ID YCGR_PSEPK Reviewed; 247 AA.
AC Q88EQ6;
DT 13-JUL-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 27-MAR-2024, entry version 106.
DE RecName: Full=Flagellar brake protein YcgR;
DE AltName: Full=Cyclic di-GMP binding protein YcgR;
GN Name=ycgR; OrderedLocusNames=PP_4397;
OS Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950
OS / KT2440).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=160488;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440;
RX PubMed=12534463; DOI=10.1046/j.1462-2920.2002.00366.x;
RA Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H.,
RA Martins dos Santos V.A.P., Fouts D.E., Gill S.R., Pop M., Holmes M.,
RA Brinkac L.M., Beanan M.J., DeBoy R.T., Daugherty S.C., Kolonay J.F.,
RA Madupu R., Nelson W.C., White O., Peterson J.D., Khouri H.M., Hance I.,
RA Chris Lee P., Holtzapple E.K., Scanlan D., Tran K., Moazzez A.,
RA Utterback T.R., Rizzo M., Lee K., Kosack D., Moestl D., Wedler H.,
RA Lauber J., Stjepandic D., Hoheisel J., Straetz M., Heim S., Kiewitz C.,
RA Eisen J.A., Timmis K.N., Duesterhoeft A., Tuemmler B., Fraser C.M.;
RT "Complete genome sequence and comparative analysis of the metabolically
RT versatile Pseudomonas putida KT2440.";
RL Environ. Microbiol. 4:799-808(2002).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS).
RG Joint center for structural genomics (JCSG);
RT "Crystal structure of hypothetical protein (NP_746511.1) from Pseudomonas
RT putida KT2440 at 2.25 A resolution.";
RL Submitted (FEB-2009) to the PDB data bank.
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH C-DI-GMP, SUBUNIT,
RP AND MUTAGENESIS OF GLN-121; ARG-122; ARG-123; ARG-127; ASP-157; SER-159 AND
RP GLY-162.
RX PubMed=20226196; DOI=10.1016/j.jmb.2010.03.007;
RA Ko J., Ryu K.S., Kim H., Shin J.S., Lee J.O., Cheong C., Choi B.S.;
RT "Structure of PP4397 reveals the molecular basis for different c-di-GMP
RT binding modes by Pilz domain proteins.";
RL J. Mol. Biol. 398:97-110(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 Increasing levels of c-di-GMP lead to decreased motility (By
CC similarity). Binds c-di-GMP with a dissociation constant of 165 nM.
CC Binds 2 intercalated (c-di-GMP) dimers per subunit. {ECO:0000250}.
CC -!- SUBUNIT: Interacts with the flagellar basal bodies (By similarity).
CC Monomer. Binding of c-di-GMP produces a dimer to monomer transition.
CC {ECO:0000250, ECO:0000269|PubMed:20226196}.
CC -!- SUBCELLULAR LOCATION: Bacterial flagellum basal body {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the YcgR family. {ECO:0000305}.
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DR EMBL; AE015451; AAN69975.1; -; Genomic_DNA.
DR RefSeq; NP_746511.1; NC_002947.4.
DR RefSeq; WP_010955107.1; NC_002947.4.
DR PDB; 2GJG; X-ray; 2.25 A; A=1-247.
DR PDB; 3KYF; X-ray; 2.10 A; A=8-238.
DR PDBsum; 2GJG; -.
DR PDBsum; 3KYF; -.
DR AlphaFoldDB; Q88EQ6; -.
DR SMR; Q88EQ6; -.
DR STRING; 160488.PP_4397; -.
DR PaxDb; 160488-PP_4397; -.
DR DNASU; 1043210; -.
DR GeneID; 83678893; -.
DR KEGG; ppu:PP_4397; -.
DR PATRIC; fig|160488.4.peg.4672; -.
DR eggNOG; COG5581; Bacteria.
DR HOGENOM; CLU_098282_0_0_6; -.
DR OrthoDB; 6746848at2; -.
DR PhylomeDB; Q88EQ6; -.
DR BioCyc; PPUT160488:G1G01-4675-MONOMER; -.
DR EvolutionaryTrace; Q88EQ6; -.
DR Proteomes; UP000000556; Chromosome.
DR GO; GO:0009425; C:bacterial-type flagellum basal body; IEA:UniProtKB-SubCell.
DR GO; GO:0035438; F:cyclic-di-GMP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0071973; P:bacterial-type flagellum-dependent cell motility; IEA:UniProtKB-UniRule.
DR GO; GO:0071945; P:regulation of bacterial-type flagellum-dependent cell motility by regulation of motor speed; IEA:UniProtKB-UniRule.
DR Gene3D; 2.40.10.220; predicted glycosyltransferase like domains; 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; PilZN; 1.
DR SUPFAM; SSF141371; PilZ domain-like; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Bacterial flagellum; c-di-GMP; Nucleotide-binding;
KW Reference proteome.
