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Protein

Serine/threonine-protein kinase PrkC

Gene

prkC

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Protein kinase that is responsible for triggering spore germination in response to muropeptides, signaling bacteria to exit dormancy. PrkC is thus a germination receptor that binds peptidoglycan fragments containing m-Dpm (meso-diaminopimelate), which act as spore germinants. Autophosphorylates and phosphorylates FusA (EF-G, elongation factor G); the latter modification is likely necessary for germination in response to peptidoglycan. PrkC is a substrate in vitro of the cotranscribed phosphatase PrpC, which suggests that they form a functional couple in vivo. Might also be involved in sporulation and biofilm formation. Does not seem to be involved in stress response.3 Publications

Catalytic activityi

ATP + a protein = ADP + a phosphoprotein.

Enzyme regulationi

Bryostatin activates PrkC activity and induces germination, whereas staurosporine inhibits PrkC and significantly reduced peptidoglycan-dependent germination.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei40 – 401ATPPROSITE-ProRule annotation
Sitei40 – 401Required for activity
Active sitei134 – 1341Proton acceptorPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi17 – 259ATPCurated

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. penicillin binding Source: InterPro
  3. peptidoglycan binding Source: UniProtKB
  4. protein serine/threonine kinase activity Source: UniProtKB

GO - Biological processi

  1. cellular response to peptidoglycan Source: UniProtKB
  2. protein phosphorylation Source: UniProtKB
  3. signal transduction Source: UniProtKB
  4. spore germination Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Serine/threonine-protein kinase, Transferase

Keywords - Biological processi

Germination

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciBSUB:BSU15770-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine/threonine-protein kinase PrkC (EC:2.7.11.1)
Short name:
Ser/Thr-protein kinase PrkC
Gene namesi
Name:prkC
Synonyms:yloP
Ordered Locus Names:BSU15770
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570: Chromosome

Organism-specific databases

GenoListiBSU15770. [Micado]

Subcellular locationi

Spore core membrane 1 Publication; Single-pass type II membrane protein 1 Publication
Note: Is associated with the inner membrane of the spore.

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 330330CytoplasmicCuratedAdd
BLAST
Transmembranei331 – 35121HelicalSequence AnalysisAdd
BLAST
Topological domaini352 – 648297ExtracellularCuratedAdd
BLAST

GO - Cellular componenti

  1. integral component of membrane Source: UniProtKB-KW
  2. plasma membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Disruption phenotypei

Spores lacking this gene fail to germinate in the presence of peptidoglycan fragments or purified GlcNAc-MurNAc tripeptides and tetrapeptides. They still respond to the nutrient germinant L-alanine and to the chemical germinant Ca2+-dipicolinic acid, indicating that the spores are still capable of germinating and that PrkC is not involved in nutrient or chemical germination.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi40 – 401K → A: Does not support germination in response to peptidoglycan. 2 Publications
Mutagenesisi40 – 401K → R: Abolishes autophosphorylation and decreases spore production and biofilm formation. 2 Publications
Mutagenesisi162 – 1621T → A: 4-fold reduction in activity. Abolished activity; when associated with A-163; A-165 and A-167. 1 Publication
Mutagenesisi163 – 1631T → A: 4-fold reduction in activity. Abolished activity; when associated with A-162; A-165 and A-167. 1 Publication
Mutagenesisi165 – 1651T → A: 4-fold reduction in activity. Abolished activity; when associated with A-162; A-163 and A-167. 1 Publication
Mutagenesisi167 – 1671T → A: 4-fold reduction in activity. Abolished activity; when associated with A-162; A-163 and A-165. 1 Publication
Mutagenesisi214 – 2141S → A: 4-fold reduction in activity. 1 Publication
Mutagenesisi290 – 2901T → A: Slightly reduced activity. 1 Publication
Mutagenesisi313 – 3131T → A: Unchanged activity. 1 Publication
Mutagenesisi320 – 3201T → A: 2-fold reduction in activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 648648Serine/threonine-protein kinase PrkCPRO_0000171183Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei162 – 1621Phosphothreonine; by autocatalysis1 Publication
Modified residuei163 – 1631Phosphothreonine; by autocatalysis1 Publication
Modified residuei165 – 1651Phosphothreonine; by autocatalysis1 Publication
Modified residuei167 – 1671Phosphothreonine; by autocatalysis1 Publication
Modified residuei214 – 2141Phosphoserine; by autocatalysis1 Publication
Modified residuei290 – 2901Phosphothreonine; by autocatalysis2 Publications
Modified residuei313 – 3131Phosphothreonine; by autocatalysis1 Publication
Modified residuei320 – 3201Phosphothreonine; by autocatalysis1 Publication

Post-translational modificationi

Autophosphorylation on threonine residue(s) and serine residue considerably increases the kinase activity of the protein. Dephosphorylated in vitro by PrpC.3 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiO34507.

PTM databases

PhosSiteiP0606169.

