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Protein

Rubredoxin

Gene

rub

Organism
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule.
Electron acceptor for cytoplasmic lactate dehydrogenase.

Cofactori

Fe3+Note: Binds 1 Fe3+ ion per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi6 – 61Iron
Metal bindingi9 – 91Iron
Metal bindingi39 – 391Iron
Metal bindingi42 – 421Iron

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Electron transport, Transport

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciDVUL883:GCJ5-2550-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Rubredoxin
Short name:
Rd
Gene namesi
Name:rub
Ordered Locus Names:DvMF_2480
OrganismiDesulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Taxonomic identifieri883 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
Proteomesi
  • UP000001361 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 5252RubredoxinPRO_0000135039Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-formylmethionine1 Publication

Keywords - PTMi

Formylation

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

STRINGi883.DvMF_2480.

Structurei

Secondary structure

1
52
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 63Combined sources
Turni7 – 93Combined sources
Turni15 – 173Combined sources
Helixi20 – 223Combined sources
Helixi30 – 323Combined sources
Turni40 – 423Combined sources
Helixi46 – 483Combined sources
Beta strandi49 – 513Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RDVX-ray2.00A1-52[»]
2RDVX-ray1.90A/B/C1-52[»]
ProteinModelPortaliP15412.
SMRiP15412. Positions 1-52.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP15412.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 5252Rubredoxin-likePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the rubredoxin family.Curated
Contains 1 rubredoxin-like domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4105VCQ. Bacteria.
COG1773. LUCA.
HOGENOMiHOG000223371.
OMAiAPKDMFE.
OrthoDBiPOG091H0FS1.

Family and domain databases

CDDicd00730. rubredoxin. 1 hit.
Gene3Di2.20.28.10. 1 hit.
InterProiIPR024922. Rubredoxin.
IPR024934. Rubredoxin-like_dom.
IPR004039. Rubredoxin-type_fold.
IPR024935. Rubredoxin_dom.
IPR018527. Rubredoxin_Fe_BS.
[Graphical view]
PfamiPF00301. Rubredoxin. 1 hit.
[Graphical view]
PIRSFiPIRSF000071. Rubredoxin. 1 hit.
PRINTSiPR00163. RUBREDOXIN.
PROSITEiPS00202. RUBREDOXIN. 1 hit.
PS50903. RUBREDOXIN_LIKE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P15412-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKYVCTVCG YEYDPAEGDP DNGVKPGTAF EDVPADWVCP ICGAPKSEFE

PA
Length:52
Mass (Da):5,598
Last modified:April 1, 1990 - v1
Checksum:i6443741A8A8063A2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D76419 Genomic DNA. Translation: BAA11175.1.
CP001197 Genomic DNA. Translation: ACL09420.1.
PIRiJX0241.
RefSeqiWP_007526280.1. NC_011769.1.

Genome annotation databases

EnsemblBacteriaiACL09420; ACL09420; DvMF_2480.
KEGGidvm:DvMF_2480.
PATRICi21775377. VBIDesVul86729_2691.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D76419 Genomic DNA. Translation: BAA11175.1.
CP001197 Genomic DNA. Translation: ACL09420.1.
PIRiJX0241.
RefSeqiWP_007526280.1. NC_011769.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RDVX-ray2.00A1-52[»]
2RDVX-ray1.90A/B/C1-52[»]
ProteinModelPortaliP15412.
SMRiP15412. Positions 1-52.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi883.DvMF_2480.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACL09420; ACL09420; DvMF_2480.
KEGGidvm:DvMF_2480.
PATRICi21775377. VBIDesVul86729_2691.

Phylogenomic databases

eggNOGiENOG4105VCQ. Bacteria.
COG1773. LUCA.
HOGENOMiHOG000223371.
OMAiAPKDMFE.
OrthoDBiPOG091H0FS1.

Enzyme and pathway databases

BioCyciDVUL883:GCJ5-2550-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP15412.

Family and domain databases

CDDicd00730. rubredoxin. 1 hit.
Gene3Di2.20.28.10. 1 hit.
InterProiIPR024922. Rubredoxin.
IPR024934. Rubredoxin-like_dom.
IPR004039. Rubredoxin-type_fold.
IPR024935. Rubredoxin_dom.
IPR018527. Rubredoxin_Fe_BS.
[Graphical view]
PfamiPF00301. Rubredoxin. 1 hit.
[Graphical view]
PIRSFiPIRSF000071. Rubredoxin. 1 hit.
PRINTSiPR00163. RUBREDOXIN.
PROSITEiPS00202. RUBREDOXIN. 1 hit.
PS50903. RUBREDOXIN_LIKE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRUBR_DESVM
AccessioniPrimary (citable) accession number: P15412
Secondary accession number(s): B8DMY0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: April 1, 1990
Last modified: September 7, 2016
This is version 106 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, Direct protein sequencing, 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.