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Protein

Vitamin K epoxide reductase homolog

Gene

CYB_2278

Organism
Synechococcus sp. (strain JA-2-3B'a(2-13)) (Cyanobacteria bacterium Yellowstone B-Prime)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Thiol-disulfide oxidoreductase that catalyzes vitamin K-dependent disulfide bond formation in periplasmic target proteins.2 Publications

Enzyme regulationi

Inhibited by ferulenol.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei50 – 501Important for the reduction of the redox-active Cys-130 and Cys-133
Sitei56 – 561Important for the reduction of the redox-active Cys-130 and Cys-133
Sitei209 – 2091Important for the reduction of the redox-active Cys-130 and Cys-133
Sitei212 – 2121Important for the reduction of the redox-active Cys-130 and Cys-133

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Enzyme and pathway databases

BioCyciSSP321332:GH1B-2277-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Vitamin K epoxide reductase homolog (EC:1.1.4.-)
Short name:
VKOR
Gene namesi
Ordered Locus Names:CYB_2278
OrganismiSynechococcus sp. (strain JA-2-3B'a(2-13)) (Cyanobacteria bacterium Yellowstone B-Prime)
Taxonomic identifieri321332 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechococcus
Proteomesi
  • UP000001938 Componenti: Chromosome

Subcellular locationi

  • Membrane 2 Publications; Multi-pass membrane protein 2 Publications

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 2020CytoplasmicAdd
BLAST
Transmembranei21 – 4121HelicalAdd
BLAST
Topological domaini42 – 6625PeriplasmicAdd
BLAST
Transmembranei67 – 8721HelicalAdd
BLAST
Topological domaini88 – 10215CytoplasmicAdd
BLAST
Transmembranei103 – 12321HelicalAdd
BLAST
Topological domaini124 – 1285Periplasmic
Transmembranei129 – 14921HelicalAdd
BLAST
Topological domaini150 – 1589Cytoplasmic
Transmembranei159 – 17921HelicalAdd
BLAST
Topological domaini180 – 283104PeriplasmicAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi41 – 411K → A: Reduces enzyme activity by about 40% with dithiothreitol as in vitro reductant. 1 Publication
Mutagenesisi41 – 411K → E: Reduces enzyme activity by about 20% with dithiothreitol as in vitro reductant. 1 Publication
Mutagenesisi41 – 411K → R: Minor effect on enzyme activity with dithiothreitol as in vitro reductant. 1 Publication
Mutagenesisi41 – 411K → S: Reduces enzyme activity by about 75% with dithiothreitol as in vitro reductant. 1 Publication
Mutagenesisi50 – 501C → A: Abolishes enzyme activity, but not with dithiothreitol as in vitro reductant. 2 Publications
Mutagenesisi56 – 561C → A: Abolishes enzyme activity, but not with dithiothreitol as in vitro reductant. 1 Publication
Mutagenesisi60 – 601L → A or G: Reduces enzyme activity. 1 Publication
Mutagenesisi130 – 1301C → A or S: Abolishes enzyme activity, also with dithiothreitol as in vitro reductant. 2 Publications
Mutagenesisi133 – 1331C → A: Abolishes enzyme activity, also with dithiothreitol as in vitro reductant. 1 Publication
Mutagenesisi209 – 2091C → A: Abolishes enzyme activity, but not with dithiothreitol as in vitro reductant. 1 Publication
Mutagenesisi212 – 2121C → A: Abolishes enzyme activity, but not with dithiothreitol as in vitro reductant. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 283283Vitamin K epoxide reductase homologPRO_0000429265Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi50 ↔ 56Redox-active1 Publication
Disulfide bondi130 ↔ 133Redox-active1 Publication
Disulfide bondi209 ↔ 212Redox-active1 Publication
Disulfide bondi231 ↔ 2441 Publication

Keywords - PTMi

Disulfide bond, Quinone

Interactioni

Protein-protein interaction databases

STRINGi321332.CYB_2278.

Structurei

Secondary structure

1
283
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi21 – 4222Combined sources
Helixi56 – 616Combined sources
Beta strandi65 – 673Combined sources
Helixi72 – 8817Combined sources
Helixi96 – 12429Combined sources
Helixi131 – 14818Combined sources
Beta strandi149 – 1513Combined sources
Helixi157 – 18125Combined sources
Helixi187 – 19913Combined sources
Beta strandi202 – 2054Combined sources
Helixi210 – 21910Combined sources
Helixi220 – 2256Combined sources
Beta strandi228 – 2314Combined sources
Helixi242 – 2465Combined sources
Beta strandi251 – 2577Combined sources
Beta strandi260 – 2645Combined sources
Helixi268 – 2758Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3KP8X-ray1.66A186-283[»]
3KP9X-ray3.60A1-283[»]
4NV2X-ray3.61A1-283[»]
4NV5X-ray2.79A/B1-283[»]
4NV6X-ray4.19A1-283[»]
ProteinModelPortaliQ2JJF6.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ2JJF6.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni59 – 657Quinone binding
Regioni111 – 12212Quinone bindingAdd
BLAST
Regioni186 – 28398Thioredoxin-like domainAdd
BLAST

Domaini

Cysteine residues from the thioredoxin-like domain participate in a series of disulfide-exchange reactions that regenerate the redox-active cysteine residues in the transmembrane domain.

