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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.
OrthoDBiEOG69SKK0.

Family and domain databases

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.
OrthoDBiEOG69SKK0.

Enzyme and pathway databases

BioCyciDVUL883:GCJ5-2550-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP15412.

Family and domain databases

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...

Publicationsi

« Hide 'large scale' publications
  1. "Amino acid sequence and function of rubredoxin from Desulfovibrio vulgaris Miyazaki."
    Shimuzu F., Ogata M., Yagi T., Wakabayashi S., Matsubara H.
    Biochimie 71:1171-1177(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE, FORMYLATION AT MET-1.
  2. "Cloning and expression of the rubredoxin gene from Desulfovibrio vulgaris (Miyazaki F) -- comparison of the primary structure of desulfoferrodoxin."
    Kitamura M., Koshino Y., Kamikawa Y., Kohno K., Kojima S., Miura K., Sagara T., Akutsu H., Kumagai I., Nakaya T.
    Biochim. Biophys. Acta 1351:239-247(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Complete sequence of Desulfovibrio vulgaris str. 'Miyazaki F'."
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Hazen T.C., Richardson P.
    Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Miyazaki F / DSM 19637.
  4. "Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms."
    Misaki S., Morimoto Y., Ogata M., Yagi T., Higuchi Y., Yasuoka N.
    Acta Crystallogr. D 55:408-413(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
    Strain: IAM 12604.

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: November 11, 2015
This is version 105 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.