FT CHAIN 1..247
FT /note="Flagellar brake protein YcgR"
FT /id="PRO_0000395282"
FT DOMAIN 121..234
FT /note="PilZ"
FT BINDING 121..127
FT /ligand="3',3'-c-di-GMP"
FT /ligand_id="ChEBI:CHEBI:58805"
FT /evidence="ECO:0000269|PubMed:20226196"
FT MUTAGEN 121
FT /note="Q->A: 1.7-fold decreased affinity for c-di-GMP."
FT /evidence="ECO:0000269|PubMed:20226196"
FT MUTAGEN 122
FT /note="R->A: 20-fold decreased affinity for c-di-GMP."
FT /evidence="ECO:0000269|PubMed:20226196"
FT MUTAGEN 122
FT /note="R->L: 4-fold decreased affinity for c-di-GMP, binds
FT 1 c-di-GMP per monomer."
FT /evidence="ECO:0000269|PubMed:20226196"
FT MUTAGEN 123
FT /note="R->A: Loss of c-di-GMP binding."
FT /evidence="ECO:0000269|PubMed:20226196"
FT MUTAGEN 127
FT /note="R->A: Loss of c-di-GMP binding."
FT /evidence="ECO:0000269|PubMed:20226196"
FT MUTAGEN 157
FT /note="D->A: Loss of c-di-GMP binding."
FT /evidence="ECO:0000269|PubMed:20226196"
FT MUTAGEN 159
FT /note="S->A: 4-fold decreased affinity for c-di-GMP."
FT /evidence="ECO:0000269|PubMed:20226196"
FT MUTAGEN 162
FT /note="G->A: Loss of c-di-GMP binding."
FT /evidence="ECO:0000269|PubMed:20226196"
FT STRAND 12..14
FT /evidence="ECO:0007829|PDB:3KYF"
FT HELIX 17..29
FT /evidence="ECO:0007829|PDB:3KYF"
FT STRAND 34..38
FT /evidence="ECO:0007829|PDB:3KYF"
FT STRAND 44..47
FT /evidence="ECO:0007829|PDB:3KYF"
FT STRAND 49..53
FT /evidence="ECO:0007829|PDB:3KYF"
FT TURN 54..57
FT /evidence="ECO:0007829|PDB:3KYF"
FT STRAND 58..62
FT /evidence="ECO:0007829|PDB:3KYF"
FT HELIX 67..69
FT /evidence="ECO:0007829|PDB:3KYF"
FT HELIX 70..74
FT /evidence="ECO:0007829|PDB:3KYF"
FT STRAND 79..85
FT /evidence="ECO:0007829|PDB:3KYF"
FT STRAND 88..94
FT /evidence="ECO:0007829|PDB:3KYF"
FT STRAND 99..103
FT /evidence="ECO:0007829|PDB:3KYF"
FT STRAND 106..111
FT /evidence="ECO:0007829|PDB:3KYF"
FT STRAND 117..120
FT /evidence="ECO:0007829|PDB:3KYF"
FT HELIX 123..129
FT /evidence="ECO:0007829|PDB:2GJG"
FT HELIX 132..134
FT /evidence="ECO:0007829|PDB:3KYF"
FT STRAND 137..140
FT /evidence="ECO:0007829|PDB:3KYF"
FT STRAND 147..149
FT /evidence="ECO:0007829|PDB:3KYF"
FT STRAND 151..158
FT /evidence="ECO:0007829|PDB:3KYF"
FT STRAND 160..169
FT /evidence="ECO:0007829|PDB:3KYF"
FT HELIX 172..174
FT /evidence="ECO:0007829|PDB:3KYF"
FT STRAND 180..186
FT /evidence="ECO:0007829|PDB:3KYF"
FT TURN 187..190
FT /evidence="ECO:0007829|PDB:3KYF"
FT STRAND 192..205
FT /evidence="ECO:0007829|PDB:3KYF"
FT HELIX 206..208
FT /evidence="ECO:0007829|PDB:3KYF"
FT STRAND 210..219
FT /evidence="ECO:0007829|PDB:3KYF"
FT HELIX 222..237
FT /evidence="ECO:0007829|PDB:3KYF"
SQ SEQUENCE 247 AA; 28449 MW; 75AFB427486A0C0E CRC64;
MFNESDAPQP PKVLSTPLEI AANLRQLQES HDPLIITFHD RSHRFQSYVV HVDRESNTLA
LDEMIPRDGE KFIENGEHFR VEGFHDGVRI AWECDHALKI SEVDGHRCYS GPLPQEVTYH
QRRNAFRAAL KLSQLVDIIL DGAHLKGNGA MRGKLLDISA TGCKLRFEGN VEDRLQLGQV
YERFKAGNPL GLVDTMVELR HLHYEERINT TFAGVRFHNL SGQAQRKIES FVYQLQREAR
RFDKDDY
//
