation of a KinD-DegS hybrid kinase using overlapping PCR, overview. DegS is a sensory histidine kinase that is able to phosphorylate DegU, a DNA-binding response regulator. The DegS-DegU system controls many genes (both positively and negatively) including the fla/che operon that encodes dozens of genes involved in motility and chemotaxis
additional information
-
generation of a KinD-DegS hybrid kinase using overlapping PCR, overview. DegS is a sensory histidine kinase that is able to phosphorylate DegU, a DNA-binding response regulator. The DegS-DegU system controls many genes (both positively and negatively) including the fla/che operon that encodes dozens of genes involved in motility and chemotaxis
additional information
-
in vivo quantitative domain-based stepwise deletion analyses to determine the minimum functional domain of KinC, overview
additional information
a truncated version of DesK, which lacks the transmembrane domain, is not pH-dependent
additional information
-
a truncated version of DesK, which lacks the transmembrane domain, is not pH-dependent
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
DEAE-agarose column chromatography, Ni-NTA column chromatography, glutathione-agarose resin column chromatography, and Superdex 200 gel filtration
-
recombinant His-tagged enzyme KinC from Escherichia coli strain BL21(DE3) by nicke affinity chromatography
-
recombinant N-terminally His6-tagged wild-type and mutant enzymes from Escherichia coli strain M15/pREP4 by nickel affinity chromatography, dialysis, and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene yycG, recombinant expression of trncated enzyme mutants. Expression of a soluble cytoplasmic YycG construct in a bacterial two-hybrid expression system using the full-length YycG or a truncated YycGDELTA211-611 that lacks all cytoplasmic domains, and cell division proteins FtsZ, FtsA, FtsW, DivIB, DivIC, FtsL, Pbp2B, EzrA, ZapA, SepF and MinJ as C-terminal fusions to the individual domains (T18 and T25) of the two-domain Bordatella pertussis adenylate cyclase protein. YycG makes specific interactions with FtsL, DivIB, Pbp2B and interactions with FtsW and EzrA appear also possible
expression of residues 10-117 of KinA, fused to an N-terminal His6Gbeta1-tag and a TEV protease site in the tag-protein linker, in Escherichia coli strain BL21(DE3), expresssion of the selenomethionine variant in Escherichia coli strain B834
gene desK, recombinant expression of N-terminally His6-tagged wild-type and mutant enzymes in Escherichia coli strain M15/pREP4
gene kinD, recombinant expression of the chimeric KinD-DegS hybrid kinase under control of the kinD native promoter in Escherichia coli strain DH5alpha, construct transfection to Bacillus subtilis strain NCIB3610 by SPP1 phage transduction
recombinant expression of His-tagged enzyme KinC in Escherichia coli strain BL21(DE3)
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Klein, C.; Entian, K.D.
Genes involved in self-protection against the lantibiotic subtilin produced by Bacillus subtilis ATCC 6633
Appl. Environ. Microbiol.
60
2793-2801
1994
Bacillus subtilis (P33113)
Hyyrylainen, H.L.; Bolhuis, A.; Darmon, E.; Muukkonen, L.; Koski, P.; Vitikainen, M.; Sarvas, M.; Pragai, Z.; Bron, S.; van Dijl, J.M.; Kontinen, V.P.
A novel two-component regulatory system in Bacillus subtilis for the survival of severe secretion stress
Mol. Microbiol.
41
1159-1172
2001
Bacillus subtilis (O32193)
Kunst, F.; Ogasawara, N.; Moszer, I.; et al
The complete genome sequence of the gram-positive bacterium Bacillus subtilis
Nature
390
249-256
1997
Bacillus subtilis (O32193), Bacillus subtilis (O34427), Bacillus subtilis (P13799), Bacillus subtilis (P16497), Bacillus subtilis (P23545), Bacillus subtilis (P29072), Bacillus subtilis (P35164), Bacillus subtilis (P39764), Bacillus subtilis (Q08430), Bacillus subtilis (Q45614)
Medina, N.; Vannier, F.; Roche, B.; Autret, S.; Levine, A.; Seror, S.J.
Sequencing of regions downstream of addA (98 degrees) and citG (289 degrees) in Bacillus subtilis
Microbiology
143
3305-3308
1997
Bacillus subtilis (O32193)
Wipat, A.; Brignell, S.C.; Guy, B.J.; et al.
The yvsA-yvqA (293 degrees-289 degrees) region of the Bacillus subtilis chromosome containing genes involved in metal ion uptake and a putative sigma factor
Microbiology
144
1593-1600
1998
Bacillus subtilis (O32193)
-
Yamamoto, H.; Murata, M.; Sekiguchi, J.
The CitST two-component system regulates the expression of the Mg-citrate transporter in Bacillus subtilis
Mol. Microbiol.
37
898-912
2000
Bacillus subtilis (O34427)
Yamamoto, H.; Uchiyama, S.; Nugroho, F.A.; Sekiguchi, J.
