Skip Header

Contribute Send feedback
Read comments (?) or add your own

Q9KNC3 (YCGRL_VIBCH) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 45. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Cyclic di-GMP binding protein VCA0042
Gene names
Ordered Locus Names:VC_A0042
OrganismVibrio cholerae
Taxonomic identifier666 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio

Protein attributes

Sequence length252 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 mM in its absence. HAMAP MF_01457

Cofactor

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. Ref.3

Subunit structure

Dimer. Ref.3

Subcellular location

Bacterial flagellum basal body Potential HAMAP MF_01457.

Sequence similarities

Belongs to the YcgR family.

Contains 1 PilZ domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 252252Cyclic di-GMP binding protein VCA0042 HAMAP MF_01457
PRO_0000395289

Regions

Domain134 – 233100PilZ

Experimental info

Mutagenesis1351L → R: Increases affinity for c-di-GMP, increases amount of c-di-GMP dimer bound to the protein. Ref.3

Secondary structure

1 ....................................... 252
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9KNC3 [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: 5FC448153DDAA6FD

FASTA25228,381
        10         20         30         40         50         60 
MNSRPAEKID NNDGQTETPR SKTVSTINST DALAMVEHSS ELTLSITTPV GTKFVCRTPF 

        70         80         90        100        110        120 
IGTHTDKFLL VEMPKISADD LQYFFQEGFW MNIRAISPRG EGALIHFRSQ LMHILQEPVP 

       130        140        150        160        170        180 
MAFLSIPNTM QVSQLRKEPR FELNLAGKVL FDEHRGDCEL RDLSRSGCRF ITPPLGKTYQ 

       190        200        210        220        230        240 
VGDLVALEIF SDLRGTKTFP PLTGKICNLQ RSLHHARYGL EFNEEGRNNA KNLLAQLKFN 

       250 
GTKLTLNAEK KA

« Hide

References

« Hide 'large scale' references
[1]"DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae."
Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L., Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R., Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D., Vamathevan J.J., Bass S. expand/collapse author list , Qin H., Dragoi I., Sellers P., McDonald L.A., Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L., Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.
Nature 406:477-483(2000) [PubMed: 10952301] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 39315 / El Tor Inaba N16961 / Serotype O1.
[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: 20226196] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF L135R MUTANT IN COMPLEX WITH C-DI-GMP, SUBUNIT, COFACTOR, MUTAGENESIS OF LEU-135.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AE003853 Genomic DNA. Translation: AAF95956.1.
PIRC82507.
RefSeqNP_232443.1. NC_002506.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1YLNX-ray2.20A1-252[»]
3KYGX-ray2.10A/B21-247[»]
ProteinModelPortalQ9KNC3.
SMRQ9KNC3. Positions 23-247.
ModBaseSearch...

Protein-protein interaction databases

MINTMINT-6178617.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID2612415.
GenomeReviewsGene locus VC_A0042 in contig AE003853_GR.
KEGGvch:VCA0042.
PATRIC20084673. VBIVibCho83274_2688.
TIGRVC_A0042.

Phylogenomic databases

HOGENOMHBG741439.
OMASHRGEGA.
ProtClustDBCLSK869471.

Family and domain databases

HAMAPMF_01457. YcgR. Divergent sequence.
[Tree]
InterProIPR009875. PilZ_domain.
IPR012349. Split_barrel_FMN-bd.
[Graphical view]
Gene3DG3DSA:2.30.110.10. PNPOx_FMN_bd. 1 hit.
PfamPF07238. PilZ. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameYCGRL_VIBCH
AccessionPrimary (citable) accession number: Q9KNC3
Entry history
Integrated into UniProtKB/Swiss-Prot: July 13, 2010
Last sequence update: October 1, 2000
Last modified: January 25, 2012
This is version 45 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents