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Database: UniProt
Entry: YCGR_ECOLI
LinkDB: YCGR_ECOLI
Original site: YCGR_ECOLI 
ID   YCGR_ECOLI              Reviewed;         244 AA.
AC   P76010; Q9R7N3;
DT   15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1997, sequence version 1.
DT   05-JUL-2017, entry version 116.
DE   RecName: Full=Flagellar brake protein YcgR;
DE   AltName: Full=Cyclic di-GMP binding protein YcgR;
GN   Name=ycgR; OrderedLocusNames=b1194, JW1183;
OS   Escherichia coli (strain K12).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA   Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A.,
RA   Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K.,
RA   Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K.,
RA   Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N.,
RA   Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y.,
RA   Yano M., Horiuchi T.;
RT   "A 718-kb DNA sequence of the Escherichia coli K-12 genome
RT   corresponding to the 12.7-28.0 min region on the linkage map.";
RL   DNA Res. 3:137-155(1996).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
RA   Mau B., Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1462(1997).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains
RT   MG1655 and W3110.";
RL   Mol. Syst. Biol. 2:E1-E5(2006).
RN   [4]
RP   ROLE IN FLAGELLAR MOTILITY.
RC   STRAIN=K12;
RX   PubMed=11031114; DOI=10.1006/jmbi.2000.4147;
RA   Ko M., Park C.;
RT   "Two novel flagellar components and H-NS are involved in the motor
RT   function of Escherichia coli.";
RL   J. Mol. Biol. 303:371-382(2000).
RN   [5]
RP   DOMAIN PILZ.
RX   PubMed=16249258; DOI=10.1093/bioinformatics/bti739;
RA   Amikam D., Galperin M.Y.;
RT   "PilZ domain is part of the bacterial c-di-GMP binding protein.";
RL   Bioinformatics 22:3-6(2006).
RN   [6]
RP   FUNCTION IN MOTILITY, C-DI-GMP-BINDING, SUBUNIT, DISRUPTION PHENOTYPE,
RP   AND MUTAGENESIS OF ARG-118 AND SER-147.
RC   STRAIN=TOB1;
RX   PubMed=16920715; DOI=10.1074/jbc.C600179200;
RA   Ryjenkov D.A., Simm R., Romling U., Gomelsky M.;
RT   "The PilZ domain is a receptor for the second messenger c-di-GMP: the
RT   PilZ domain protein YcgR controls motility in enterobacteria.";
RL   J. Biol. Chem. 281:30310-30314(2006).
RN   [7]
RP   FUNCTION AS A FLAGELLAR BRAKE, INTERACTION WITH MOTA, SUBCELLULAR
RP   LOCATION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=20303158; DOI=10.1016/j.cell.2010.01.018;
RA   Boehm A., Kaiser M., Li H., Spangler C., Kasper C.A., Ackermann M.,
RA   Kaever V., Sourjik V., Roth V., Jenal U.;
RT   "Second messenger-mediated adjustment of bacterial swimming
RT   velocity.";
RL   Cell 141:107-116(2010).
RN   [8]
RP   FUNCTION AS A FLAGELLAR BRAKE, INTERACTION WITH FLIG AND FLIM, AND
RP   MUTAGENESIS OF LYS-42; ASN-62; LYS-81; GLN-223 AND ILE-227.
RC   STRAIN=K12 / RP3098;
RX   PubMed=20346719; DOI=10.1016/j.molcel.2010.03.001;
RA   Paul K., Nieto V., Carlquist W.C., Blair D.F., Harshey R.M.;
RT   "The c-di-GMP binding protein YcgR controls flagellar motor direction
RT   and speed to affect chemotaxis by a 'backstop brake' mechanism.";
RL   Mol. Cell 38:128-139(2010).
CC   -!- FUNCTION: Acts as a flagellar brake, regulating swimming and
CC       swarming in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)-
CC       dependent manner. When bound to c-di-GMP it binds to elements of
CC       the flagellar motor (MotA (PubMed:20303158) and/or FliG and FliM
CC       (PubMed:20346719), binding to FliM also occurs in the absence of
CC       c-di-GMP), causing the motor to slow down. Thus, increasing levels
CC       of c-di-GMP lead to decreased motility. Probably binds 1 c-di-GMP
CC       dimer per subunit. {ECO:0000269|PubMed:11031114,
CC       ECO:0000269|PubMed:16920715, ECO:0000269|PubMed:20303158,
CC       ECO:0000269|PubMed:20346719}.
CC   -!- SUBUNIT: Monomer (Probable). Interacts with MotA in the flagellar
CC       basal bodies (PubMed:20303158). In another study (PubMed:20346719)
CC       it was not seen to interact with MotA, but instead with FliM and
CC       FliG, also in the flagellar basal body.
CC       {ECO:0000269|PubMed:16920715, ECO:0000269|PubMed:20303158,
CC       ECO:0000269|PubMed:20346719, ECO:0000305}.
CC   -!- INTERACTION:
CC       P0ABZ1:fliG; NbExp=3; IntAct=EBI-554507, EBI-1126524;
CC       P06974:fliM; NbExp=3; IntAct=EBI-554507, EBI-560439;
CC   -!- SUBCELLULAR LOCATION: Bacterial flagellum basal body
CC       {ECO:0000269|PubMed:20303158}.
CC   -!- DOMAIN: The N-terminal domain is involved in FliG binding, the C-
CC       terminal domain is involved in FliM binding.
CC       {ECO:0000269|PubMed:16249258}.
CC   -!- DOMAIN: The PilZ domain is able to bind c-di-GMP, but with a lower
CC       affinity (dissociation constant of 1.45 uM) compared to the whole
CC       protein (dissociation constant of 0.84 uM).