Cloning and sequencing of a 35.7 kb in the 70 degree-73 degree region of the Bacillus subtilis genome reveal genes for a new two-component system, three spore germination proteins, an iron uptake system and a general stress response protein
Gene
194
191-199
1997
Bacillus subtilis (O34427)
Henner, D.J.; Yang, M.; Ferrari, E.
Localization of Bacillus subtilis sacU(Hy) mutations to two linked genes with similarities to the conserved procaryotic family of two-component signalling systems
J. Bacteriol.
170
5102-5109
1988
Bacillus subtilis (P13799)
Kunst, F.; Debarbouille, M.; Msadek, T.; Young, M.; Mauel, C.; Karamata, D.; Klier, A.; Rapoport, G.; Dedonder, R.
Deduced polypeptides encoded by the Bacillus subtilis sacU locus share homology with two-component sensor-regulator systems
J. Bacteriol.
170
5093-5101
1988
Bacillus subtilis (P13799)
Tanaka, T.; Kawata, M.
Cloning and characterization of Bacillus subtilis iep, which has positive and negative effects on production of extracellular proteases
J. Bacteriol.
170
3593-3600
1988
Bacillus subtilis (P13799)
Antoniewski, C.; Savelli, B.; Stragier, P.
The spoIIJ gene, which regulates early developmental steps in Bacillus subtilis, belongs to a class of environmentally responsive genes
J. Bacteriol.
172
86-93
1990
Bacillus subtilis (P16497)
Perego, M.; Cole, S.P.; Burbulys, D.; Trach, K.; Hoch, J.A.
Characterization of the gene for a protein kinase which phosphorylates the sporulation-regulatory proteins Spo0A and Spo0F of Bacillus subtilis
J. Bacteriol.
171
6187-6196
1989
Bacillus subtilis (P16497)
Lapidus, A.; Galleron, N.; Sorokin, A.; Ehrlich, S.D.
Sequencing and functional annotation of the Bacillus subtilis genes in the 200 kb rrnB-dnaB region
Microbiology
143
3431-3441
1997
Bacillus subtilis (P23545)
-
Seki, T.; Yoshikawa, H.; Takahashi, H.; Saito, H.
Nucleotide sequence of the Bacillus subtilis phoR gene
J. Bacteriol.
170
5935-5938
1988
Bacillus subtilis (P23545)
Fuhrer, D.K.; Ordal, G.W.
Bacillus subtilis CheN, a homolog of CheA, the central regulator of chemotaxis in Escherichia coli
J. Bacteriol.
173
7443-7448
1991
Bacillus subtilis (P29072), Bacillus subtilis
Klein, C.; Kaletta, C.; Entian, K.D.
Biosynthesis of the lantibiotic subtilin is regulated by a histidine kinase/response regulator system
Appl. Environ. Microbiol.
59
296-303
1993
Bacillus subtilis (P33113)
Sorokin, A.; Zumstein, E.; Azevedo, V.; Ehrlich, S.D.; Serror, P.
The organization of the Bacillus subtilis 168 chromosome region between the spoVA and serA genetic loci, based on sequence data
Mol. Microbiol.
10
385-395
1993
Bacillus subtilis (P35164)
Sun, G.; Sharkova, E.; Chesnut, R.; Birkey, S.; Duggan, M.F.; Sorokin, A.; Pujic, P.; Ehrlich, S.D.; Hulett, F.M.
Regulators of aerobic and anaerobic respiration in Bacillus subtilis
J. Bacteriol.
178
1374-1385
1996
Bacillus subtilis (P35164)
Kobayashi, K.; Shoji, K.; Shimizu, T.; Nakano, K.; Sato, T.; Kobayashi, Y.
Analysis of a suppressor mutation ssb (kinC) of sur0B20 (spo0A) mutation in Bacillus subtilis reveals that kinC encodes a histidine protein kinase
J. Bacteriol.
177
176-182
1995
Bacillus subtilis (P39764)
LeDeaux, J.R.; Grossman, A.D.
Isolation and characterization of kinC, a gene that encodes a sensor kinase homologous to the sporulation sensor kinases KinA and KinB in Bacillus subtilis
J. Bacteriol.
177
166-175
1995
Bacillus subtilis (P39764), Bacillus subtilis
Winters, P.; Caldwell, R.; Enfield, L.; Ferrari, E.
The ampS-nprE (124 degrees-127 degrees) region of the Bacillus subtilis 168 chromosome: sequencing of a 27 kb segment and identification of several genes in the area
Microbiology
142
3033-3037
1996
Bacillus subtilis (P39764)
-
Oudega, B.; Koningstein, G.; Rodrigues, L.; de Sales Ramon, M.; Hilbert, H.; Dusterhoft, A.; Pohl, T.M.; Weitzenegger, T.
Analysis of the Bacillus subtilis genome: cloning and nucleotide sequence of a 62 kb region between 275 degrees (rrnB) and 284 degrees (pai)
Microbiology
143
2769-2774
1997
Bacillus subtilis (Q08430)
-
Trach, K.A.; Hoch, J.A.
Multisensory activation of the phosphorelay initiating sporulation in Bacillus subtilis: identification and sequence of the protein kinase of the alternate pathway
Mol. Microbiol.