Interactioni

Subunit structurei

Homodimer.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
yabTP375622EBI-6667154,EBI-9303331
ybdMO314353EBI-6667154,EBI-5255200
ywqDP967162EBI-6667154,EBI-9302929

Protein-protein interaction databases

IntActiO34507. 8 interactions.
STRINGi224308.BSU15770.

Structurei

3D structure databases

ProteinModelPortaliO34507.
SMRiO34507. Positions 6-277.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini11 – 271261Protein kinasePROSITE-ProRule annotationAdd
BLAST
Domaini356 – 42469PASTA 1PROSITE-ProRule annotationAdd
BLAST
Domaini425 – 49268PASTA 2PROSITE-ProRule annotationAdd
BLAST
Domaini493 – 55967PASTA 3PROSITE-ProRule annotationAdd
BLAST

Domaini

The C-terminal extracellular domain containing the PASTA repeats binds peptidoglycan.

Sequence similaritiesi

Belongs to the protein kinase superfamily. Ser/Thr protein kinase family.PROSITE-ProRule annotation
Contains 3 PASTA domains.PROSITE-ProRule annotation
Contains 1 protein kinase domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal-anchor, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG0515.
HOGENOMiHOG000037186.
InParanoidiO34507.
KOiK08884.
OMAiPANIMIN.
OrthoDBiEOG6B35XT.
PhylomeDBiO34507.

Family and domain databases

InterProiIPR011009. Kinase-like_dom.
IPR005543. PASTA_dom.
IPR000719. Prot_kinase_dom.
IPR017441. Protein_kinase_ATP_BS.
IPR002290. Ser/Thr_dual-sp_kinase.
IPR008271. Ser/Thr_kinase_AS.
[Graphical view]
PfamiPF03793. PASTA. 3 hits.
PF00069. Pkinase. 1 hit.
[Graphical view]
SMARTiSM00740. PASTA. 3 hits.
SM00220. S_TKc. 1 hit.
[Graphical view]
SUPFAMiSSF56112. SSF56112. 1 hit.
PROSITEiPS51178. PASTA. 3 hits.
PS00107. PROTEIN_KINASE_ATP. 1 hit.
PS50011. PROTEIN_KINASE_DOM. 1 hit.
PS00108. PROTEIN_KINASE_ST. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O34507-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MLIGKRISGR YQILRVIGGG GMANVYLAED IILDREVAIK ILRFDYANDN
60 70 80 90 100
EFIRRFRREA QSASSLDHPN IVSIYDLGEE DDIYYIVMEY VEGMTLKEYI
110 120 130 140 150
TANGPLHPKE ALNIMEQIVS AIAHAHQNQI VHRDIKPHNI LIDHMGNIKV
160 170 180 190 200
TDFGIATALS STTITHTNSV LGSVHYLSPE QARGGLATKK SDIYALGIVL
210 220 230 240 250
FELLTGRIPF DGESAVSIAL KHLQAETPSA KRWNPSVPQS VENIILKATA
260 270 280 290 300
KDPFHRYETA EDMEADIKTA FDADRLNEKR FTIQEDEEMT KAIPIIKDEE
310 320 330 340 350
LAKAAGEKEA EVTTAQENKT KKNGKRKKWP WVLLTICLVF ITAGILAVTV
360 370 380 390 400
FPSLFMPKDV KIPDVSGMEY EKAAGLLEKE GLQVDSEVLE ISDEKIEEGL
410 420 430 440 450
MVKTDPKADT TVKEGATVTL YKSTGKAKTE IGDVTGQTVD QAKKALKDQG
460 470 480 490 500
FNHVTVNEVN DEKNAGTVID QNPSAGTELV PSEDQVKLTV SIGPEDITLR
510 520 530 540 550
DLKTYSKEAA SGYLEDNGLK LVEKEAYSDD VPEGQVVKQK PAAGTAVKPG
560 570 580 590 600
NEVEVTFSLG PEKKPAKTVK EKVKIPYEPE NEGDELQVQI AVDDADHSIS
610 620 630 640
DTYEEFKIKE PTERTIELKI EPGQKGYYQV MVNNKVVSYK TIEYPKDE
Length:648
Mass (Da):71,866
Last modified:January 1, 1998 - v1
Checksum:i9653AB5CFBAA7900
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y13937 Genomic DNA. Translation: CAA74267.1.
AL009126 Genomic DNA. Translation: CAB13450.1.
PIRiH69878.
RefSeqiNP_389459.1. NC_000964.3.

Genome annotation databases

EnsemblBacteriaiCAB13450; CAB13450; BSU15770.
GeneIDi936132.
KEGGibsu:BSU15770.
PATRICi18974961. VBIBacSub10457_1672.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y13937 Genomic DNA. Translation: CAA74267.1.
AL009126 Genomic DNA. Translation: CAB13450.1.
PIRiH69878.
RefSeqiNP_389459.1. NC_000964.3.

3D structure databases

ProteinModelPortaliO34507.
SMRiO34507. Positions 6-277.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiO34507. 8 interactions.
STRINGi224308.BSU15770.