Sequence similaritiesi

Belongs to the VKOR family.Curated

Keywords - Domaini

Redox-active center, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105CVB. Bacteria.
COG4243. LUCA.
HOGENOMiHOG000232446.
OMAiCPHCHEQ.
OrthoDBiEOG65N1CR.

Family and domain databases

Gene3Di3.40.30.10. 1 hit.
InterProiIPR012336. Thioredoxin-like_fold.
IPR012932. VKOR.
[Graphical view]
PfamiPF07884. VKOR. 1 hit.
[Graphical view]
SMARTiSM00756. VKc. 1 hit.
[Graphical view]
SUPFAMiSSF52833. SSF52833. 1 hit.

Sequencei

Sequence statusi: Complete.

Q2JJF6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASYLKLKAQ EETWLQRHSR LILAILAGLG SLLTAYLTYT KLTEQPAAFC
60 70 80 90 100
TGDGGCDLVL SSRWAEFLGI PTAAVGLLGF LGVLALAVLP DGLPLVKRWR
110 120 130 140 150
WPALFGLVSA MTAFEMYMLY LMVAVLRQFC MYCTTAIILV AGLGLVTVLG
160 170 180 190 200
HRWLDGGKLA FSYILVAFLT LVTTIGVYAN QVPPPSPLAV GLAAHLRQIG
210 220 230 240 250
GTMYGAYWCP HCQDQKELFG AAFDQVPYVE CSPNGPGTPQ AQECTEAGIT
260 270 280
SYPTWIINGR TYTGVRSLEA LAVASGYPLE EGR
Length:283
Mass (Da):30,593
Last modified:March 7, 2006 - v1
Checksum:i615561731469DF16
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000240 Genomic DNA. Translation: ABD03218.1.
RefSeqiWP_011433847.1. NC_007776.1.

Genome annotation databases

EnsemblBacteriaiABD03218; ABD03218; CYB_2278.
KEGGicyb:CYB_2278.
PATRICi23806900. VBISynSp29577_2279.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000240 Genomic DNA. Translation: ABD03218.1.
RefSeqiWP_011433847.1. NC_007776.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3KP8X-ray1.66A186-283[»]
3KP9X-ray3.60A1-283[»]
4NV2X-ray3.61A1-283[»]
4NV5X-ray2.79A/B1-283[»]
4NV6X-ray4.19A1-283[»]
ProteinModelPortaliQ2JJF6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi321332.CYB_2278.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABD03218; ABD03218; CYB_2278.
KEGGicyb:CYB_2278.
PATRICi23806900. VBISynSp29577_2279.

Phylogenomic databases

eggNOGiENOG4105CVB. Bacteria.
COG4243. LUCA.
HOGENOMiHOG000232446.
OMAiCPHCHEQ.
OrthoDBiEOG65N1CR.

Enzyme and pathway databases

BioCyciSSP321332:GH1B-2277-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ2JJF6.

Family and domain databases

Gene3Di3.40.30.10. 1 hit.
InterProiIPR012336. Thioredoxin-like_fold.
IPR012932. VKOR.
[Graphical view]
PfamiPF07884. VKOR. 1 hit.
[Graphical view]
SMARTiSM00756. VKc. 1 hit.
[Graphical view]
SUPFAMiSSF52833. SSF52833. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses."
    Bhaya D., Grossman A.R., Steunou A.-S., Khuri N., Cohan F.M., Hamamura N., Melendrez M.C., Bateson M.M., Ward D.M., Heidelberg J.F.
    ISME J. 1:703-713(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: JA-2-3B'a(2-13).
  2. "Structure of a bacterial homologue of vitamin K epoxide reductase."
    Li W., Schulman S., Dutton R.J., Boyd D., Beckwith J., Rapoport T.A.
    Nature 463:507-512(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.66 ANGSTROMS) OF MUTANT SER-56 IN COMPLEX WITH UBIQUINONE, SUBCELLULAR LOCATION, TOPOLOGY, DISULFIDE BOND, FUNCTION, MUTAGENESIS OF CYS-50; CYS-56; CYS-130; CYS-133; CYS-209 AND CYS-212, ENZYME REGULATION, REDOX-ACTIVE SITE, REGION.
  3. "Structures of an intramembrane vitamin K epoxide reductase homolog reveal control mechanisms for electron transfer."
    Liu S., Cheng W., Fowle Grider R., Shen G., Li W.
    Nat. Commun. 5:3110-3110(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.79 ANGSTROMS) OF 186-283 OF MUTANTS ALA-50 AND ALA-212 IN COMPLEX WITH UBIQUINONE, FUNCTION, SUBCELLULAR LOCATION, TOPOLOGY, MUTAGENESIS OF LYS-41; CYS-50; LEU-60; CYS-130 AND CYS-212, REDOX-ACTIVE SITE, SITE, THIOREDOXIN-LIKE REGION.

Entry informationi

Entry nameiVKOR_SYNJB
AccessioniPrimary (citable) accession number: Q2JJF6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 11, 2014
Last sequence update: March 7, 2006
Last modified: December 9, 2015
This is version 64 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.