YCGRL_VIBCH
ID YCGRL_VIBCH Reviewed; 252 AA.
AC Q9KNC3;
DT 13-JUL-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 95.
DE RecName: Full=Cyclic di-GMP binding protein VCA0042;
GN OrderedLocusNames=VC_A0042;
OS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=243277;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 39315 / El Tor Inaba N16961;
RX PubMed=10952301; DOI=10.1038/35020000;
RA Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L.,
RA Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R.,
RA Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D.,
RA Vamathevan J.J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L.A.,
RA Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L.,
RA Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.;
RT "DNA sequence of both chromosomes of the cholera pathogen Vibrio
RT cholerae.";
RL Nature 406:477-483(2000).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
RG Midwest center for structural genomics (MCSG);
RT "The crystal structure of the hypothetical protein VCA0042 from Vibrio
RT cholerae O1.";
RL Submitted (FEB-2009) to the PDB data bank.
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF L135R MUTANT IN COMPLEX WITH
RP C-DI-GMP, SUBUNIT, AND MUTAGENESIS OF LEU-135.
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: May act as a flagellar brake, regulating swimming and
CC swarming in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)-dependent
CC manner. Increasing levels of c-di-GMP lead to decreased motility
CC (Potential). Binds bis-(3'-5') cyclic diguanylic acid (c-di-GMP) with a
CC dissociation constant of 170 nM in the presence of 10 mM KCl and with
CC 100 nM in its absence. Binds 1 to 2 c-di-GMP per subunit. Only 1 c-di-
CC GMP is seen in the wild-type crystal, while 2 are seen in the mutant.
CC Depending on the concentration of K(+) stoichiometries of 1:1, 1.43:1
CC and 2:1 are determined by isothermal titration calorimetry.
CC {ECO:0000305}.
CC -!- SUBUNIT: Dimer. {ECO:0000269|PubMed:20226196}.
CC -!- INTERACTION:
CC Q9KNC3; Q9KU70: VC_0653; NbExp=4; IntAct=EBI-7698724, EBI-7698739;
CC -!- SUBCELLULAR LOCATION: Bacterial flagellum basal body {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the YcgR family. {ECO:0000305}.
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DR EMBL; AE003853; AAF95956.1; -; Genomic_DNA.
DR PIR; C82507; C82507.
DR RefSeq; NP_232443.1; NC_002506.1.
DR RefSeq; WP_001088585.1; NZ_LT906615.1.
DR PDB; 1YLN; X-ray; 2.20 A; A=1-252.
DR PDB; 3KYG; X-ray; 2.10 A; A/B=21-247.
DR PDBsum; 1YLN; -.
DR PDBsum; 3KYG; -.
DR AlphaFoldDB; Q9KNC3; -.
DR SMR; Q9KNC3; -.
DR IntAct; Q9KNC3; 1.
DR MINT; Q9KNC3; -.
DR STRING; 243277.VC_A0042; -.
DR DNASU; 2612415; -.
DR EnsemblBacteria; AAF95956; AAF95956; VC_A0042.
DR GeneID; 57741516; -.
DR KEGG; vch:VC_A0042; -.
DR PATRIC; fig|243277.26.peg.2688; -.
DR eggNOG; ENOG5033HT2; Bacteria.
DR HOGENOM; CLU_1119806_0_0_6; -.
DR OMA; SKSGCRF; -.
DR BioCyc; VCHO:VCA0042-MON; -.
DR EvolutionaryTrace; Q9KNC3; -.
DR Proteomes; UP000000584; Chromosome 2.
DR GO; GO:0009425; C:bacterial-type flagellum basal body; IEA:UniProtKB-SubCell.
DR GO; GO:0035438; F:cyclic-di-GMP binding; IEA:InterPro.
DR Gene3D; 2.30.110.10; -; 1.
DR InterPro; IPR009875; PilZ_domain.
DR InterPro; IPR012349; Split_barrel_FMN-bd.
DR InterPro; IPR009926; T3SS_YcgR_PilZN.
DR Pfam; PF07238; PilZ; 1.
DR Pfam; PF12945; YcgR_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Bacterial flagellum; c-di-GMP; Nucleotide-binding;
KW Reference proteome.
FT CHAIN 1..252
FT /note="Cyclic di-GMP binding protein VCA0042"
FT /id="PRO_0000395289"
FT DOMAIN 134..233
FT /note="PilZ"
FT REGION 1..24
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 135
FT /note="L->R: Increases affinity for c-di-GMP, increases
FT amount of c-di-GMP dimer bound to the protein."
FT /evidence="ECO:0000269|PubMed:20226196"
FT STRAND 23..28
FT /evidence="ECO:0007829|PDB:3KYG"
FT HELIX 29..33
FT /evidence="ECO:0007829|PDB:3KYG"
FT STRAND 41..47
FT /evidence="ECO:0007829|PDB:3KYG"
FT STRAND 53..64
FT /evidence="ECO:0007829|PDB:3KYG"
FT TURN 65..67
FT /evidence="ECO:0007829|PDB:3KYG"
FT STRAND 68..72
FT /evidence="ECO:0007829|PDB:3KYG"
FT HELIX 78..84
FT /evidence="ECO:0007829|PDB:3KYG"
FT STRAND 90..97
FT /evidence="ECO:0007829|PDB:3KYG"
FT STRAND 103..115
FT /evidence="ECO:0007829|PDB:3KYG"
FT STRAND 117..119
FT /evidence="ECO:0007829|PDB:3KYG"
FT STRAND 121..124
FT /evidence="ECO:0007829|PDB:3KYG"
FT STRAND 128..135
FT /evidence="ECO:0007829|PDB:3KYG"
FT STRAND 141..151
FT /evidence="ECO:0007829|PDB:3KYG"
FT STRAND 154..163
FT /evidence="ECO:0007829|PDB:3KYG"
FT STRAND 165..171
FT /evidence="ECO:0007829|PDB:3KYG"
FT STRAND 184..192
FT /evidence="ECO:0007829|PDB:3KYG"
FT STRAND 195..198
FT /evidence="ECO:0007829|PDB:3KYG"
FT STRAND 202..214
FT /evidence="ECO:0007829|PDB:3KYG"
FT STRAND 216..222
FT /evidence="ECO:0007829|PDB:3KYG"
FT HELIX 224..235
FT /evidence="ECO:0007829|PDB:3KYG"
FT STRAND 237..239
FT /evidence="ECO:0007829|PDB:1YLN"
FT STRAND 241..245
FT /evidence="ECO:0007829|PDB:3KYG"
SQ SEQUENCE 252 AA; 28381 MW; 5FC448153DDAA6FD CRC64;
MNSRPAEKID NNDGQTETPR SKTVSTINST DALAMVEHSS ELTLSITTPV GTKFVCRTPF
IGTHTDKFLL VEMPKISADD LQYFFQEGFW MNIRAISPRG EGALIHFRSQ LMHILQEPVP
MAFLSIPNTM QVSQLRKEPR FELNLAGKVL FDEHRGDCEL RDLSRSGCRF ITPPLGKTYQ
VGDLVALEIF SDLRGTKTFP PLTGKICNLQ RSLHHARYGL EFNEEGRNNA KNLLAQLKFN
GTKLTLNAEK KA
