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Protein

GTP-sensing transcriptional pleiotropic repressor CodY

Gene

codY

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

DNA-binding protein that represses the expression of many genes that are induced as cells make the transition from rapid exponential growth to stationary phase and sporulation. It is a GTP-binding protein that senses the intracellular GTP concentration as an indicator of nutritional limitations. At low GTP concentration it no longer binds GTP and stop to act as a transcriptional repressor.2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi202 – 22120H-T-H motifSequence analysisAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • negative regulation of transcription, DNA-templated Source: UniProtKB-HAMAP
  • regulation of transcription, DNA-templated Source: CACAO
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, GTP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciBSUB:BSU16170-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
GTP-sensing transcriptional pleiotropic repressor CodY
Alternative name(s):
Vegetative protein 286B
Short name:
VEG286B
Gene namesi
Name:codY
Ordered Locus Names:BSU16170
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 259258GTP-sensing transcriptional pleiotropic repressor CodYPRO_0000213221Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei215 – 2151Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP39779.

PTM databases

iPTMnetiP39779.

Expressioni

Gene expression databases

CollecTFiEXPREG_00000a80.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
ccpAP251443EBI-7827914,EBI-5247535
rpoAP204292EBI-7827914,EBI-5247865

Protein-protein interaction databases

IntActiP39779. 2 interactions.
MINTiMINT-8366926.
STRINGi224308.Bsubs1_010100008906.

Structurei

Secondary structure

1
259
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi2 – 1514Combined sources
Helixi24 – 3512Combined sources
Beta strandi37 – 437Combined sources
Beta strandi46 – 527Combined sources
Helixi60 – 689Combined sources
Helixi73 – 808Combined sources
Beta strandi86 – 894Combined sources
Helixi100 – 1067Combined sources
Beta strandi107 – 11812Combined sources
Beta strandi121 – 13212Combined sources
Helixi137 – 15822Combined sources
Helixi168 – 17710Combined sources
Helixi181 – 19010Combined sources
Beta strandi193 – 1953Combined sources
Beta strandi198 – 2014Combined sources
Helixi203 – 2108Combined sources
Helixi214 – 22613Combined sources
Beta strandi229 – 2346Combined sources
Beta strandi236 – 2383Combined sources
Beta strandi240 – 2445Combined sources
Helixi248 – 2558Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2B0LX-ray2.90A/B/C168-259[»]
2B18X-ray1.80A1-155[»]
2GX5X-ray1.74A/B/C/D2-160[»]
2HGVX-ray2.30A1-155[»]
ProteinModelPortaliP39779.
SMRiP39779. Positions 1-160, 168-257.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP39779.

Family & Domainsi

Sequence similaritiesi

Belongs to the CodY family.Curated

Phylogenomic databases

eggNOGiCOG4465. LUCA.
HOGENOMiHOG000058075.
KOiK03706.
OMAiREKHNEV.
OrthoDBiEOG60GRZT.
PhylomeDBiP39779.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
HAMAPiMF_00621. HTH_type_CodY.
InterProiIPR014154. CodY.
IPR010312. GTP_sensing_CodY_N.
IPR013198. GTP_sensing_HTH_CodY_C.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF06018. CodY. 1 hit.
PF08222. HTH_CodY. 1 hit.
[Graphical view]
PIRSFiPIRSF011572. GTP_sensing_CodY. 1 hit.
SUPFAMiSSF46785. SSF46785. 1 hit.
TIGRFAMsiTIGR02787. codY_Gpos. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P39779-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALLQKTRII NSMLQAAAGK PVNFKEMAET LRDVIDSNIF VVSRRGKLLG
60 70 80 90 100
YSINQQIEND RMKKMLEDRQ FPEEYTKNLF NVPETSSNLD INSEYTAFPV
110 120 130 140 150
ENRDLFQAGL TTIVPIIGGG ERLGTLILSR LQDQFNDDDL ILAEYGATVV
160 170 180 190 200
GMEILREKAE EIEEEARSKA VVQMAISSLS YSELEAIEHI FEELDGNEGL
210 220 230 240 250
LVASKIADRV GITRSVIVNA LRKLESAGVI ESRSLGMKGT YIKVLNNKFL