CC       {ECO:0000269|PubMed:16249258}.
CC   -!- DISRUPTION PHENOTYPE: No visible motility phenotype. Disruption of
CC       this gene suppresses the reduced motility of a yhjH disruption,
CC       thus the double disruption is motile.
CC       {ECO:0000269|PubMed:16920715, ECO:0000269|PubMed:20303158}.
CC   -!- SIMILARITY: Belongs to the YcgR family. {ECO:0000305}.
DR   EMBL; U00096; AAC74278.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAA36052.2; -; Genomic_DNA.
DR   PIR; G64865; G64865.
DR   RefSeq; NP_415712.1; NC_000913.3.
DR   RefSeq; WP_000020169.1; NZ_LN832404.1.
DR   ProteinModelPortal; P76010; -.
DR   SMR; P76010; -.
DR   BioGrid; 4260858; 131.
DR   DIP; DIP-11561N; -.
DR   IntAct; P76010; 7.
DR   STRING; 316385.ECDH10B_1247; -.
DR   PaxDb; P76010; -.
DR   PRIDE; P76010; -.
DR   EnsemblBacteria; AAC74278; AAC74278; b1194.
DR   EnsemblBacteria; BAA36052; BAA36052; BAA36052.
DR   GeneID; 947609; -.
DR   KEGG; ecj:JW1183; -.
DR   KEGG; eco:b1194; -.
DR   PATRIC; fig|1411691.4.peg.1092; -.
DR   EchoBASE; EB3658; -.
DR   EcoGene; EG13899; ycgR.
DR   eggNOG; ENOG4108T7K; Bacteria.
DR   eggNOG; COG5581; LUCA.
DR   HOGENOM; HOG000265609; -.
DR   KO; K21087; -.
DR   BioCyc; EcoCyc:G6623-MONOMER; -.
DR   PRO; PR:P76010; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0009425; C:bacterial-type flagellum basal body; IEA:UniProtKB-SubCell.
DR   GO; GO:0048037; F:cofactor binding; IEA:InterPro.
DR   GO; GO:0035438; F:cyclic-di-GMP binding; IDA:UniProtKB.
DR   GO; GO:0071973; P:bacterial-type flagellum-dependent cell motility; IMP:EcoCyc.
DR   GO; GO:0071945; P:regulation of bacterial-type flagellum-dependent cell motility by regulation of motor speed; IGI:UniProtKB.
DR   Gene3D; 2.30.110.10; -; 1.
DR   HAMAP; MF_01457; YcgR; 1.
DR   InterPro; IPR009875; PilZ_domain.
DR   InterPro; IPR012349; Split_barrel_FMN-bd.
DR   InterPro; IPR023787; T3SS_YcgR.
DR   InterPro; IPR009926; T3SS_YcgR_N.
DR   Pfam; PF07238; PilZ; 1.
DR   Pfam; PF07317; YcgR; 1.
PE   1: Evidence at protein level;
KW   Bacterial flagellum; c-di-GMP; Complete proteome; Nucleotide-binding;
KW   Reference proteome.
FT   CHAIN         1    244       Flagellar brake protein YcgR.
FT                                /FTId=PRO_0000168858.
FT   DOMAIN      112    230       PilZ.
FT   MUTAGEN      42     42       K->D: Suppression of the yhjH disruption
FT                                motility phenotype.
FT                                {ECO:0000269|PubMed:20346719}.
FT   MUTAGEN      62     62       N->W: Significant suppression of the yhjH
FT                                disruption motility phenotype, less
FT                                binding to FliG.
FT                                {ECO:0000269|PubMed:20346719}.
FT   MUTAGEN      81     81       K->D: Significant suppression of the yhjH
FT                                disruption motility phenotype, less
FT                                binding to FliG.
FT                                {ECO:0000269|PubMed:20346719}.
FT   MUTAGEN     118    118       R->D: Complete loss of c-di-GMP binding
FT                                in vitro, suppresses yhjH disruption
FT                                (PubMed:16920715). Somewhat reduced
FT                                binding to FliM, stimulated by c-di-GMP,
FT                                greatly reduced binding to FliG
FT                                (PubMed:20346719).
FT                                {ECO:0000269|PubMed:16920715,
FT                                ECO:0000269|PubMed:20346719}.
FT   MUTAGEN     147    147       S->A: Slight increase in affinity for c-
FT                                di-GMP. {ECO:0000269|PubMed:16920715}.
FT   MUTAGEN     223    223       Q->P: Significant suppression of the yhjH
FT                                disruption motility phenotype, no binding
FT                                to FliM. {ECO:0000269|PubMed:20346719}.
FT   MUTAGEN     223    223       Q->W: Significant suppression of the yhjH
FT                                disruption motility phenotype.
FT                                {ECO:0000269|PubMed:20346719}.
FT   MUTAGEN     227    227       I->W: Some suppression of the yhjH
FT                                disruption motility phenotype, no binding
FT                                to FliM. {ECO:0000269|PubMed:20346719}.
SQ   SEQUENCE   244 AA;  27857 MW;  85D76B51DAC7BAB9 CRC64;
     MSHYHEQFLK QNPLAVLGVL RDLHKAAIPL RLSWNGGQLI SKLLAITPDK LVLDFGSQAE
     DNIAVLKAQH ITITAETQGA KVEFTVEQLQ QSEYLQLPAF ITVPPPTLWF VQRRRYFRIS
     APLHPPYFCQ TKLADNSTLR FRLYDLSLGG MGALLETAKP AELQEGMRFA QIEVNMGQWG
     VFHFDAQLIS ISERKVIDGK NETITTPRLS FRFLNVSPTV ERQLQRIIFS LEREAREKAD
     KVRD
//
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