8
69-79
1993
Bacillus subtilis (Q08430)
Fabret, C.; Hoch, J.A.
A two-component signal transduction system essential for growth of Bacillus subtilis: implications for anti-infective therapy
J. Bacteriol.
180
6375-6383
1998
Bacillus subtilis (Q45614)
Fukuchi, K.; Kasahara, Y.; Asai, K.; Kobayashi, K.; Moriya, S.; Ogasawara, N.
The essential two-component regulatory system encoded by yycF and yycG modulates expression of the ftsAZ operon in Bacillus subtilis
Microbiology
146
1573-1583
2000
Bacillus subtilis (Q45614)
-
Lee, J.; Tomchick, D.R.; Brautigam, C.A.; Machius, M.; Kort, R.; Hellingwerf, K.J.; Gardner, K.H.
Changes at the KinA PAS-A dimerization interface influence histidine kinase function
Biochemistry
47
4051-4064
2008
Bacillus subtilis (P16497), Bacillus subtilis, Bacillus subtilis 168 (P16497)
Fukushima, T.; Szurmant, H.; Kim, E.J.; Perego, M.; Hoch, J.A.
A sensor histidine kinase co-ordinates cell wall architecture with cell division in Bacillus subtilis
Mol. Microbiol.
69
621-632
2008
Bacillus subtilis (Q45614), Bacillus subtilis
Kim, Y.P.; Yeo, K.J.; Kim, M.H.; Kim, Y.C.; Jeon, Y.H.
Structural characterization of the intra-membrane histidine kinase YbdK from Bacillus subtilis in DPC micelles
Biochem. Biophys. Res. Commun.
391
1506-1511
2010
Bacillus subtilis
Jacques, D.A.; Langley, D.B.; Jeffries, C.M.; Cunningham, K.A.; Burkholder, W.F.; Guss, J.M.; Trewhella, J.
Histidine kinase regulation by a cyclophilin-like inhibitor
J. Mol. Biol.
384
422-435
2008
Bacillus subtilis, Bacillus subtilis 168
Cunningham, K.A.; Burkholder, W.F.
The histidine kinase inhibitor Sda binds near the site of autophosphorylation and may sterically hinder autophosphorylation and phosphotransfer to Spo0F
Mol. Microbiol.
71
659-677
2009
Bacillus subtilis
Buelow, D.R.; Raivio, T.L.
Three (and more) component regulatory systems - auxiliary regulators of bacterial histidine kinases
Mol. Microbiol.
75
547-566
2010
Bacillus subtilis, Bordetella pertussis, Caulobacter vibrioides, Escherichia coli, Sinorhizobium meliloti, Vibrio harveyi (P54302)
Albanesi, D.; Martin, M.; Trajtenberg, F.; Mansilla, M.C.; Haouz, A.; Alzari, P.M.; de Mendoza, D.; Buschiazzo, A.
Structural plasticity and catalysis regulation of a thermosensor histidine kinase
Proc. Natl. Acad. Sci. USA
106
16185-16190
2009
Bacillus subtilis (O34757), Bacillus subtilis
Shemesh, M.; Chai, Y.
A combination of glycerol and manganese promotes biofilm formation in Bacillus subtilis via histidine kinase KinD signaling
J. Bacteriol.
195
2747-2754
2013
Bacillus subtilis (O31671), Bacillus subtilis, Bacillus subtilis 168 (O31671)
Trajtenberg, F.; Grana, M.; Ruetalo, N.; Botti, H.; Buschiazzo, A.
Structural and enzymatic insights into the ATP binding and autophosphorylation mechanism of a sensor histidine kinase
J. Biol. Chem.
285
24892-24903
2010
Bacillus subtilis (O34757), Bacillus subtilis, Bacillus subtilis 168 (O34757)
Devi, S.N.; Vishnoi, M.; Kiehler, B.; Haggett, L.; Fujita, M.
In vivo functional characterization of the transmembrane histidine kinase KinC in Bacillus subtilis
Microbiology
161
1092-1104
2015
Bacillus subtilis, Bacillus subtilis 168
Fukushima, T.; Furihata, I.; Emmins, R.; Daniel, R.A.; Hoch, J.A.; Szurmant, H.
A role for the essential YycG sensor histidine kinase in sensing cell division
Mol. Microbiol.
79
503-522
2011
Bacillus subtilis (Q45614), Bacillus subtilis, Bacillus subtilis 168 (Q45614)
Geiger, C.; Spiess, T.; Korn, S.; Koetter, P.; Entian, K.
Specificity of subtilin-mediated activation of histidine kinase SpaK
Appl. Environ. Microbiol.
83
e00781
2017
Bacillus subtilis (P33113), Bacillus subtilis
EXTERNAL LINKS (specific for EC-Number 2.7.13.3)
Transporter Classification Database (TCDB): 9.B.33.1.1, 9.B.238.3.5, 9.B.33.1.2, 2.A.21.9.1, 2.A.21.9.2, 2.A.123.2.13
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