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 03-AUG-2022, entry version 140.
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., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT 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., Mau B.,
RA 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 MG1655
RT 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 function
RT 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, AND
RP 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 PilZ
RT 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 LOCATION,
RP 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 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 and
RT 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 swarming
CC in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)-dependent manner.
CC When bound to c-di-GMP it binds to elements of the flagellar motor
CC (MotA (PubMed:20303158) and/or FliG and FliM (PubMed:20346719), binding
CC to FliM also occurs in the absence of c-di-GMP), causing the motor to
CC slow down. Thus, increasing levels of c-di-GMP lead to decreased
CC motility. Probably binds 1 c-di-GMP dimer per subunit.
CC {ECO:0000269|PubMed:11031114, ECO:0000269|PubMed:16920715,
CC ECO:0000269|PubMed:20303158, ECO:0000269|PubMed:20346719}.
CC -!- SUBUNIT: Monomer (Probable). Interacts with MotA in the flagellar basal
CC bodies (PubMed:20303158). In another study (PubMed:20346719) it was not
CC seen to interact with MotA, but instead with FliM and FliG, also in the
CC flagellar basal body. {ECO:0000269|PubMed:16920715,
CC ECO:0000269|PubMed:20303158, ECO:0000269|PubMed:20346719, ECO:0000305}.
CC -!- INTERACTION:
CC P76010; P0ABZ1: fliG; NbExp=3; IntAct=EBI-554507, EBI-1126524;
CC P76010; 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 this
CC gene suppresses the reduced motility of a pdeH disruption, thus the
CC double disruption is motile. {ECO:0000269|PubMed:16920715,
CC ECO:0000269|PubMed:20303158}.
CC -!- SIMILARITY: Belongs to the YcgR family. {ECO:0000305}.
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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_SSZK01000010.1.
DR PDB; 5Y6F; X-ray; 2.30 A; A=1-244.
DR PDB; 5Y6G; X-ray; 2.30 A; A=111-244.
DR PDB; 5Y6H; X-ray; 1.77 A; A=1-111.
DR PDBsum; 5Y6F; -.
DR PDBsum; 5Y6G; -.
DR PDBsum; 5Y6H; -.
DR AlphaFoldDB; P76010; -.
DR SASBDB; P76010; -.
DR SMR; P76010; -.
DR BioGRID; 4260858; 131.
DR BioGRID; 851925; 1.
DR DIP; DIP-11561N; -.
DR IntAct; P76010; 7.
DR STRING; 511145.b1194; -.
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 eggNOG; COG5581; Bacteria.
DR HOGENOM; CLU_086025_1_0_6; -.
DR OMA; REYFRVN; -.
DR PhylomeDB; P76010; -.
DR BioCyc; EcoCyc:G6623-MON; -.
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:0035438; F:cyclic-di-GMP binding; IDA:UniProtKB.
DR GO; GO:0071973; P:bacterial-type flagellum-dependent cell motility; IMP:EcoCyc.
DR GO; GO:1902201; P:negative regulation of 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_PilZN.
DR Pfam; PF07238; PilZ; 1.
DR Pfam; PF07317; YcgR; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Bacterial flagellum; c-di-GMP; Nucleotide-binding;
KW Reference proteome.
FT CHAIN 1..244
FT /note="Flagellar brake protein YcgR"
FT /id="PRO_0000168858"
FT DOMAIN 112..230
FT /note="PilZ"
FT MUTAGEN 42
FT /note="K->D: Suppression of the pdeH disruption motility
FT phenotype."
FT /evidence="ECO:0000269|PubMed:20346719"
FT MUTAGEN 62
FT /note="N->W: Significant suppression of the pdeH disruption
FT motility phenotype, less binding to FliG."
FT /evidence="ECO:0000269|PubMed:20346719"
FT MUTAGEN 81
FT /note="K->D: Significant suppression of the pdeH disruption
FT motility phenotype, less binding to FliG."
FT /evidence="ECO:0000269|PubMed:20346719"
FT MUTAGEN 118
FT /note="R->D: Complete loss of c-di-GMP binding in vitro,
FT suppresses pdeH disruption (PubMed:16920715). Somewhat
FT reduced binding to FliM, stimulated by c-di-GMP, greatly
FT reduced binding to FliG (PubMed:20346719)."
FT /evidence="ECO:0000269|PubMed:16920715,
FT ECO:0000269|PubMed:20346719"
FT MUTAGEN 147
FT /note="S->A: Slight increase in affinity for c-di-GMP."
FT /evidence="ECO:0000269|PubMed:16920715"
FT MUTAGEN 223
FT /note="Q->P: Significant suppression of the pdeH disruption
FT motility phenotype, no binding to FliM."
FT /evidence="ECO:0000269|PubMed:20346719"
FT MUTAGEN 223
FT /note="Q->W: Significant suppression of the pdeH disruption
FT motility phenotype."
FT /evidence="ECO:0000269|PubMed:20346719"
FT MUTAGEN 227
FT /note="I->W: Some suppression of the pdeH disruption
FT motility phenotype, no binding to FliM."
FT /evidence="ECO:0000269|PubMed:20346719"
FT HELIX 6..8
FT /evidence="ECO:0007829|PDB:5Y6H"
FT HELIX 13..26
FT /evidence="ECO:0007829|PDB:5Y6H"
FT STRAND 30..34
FT /evidence="ECO:0007829|PDB:5Y6H"
FT STRAND 37..41
FT /evidence="ECO:0007829|PDB:5Y6H"
FT STRAND 43..47
FT /evidence="ECO:0007829|PDB:5Y6H"
FT STRAND 50..54
FT /evidence="ECO:0007829|PDB:5Y6H"
FT HELIX 59..67
FT /evidence="ECO:0007829|PDB:5Y6H"
FT STRAND 71..77
FT /evidence="ECO:0007829|PDB:5Y6H"
FT STRAND 80..87
FT /evidence="ECO:0007829|PDB:5Y6H"
FT STRAND 90..94
FT /evidence="ECO:0007829|PDB:5Y6H"
FT STRAND 97..102
FT /evidence="ECO:0007829|PDB:5Y6H"
FT STRAND 108..111
FT /evidence="ECO:0007829|PDB:5Y6H"
FT STRAND 123..125
FT /evidence="ECO:0007829|PDB:5Y6G"
FT STRAND 128..132
FT /evidence="ECO:0007829|PDB:5Y6F"
FT STRAND 138..147
FT /evidence="ECO:0007829|PDB:5Y6F"
FT STRAND 150..154
FT /evidence="ECO:0007829|PDB:5Y6F"
FT STRAND 172..175
FT /evidence="ECO:0007829|PDB:5Y6F"
FT HELIX 177..179
FT /evidence="ECO:0007829|PDB:5Y6G"
FT STRAND 181..193
FT /evidence="ECO:0007829|PDB:5Y6F"
FT STRAND 207..215
FT /evidence="ECO:0007829|PDB:5Y6F"
FT HELIX 218..240
FT /evidence="ECO:0007829|PDB:5Y6F"
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