IELENLKSH
Length:259
Mass (Da):29,013
Last modified:January 23, 2007 - v3
Checksum:i8CC11CCAFCCA43D4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U13634 Genomic DNA. Translation: AAB03372.1.
AL009126 Genomic DNA. Translation: CAB13490.1.
PIRiS61496.
RefSeqiNP_389499.1. NC_000964.3.
WP_003220850.1. NZ_JNCM01000035.1.

Genome annotation databases

EnsemblBacteriaiCAB13490; CAB13490; BSU16170.
GeneIDi11239478.
936491.
KEGGibsu:BSU16170.
PATRICi18975039. VBIBacSub10457_1711.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U13634 Genomic DNA. Translation: AAB03372.1.
AL009126 Genomic DNA. Translation: CAB13490.1.
PIRiS61496.
RefSeqiNP_389499.1. NC_000964.3.
WP_003220850.1. NZ_JNCM01000035.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2B0LX-ray2.90A/B/C168-259[»]
2B18X-ray1.80A1-155[»]
2GX5X-ray1.74A/B/C/D2-160[»]
2HGVX-ray2.30A1-155[»]
ProteinModelPortaliP39779.
SMRiP39779. Positions 1-160, 168-257.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP39779. 2 interactions.
MINTiMINT-8366926.
STRINGi224308.Bsubs1_010100008906.

PTM databases

iPTMnetiP39779.

Proteomic databases

PaxDbiP39779.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB13490; CAB13490; BSU16170.
GeneIDi11239478.
936491.
KEGGibsu:BSU16170.
PATRICi18975039. VBIBacSub10457_1711.

Phylogenomic databases

eggNOGiCOG4465. LUCA.
HOGENOMiHOG000058075.
KOiK03706.
OMAiREKHNEV.
OrthoDBiEOG60GRZT.
PhylomeDBiP39779.

Enzyme and pathway databases

BioCyciBSUB:BSU16170-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP39779.

Gene expression databases

CollecTFiEXPREG_00000a80.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
HAMAPiMF_00621. HTH_type_CodY.
InterProiIPR014154. CodY.
IPR010312. GTP_sensing_CodY_N.
IPR013198. GTP_sensing_HTH_CodY_C.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF06018. CodY. 1 hit.
PF08222. HTH_CodY. 1 hit.
[Graphical view]
PIRSFiPIRSF011572. GTP_sensing_CodY. 1 hit.
SUPFAMiSSF46785. SSF46785. 1 hit.
TIGRFAMsiTIGR02787. codY_Gpos. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A gene required for nutritional repression of the Bacillus subtilis dipeptide permease operon."
    Slack F.J., Serror P., Joyce E., Sonenshein A.L.
    Mol. Microbiol. 15:689-702(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / JH642.
  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. "First steps from a two-dimensional protein index towards a response-regulation map for Bacillus subtilis."
    Antelmann H., Bernhardt J., Schmid R., Mach H., Voelker U., Hecker M.
    Electrophoresis 18:1451-1463(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-15.
    Strain: 168 / IS58.
  4. "CodY is required for nutritional repression of Bacillus subtilis genetic competence."
    Serror P., Sonenshein A.L.
    J. Bacteriol. 178:5910-5915(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  5. "Bacillus subtilis CodY represses early-stationary-phase genes by sensing GTP levels."
    Ratnayake-Lecamwasam M., Serror P., Wong K.W., Sonenshein A.L.
    Genes Dev. 15:1093-1103(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  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 SER-215, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: 168.

Entry informationi

Entry nameiCODY_BACSU
AccessioniPrimary (citable) accession number: P39779
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: January 23, 2007
Last modified: February 17, 2016
This is version 133 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

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

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 one 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.