CODY_BACSU
ID CODY_BACSU Reviewed; 259 AA.
AC P39779;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 164.
DE RecName: Full=GTP-sensing transcriptional pleiotropic repressor CodY;
DE AltName: Full=Vegetative protein 286B;
DE Short=VEG286B;
GN Name=codY; OrderedLocusNames=BSU16170;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / JH642;
RX PubMed=7783641; DOI=10.1111/j.1365-2958.1995.tb02378.x;
RA Slack F.J., Serror P., Joyce E., Sonenshein A.L.;
RT "A gene required for nutritional repression of the Bacillus subtilis
RT dipeptide permease operon.";
RL Mol. Microbiol. 15:689-702(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP PROTEIN SEQUENCE OF 2-15.
RC STRAIN=168 / IS58;
RX PubMed=9298659; DOI=10.1002/elps.1150180820;
RA Antelmann H., Bernhardt J., Schmid R., Mach H., Voelker U., Hecker M.;
RT "First steps from a two-dimensional protein index towards a response-
RT regulation map for Bacillus subtilis.";
RL Electrophoresis 18:1451-1463(1997).
RN [4]
RP FUNCTION.
RX PubMed=8830686; DOI=10.1128/jb.178.20.5910-5915.1996;
RA Serror P., Sonenshein A.L.;
RT "CodY is required for nutritional repression of Bacillus subtilis genetic
RT competence.";
RL J. Bacteriol. 178:5910-5915(1996).
RN [5]
RP FUNCTION.
RX PubMed=11331605; DOI=10.1101/gad.874201;
RA Ratnayake-Lecamwasam M., Serror P., Wong K.W., Sonenshein A.L.;
RT "Bacillus subtilis CodY represses early-stationary-phase genes by sensing
RT GTP levels.";
RL Genes Dev. 15:1093-1103(2001).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-215, AND IDENTIFICATION BY
RP MASS SPECTROMETRY.
RC STRAIN=168;
RX PubMed=17218307; DOI=10.1074/mcp.m600464-mcp200;
RA Macek B., Mijakovic I., Olsen J.V., Gnad F., Kumar C., Jensen P.R.,
RA Mann M.;
RT "The serine/threonine/tyrosine phosphoproteome of the model bacterium
RT Bacillus subtilis.";
RL Mol. Cell. Proteomics 6:697-707(2007).
CC -!- FUNCTION: DNA-binding protein that represses the expression of many
CC genes that are induced as cells make the transition from rapid
CC exponential growth to stationary phase and sporulation. It is a GTP-
CC binding protein that senses the intracellular GTP concentration as an
CC indicator of nutritional limitations. At low GTP concentration it no
CC longer binds GTP and stop to act as a transcriptional repressor.
CC {ECO:0000269|PubMed:11331605, ECO:0000269|PubMed:8830686}.
CC -!- INTERACTION:
CC P39779; P25144: ccpA; NbExp=3; IntAct=EBI-7827914, EBI-5247535;
CC P39779; P20429: rpoA; NbExp=2; IntAct=EBI-7827914, EBI-5247865;
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- SIMILARITY: Belongs to the CodY family. {ECO:0000305}.
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DR EMBL; U13634; AAB03372.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB13490.1; -; Genomic_DNA.
DR PIR; S61496; S61496.
DR RefSeq; NP_389499.1; NC_000964.3.
DR RefSeq; WP_003220850.1; NZ_JNCM01000035.1.
DR PDB; 2B0L; X-ray; 2.90 A; A/B/C=168-259.
DR PDB; 2B18; X-ray; 1.80 A; A=1-155.
DR PDB; 2GX5; X-ray; 1.74 A; A/B/C/D=2-160.
DR PDB; 2HGV; X-ray; 2.30 A; A=1-155.
DR PDB; 5LNH; X-ray; 3.00 A; A/B/C/D/E/F/G/H/I/K=2-259.
DR PDB; 5LOE; X-ray; 3.00 A; A/B/C/D=1-259.
DR PDB; 5LOJ; X-ray; 3.71 A; A/B=2-259.
DR PDB; 5LOO; X-ray; 4.50 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N=2-259.
DR PDBsum; 2B0L; -.
DR PDBsum; 2B18; -.
DR PDBsum; 2GX5; -.
DR PDBsum; 2HGV; -.
DR PDBsum; 5LNH; -.
DR PDBsum; 5LOE; -.
DR PDBsum; 5LOJ; -.
DR PDBsum; 5LOO; -.
DR AlphaFoldDB; P39779; -.
DR SMR; P39779; -.
DR IntAct; P39779; 2.
DR MINT; P39779; -.
DR STRING; 224308.BSU16170; -.
DR iPTMnet; P39779; -.
DR jPOST; P39779; -.
DR PaxDb; P39779; -.
DR PRIDE; P39779; -.
DR EnsemblBacteria; CAB13490; CAB13490; BSU_16170.
DR GeneID; 50133528; -.
DR GeneID; 64303509; -.