PTM databases

PhosSiteiP0606169.

Proteomic databases

PaxDbiO34507.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB13450; CAB13450; BSU15770.
GeneIDi936132.
KEGGibsu:BSU15770.
PATRICi18974961. VBIBacSub10457_1672.

Organism-specific databases

GenoListiBSU15770. [Micado]

Phylogenomic databases

eggNOGiCOG0515.
HOGENOMiHOG000037186.
InParanoidiO34507.
KOiK08884.
OMAiPANIMIN.
OrthoDBiEOG6B35XT.
PhylomeDBiO34507.

Enzyme and pathway databases

BioCyciBSUB:BSU15770-MONOMER.

Family and domain databases

InterProiIPR011009. Kinase-like_dom.
IPR005543. PASTA_dom.
IPR000719. Prot_kinase_dom.
IPR017441. Protein_kinase_ATP_BS.
IPR002290. Ser/Thr_dual-sp_kinase.
IPR008271. Ser/Thr_kinase_AS.
[Graphical view]
PfamiPF03793. PASTA. 3 hits.
PF00069. Pkinase. 1 hit.
[Graphical view]
SMARTiSM00740. PASTA. 3 hits.
SM00220. S_TKc. 1 hit.
[Graphical view]
SUPFAMiSSF56112. SSF56112. 1 hit.
PROSITEiPS51178. PASTA. 3 hits.
PS00107. PROTEIN_KINASE_ATP. 1 hit.
PS50011. PROTEIN_KINASE_DOM. 1 hit.
PS00108. PROTEIN_KINASE_ST. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "DNA sequence of a 28 Kbp seqment of DNA from the spoVM region of Bacillus subtilis."
    Foulger D., Errington J.
    Submitted (AUG-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  3. "The PrpC serine-threonine phosphatase and PrkC kinase have opposing physiological roles in stationary-phase Bacillus subtilis cells."
    Gaidenko T.A., Kim T.-J., Price C.W.
    J. Bacteriol. 184:6109-6114(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
    Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.
  4. "Characterization of a membrane-linked Ser/Thr protein kinase in Bacillus subtilis, implicated in developmental processes."
    Madec E., Laszkiewicz A., Iwanicki A., Obuchowski M., Seror S.
    Mol. Microbiol. 46:571-586(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT, PHOSPHORYLATION, MUTAGENESIS OF LYS-40.
    Strain: 168.
  5. "Mass spectrometry and site-directed mutagenesis identify several autophosphorylated residues required for the activity of PrkC, a Ser/Thr kinase from Bacillus subtilis."
    Madec E., Stensballe A., Kjellstrom S., Cladiere L., Obuchowski M., Jensen O.N., Seror S.J.
    J. Mol. Biol. 330:459-472(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT THR-162; THR-163; THR-165; THR-167; SER-214; THR-290; THR-313 AND THR-320, MUTAGENESIS OF THR-162; THR-163; THR-165; THR-167; SER-214; THR-290; THR-313 AND THR-320, IDENTIFICATION BY MASS SPECTROMETRY.
  6. "The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis."
    Macek B., Mijakovic I., Olsen J.V., Gnad F., Kumar C., Jensen P.R., Mann M.
    Mol. Cell. Proteomics 6:697-707(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-290, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: 168.
  7. "A eukaryotic-like Ser/Thr kinase signals bacteria to exit dormancy in response to peptidoglycan fragments."
    Shah I.M., Laaberki M.H., Popham D.L., Dworkin J.
    Cell 135:486-496(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN PEPTIDOGLYCAN-DEPENDENT GERMINATION, DISRUPTION PHENOTYPE, PEPTIDOGLYCAN-BINDING, SUBCELLULAR LOCATION, MUTAGENESIS OF LYS-40.
    Strain: 168 / PY79.
  8. "Theoretical modeling of PrkCc, serine-threonine protein kinase intracellular domain, complexed with ATP derivatives."
    Gruszczyski P., Kamierkiewicz R., Obuchowski M., Lammek B.
    QSAR Comb. Sci. 27:437-444(2008)
    Cited for: 3D-STRUCTURE MODELING OF 6-269 IN COMPLEX WITH ATP ANALOGS.
  9. "Phosphorylation and ATP-binding induced conformational changes in the PrkC, Ser/Thr kinase from B. subtilis."
    Gruszczynski P., Obuchowski M., Kazmierkiewicz R.
    J. Comput. Aided Mol. Des. 24:733-747(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: 3D-STRUCTURE MODELING OF CATALYTIC DOMAIN.

Entry informationi

Entry nameiPRKC_BACSU
AccessioniPrimary (citable) accession number: O34507
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 4, 2003
Last sequence update: January 1, 1998
Last modified: January 7, 2015
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

PubMed:18984160 shows that peptidoglycan fragments serve as a novel mechanism of interspecies bacterial signaling that likely indicates the presence of growing bacteria and thus serve as a signal for dormant cells that growth-promoting conditions exist.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.