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Protein

Cyclic di-GMP binding protein VCA0042

Gene

VC_A0042

Organism
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

May act as a flagellar brake, regulating swimming and swarming in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)-dependent manner. Increasing levels of c-di-GMP lead to decreased motility (Potential). Binds bis-(3'-5') cyclic diguanylic acid (c-di-GMP) with a dissociation constant of 170 nM in the presence of 10 mM KCl and with 100 nM in its absence. Binds 1 to 2 c-di-GMP per subunit. Only 1 c-di-GMP is seen in the wild-type crystal, while 2 are seen in the mutant. Depending on the concentration of K+ stoichiometries of 1:1, 1.43:1 and 2:1 are determined by isothermal titration calorimetry.Curated

GO - Molecular functioni

Complete GO annotation...

Keywords - Ligandi

c-di-GMP, Nucleotide-binding

Enzyme and pathway databases

BioCyciVCHO:VCA0042-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Cyclic di-GMP binding protein VCA0042
Gene namesi
Ordered Locus Names:VC_A0042
OrganismiVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Taxonomic identifieri243277 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
Proteomesi
  • UP000000584 Componenti: Chromosome 2

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Bacterial flagellum

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi135 – 1351L → R: Increases affinity for c-di-GMP, increases amount of c-di-GMP dimer bound to the protein. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 252252Cyclic di-GMP binding protein VCA0042PRO_0000395289Add
BLAST

Interactioni

Subunit structurei

Dimer.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
VC_0653Q9KU704EBI-7698724,EBI-7698739

Protein-protein interaction databases

IntActiQ9KNC3. 1 interaction.
MINTiMINT-6178617.
STRINGi243277.VCA0042.

Structurei

Secondary structure

1
252
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi23 – 286Combined sources
Helixi29 – 335Combined sources
Beta strandi41 – 477Combined sources
Beta strandi53 – 6412Combined sources
Turni65 – 673Combined sources
Beta strandi68 – 725Combined sources
Helixi78 – 847Combined sources
Beta strandi90 – 978Combined sources
Beta strandi103 – 11513Combined sources
Beta strandi117 – 1193Combined sources
Beta strandi121 – 1244Combined sources
Beta strandi128 – 1358Combined sources
Beta strandi141 – 15111Combined sources
Beta strandi154 – 16310Combined sources
Beta strandi165 – 1717Combined sources
Beta strandi184 – 1929Combined sources
Beta strandi195 – 1984Combined sources
Beta strandi202 – 21413Combined sources
Beta strandi216 – 2227Combined sources
Helixi224 – 23512Combined sources
Beta strandi237 – 2393Combined sources
Beta strandi241 – 2455Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1YLNX-ray2.20A1-252[»]
3KYGX-ray2.10A/B21-247[»]
ProteinModelPortaliQ9KNC3.
SMRiQ9KNC3. Positions 23-247.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9KNC3.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini134 – 233100PilZAdd
BLAST

Sequence similaritiesi

Belongs to the YcgR family.Curated
Contains 1 PilZ domain.Curated

Phylogenomic databases

eggNOGiENOG4105YE1. Bacteria.
ENOG41126C4. LUCA.
OMAiSKSGCRF.
OrthoDBiEOG6G20K3.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
InterProiIPR009875. PilZ_domain.
IPR012349. Split_barrel_FMN-bd.
IPR009926. T3SS_YcgR_N.
[Graphical view]
PfamiPF07238. PilZ. 1 hit.
PF12945. YcgR_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9KNC3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNSRPAEKID NNDGQTETPR SKTVSTINST DALAMVEHSS ELTLSITTPV
60 70 80 90 100
GTKFVCRTPF IGTHTDKFLL VEMPKISADD LQYFFQEGFW MNIRAISPRG
110 120 130 140 150
EGALIHFRSQ LMHILQEPVP MAFLSIPNTM QVSQLRKEPR FELNLAGKVL
160 170 180 190 200
FDEHRGDCEL RDLSRSGCRF ITPPLGKTYQ VGDLVALEIF SDLRGTKTFP
210 220 230 240 250
PLTGKICNLQ RSLHHARYGL EFNEEGRNNA KNLLAQLKFN GTKLTLNAEK

KA
Length:252
Mass (Da):28,381
Last modified:October 1, 2000 - v1
Checksum:i5FC448153DDAA6FD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003853 Genomic DNA. Translation: AAF95956.1.
PIRiC82507.
RefSeqiNP_232443.1. NC_002506.1.
WP_001088585.1. NC_002506.1.

Genome annotation databases

EnsemblBacteriaiAAF95956; AAF95956; VC_A0042.
GeneIDi2612415.
KEGGivch:VCA0042.
PATRICi20084673. VBIVibCho83274_2688.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003853 Genomic DNA. Translation: AAF95956.1.
PIRiC82507.
RefSeqiNP_232443.1. NC_002506.1.
WP_001088585.1. NC_002506.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1YLNX-ray2.20A1-252[»]
3KYGX-ray2.10A/B21-247[»]
ProteinModelPortaliQ9KNC3.
SMRiQ9KNC3. Positions 23-247.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ9KNC3. 1 interaction.
MINTiMINT-6178617.
STRINGi243277.VCA0042.

Protocols and materials databases

DNASUi2612415.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF95956; AAF95956; VC_A0042.
GeneIDi2612415.
KEGGivch:VCA0042.
PATRICi20084673. VBIVibCho83274_2688.

Phylogenomic databases

eggNOGiENOG4105YE1. Bacteria.
ENOG41126C4. LUCA.
OMAiSKSGCRF.
OrthoDBiEOG6G20K3.

Enzyme and pathway databases

BioCyciVCHO:VCA0042-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9KNC3.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
InterProiIPR009875. PilZ_domain.
IPR012349. Split_barrel_FMN-bd.
IPR009926. T3SS_YcgR_N.
[Graphical view]
PfamiPF07238. PilZ. 1 hit.
PF12945. YcgR_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 39315 / El Tor Inaba N16961.
  2. "The crystal structure of the hypothetical protein VCA0042 from Vibrio cholerae O1."
    Midwest center for structural genomics (MCSG)
    Submitted (FEB-2009) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
  3. "Structure of PP4397 reveals the molecular basis for different c-di-GMP binding modes by Pilz domain proteins."
    Ko J., Ryu K.S., Kim H., Shin J.S., Lee J.O., Cheong C., Choi B.S.
    J. Mol. Biol. 398:97-110(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF L135R MUTANT IN COMPLEX WITH C-DI-GMP, SUBUNIT, MUTAGENESIS OF LEU-135.

Entry informationi

Entry nameiYCGRL_VIBCH
AccessioniPrimary (citable) accession number: Q9KNC3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 13, 2010
Last sequence update: October 1, 2000
Last modified: December 9, 2015
This is version 74 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.