DR GeneID; 936491; -.
DR KEGG; bsu:BSU16170; -.
DR PATRIC; fig|224308.179.peg.1757; -.
DR eggNOG; COG4465; Bacteria.
DR OMA; MPFVNVD; -.
DR PhylomeDB; P39779; -.
DR BioCyc; BSUB:BSU16170-MON; -.
DR EvolutionaryTrace; P39779; -.
DR PRO; PR:P39779; -.
DR Proteomes; UP000001570; Chromosome.
DR CollecTF; EXPREG_00000a80; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0032993; C:protein-DNA complex; IMP:CollecTF.
DR GO; GO:0001217; F:DNA-binding transcription repressor activity; IMP:CollecTF.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IMP:CollecTF.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IMP:CACAO.
DR Gene3D; 1.10.10.10; -; 1.
DR Gene3D; 3.30.450.40; -; 1.
DR HAMAP; MF_00621; HTH_type_CodY; 1.
DR InterPro; IPR014154; CodY.
DR InterPro; IPR029016; GAF-like_dom_sf.
DR InterPro; IPR010312; GTP_sensing_CodY_N.
DR InterPro; IPR013198; GTP_sensing_HTH_CodY_C.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR InterPro; IPR036390; WH_DNA-bd_sf.
DR PANTHER; PTHR40062; PTHR40062; 1.
DR Pfam; PF06018; CodY; 1.
DR Pfam; PF08222; HTH_CodY; 1.
DR PIRSF; PIRSF011572; GTP_sensing_CodY; 1.
DR SUPFAM; SSF46785; SSF46785; 1.
DR TIGRFAMs; TIGR02787; codY_Gpos; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; DNA-binding;
KW GTP-binding; Nucleotide-binding; Phosphoprotein; Reference proteome;
KW Repressor; Transcription; Transcription regulation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:9298659"
FT CHAIN 2..259
FT /note="GTP-sensing transcriptional pleiotropic repressor
FT CodY"
FT /id="PRO_0000213221"
FT DNA_BIND 202..221
FT /note="H-T-H motif"
FT /evidence="ECO:0000255"
FT MOD_RES 215
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:17218307"
FT HELIX 2..15
FT /evidence="ECO:0007829|PDB:2GX5"
FT STRAND 18..20
FT /evidence="ECO:0007829|PDB:5LOE"
FT HELIX 24..35
FT /evidence="ECO:0007829|PDB:2GX5"
FT STRAND 37..43
FT /evidence="ECO:0007829|PDB:2GX5"
FT STRAND 46..52
FT /evidence="ECO:0007829|PDB:2GX5"
FT HELIX 60..68
FT /evidence="ECO:0007829|PDB:2GX5"
FT HELIX 73..80
FT /evidence="ECO:0007829|PDB:2GX5"
FT STRAND 86..89
FT /evidence="ECO:0007829|PDB:2GX5"
FT STRAND 96..98
FT /evidence="ECO:0007829|PDB:5LNH"
FT HELIX 100..106
FT /evidence="ECO:0007829|PDB:2GX5"
FT STRAND 107..118
FT /evidence="ECO:0007829|PDB:2GX5"
FT STRAND 121..132
FT /evidence="ECO:0007829|PDB:2GX5"
FT HELIX 137..158
FT /evidence="ECO:0007829|PDB:2GX5"
FT HELIX 168..177
FT /evidence="ECO:0007829|PDB:2B0L"
FT HELIX 181..190
FT /evidence="ECO:0007829|PDB:2B0L"
FT STRAND 193..195
FT /evidence="ECO:0007829|PDB:2B0L"
FT STRAND 198..201
FT /evidence="ECO:0007829|PDB:2B0L"
FT HELIX 203..210
FT /evidence="ECO:0007829|PDB:2B0L"
FT HELIX 214..226
FT /evidence="ECO:0007829|PDB:2B0L"
FT STRAND 229..234
FT /evidence="ECO:0007829|PDB:2B0L"
FT STRAND 236..238
FT /evidence="ECO:0007829|PDB:2B0L"
FT STRAND 240..244
FT /evidence="ECO:0007829|PDB:2B0L"
FT HELIX 248..255
FT /evidence="ECO:0007829|PDB:2B0L"
SQ SEQUENCE 259 AA; 29013 MW; 8CC11CCAFCCA43D4 CRC64;
MALLQKTRII NSMLQAAAGK PVNFKEMAET LRDVIDSNIF VVSRRGKLLG YSINQQIEND
RMKKMLEDRQ FPEEYTKNLF NVPETSSNLD INSEYTAFPV ENRDLFQAGL TTIVPIIGGG
ERLGTLILSR LQDQFNDDDL ILAEYGATVV GMEILREKAE EIEEEARSKA VVQMAISSLS
YSELEAIEHI FEELDGNEGL LVASKIADRV GITRSVIVNA LRKLESAGVI ESRSLGMKGT
YIKVLNNKFL IELENLKSH
