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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)DescriptionActionsGraphical viewLength
Mutagenesisi135L → R: Increases affinity for c-di-GMP, increases amount of c-di-GMP dimer bound to the protein. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003952891 – 252Cyclic di-GMP binding protein VCA0042Add BLAST252

Interactioni

Subunit structurei

Dimer.1 Publication

Binary interactionsi

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

Protein-protein interaction databases

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

Structurei

Secondary structure

1252
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi23 – 28Combined sources6
Helixi29 – 33Combined sources5
Beta strandi41 – 47Combined sources7
Beta strandi53 – 64Combined sources12
Turni65 – 67Combined sources3
Beta strandi68 – 72Combined sources5
Helixi78 – 84Combined sources7
Beta strandi90 – 97Combined sources8
Beta strandi103 – 115Combined sources13
Beta strandi117 – 119Combined sources3
Beta strandi121 – 124Combined sources4
Beta strandi128 – 135Combined sources8
Beta strandi141 – 151Combined sources11
Beta strandi154 – 163Combined sources10
Beta strandi165 – 171Combined sources7
Beta strandi184 – 192Combined sources9
Beta strandi195 – 198Combined sources4
Beta strandi202 – 214Combined sources13
Beta strandi216 – 222Combined sources7
Helixi224 – 235Combined sources12
Beta strandi237 – 239Combined sources3
Beta strandi241 – 245Combined sources5

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ9KNC3.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini134 – 233PilZAdd BLAST100

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105YE1. Bacteria.
ENOG41126C4. LUCA.
OMAiSKSGCRF.

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1YLNX-ray2.20A1-252[»]
3KYGX-ray2.10A/B21-247[»]
ProteinModelPortaliQ9KNC3.
SMRiQ9KNC3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ9KNC3. 1 interactor.
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.

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...

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: November 2, 2016
This is version 77 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.