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Protein

Rubredoxin

Gene

rub

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed-Annotation score: Annotation score: 3 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.

Cofactori

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

Temperature dependencei

Extremely thermostable, being unaffected after incubation for 24 hours at 95 degrees Celsius.

Sites

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

GO - Molecular functioni

  1. electron carrier activity Source: InterPro
  2. iron ion binding Source: InterPro

GO - Biological processi

  1. oxidation-reduction process Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Electron transport, Transport

Keywords - Ligandi

Iron, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Rubredoxin
Short name:
Rd
Gene namesi
Name:rub
Ordered Locus Names:PF1282
OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Taxonomic identifieri186497 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
ProteomesiUP000001013: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 5453RubredoxinPRO_0000135063Add
BLAST

Proteomic databases

PRIDEiP24297.

Interactioni

Protein-protein interaction databases

STRINGi186497.PF1282.

Structurei

Secondary structure

1
54
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 64Combined sources
Turni7 – 93Combined sources
Beta strandi12 – 143Combined sources
Turni15 – 173Combined sources
Helixi20 – 223Combined sources
Helixi30 – 323Combined sources
Turni40 – 423Combined sources
Helixi46 – 483Combined sources
Beta strandi49 – 524Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BQ8X-ray1.10A1-54[»]
1BQ9X-ray1.20A1-54[»]
1BRFX-ray0.95A2-54[»]
1CAAX-ray1.80A2-54[»]
1CADX-ray1.80A2-54[»]
1IU5X-ray1.50A2-54[»]
1IU6neutron diffraction1.60A2-54[»]
1QCVNMR-A2-54[»]
1RWDNMR-A2-54[»]
1VCXneutron diffraction1.50A2-54[»]
1ZRPNMR-A2-54[»]
2PVXX-ray1.04A/B/C/D/E/F/G/H1-54[»]
3KYUX-ray1.10A1-54[»]
3KYVX-ray1.10A1-54[»]
3KYWX-ray1.10A1-54[»]
3KYXOther1.68A1-54[»]
3KYYX-ray1.10A1-54[»]
3RYGneutron diffraction1.75A1-54[»]
3RZ6neutron diffraction1.75A1-54[»]
3RZTneutron diffraction1.75A1-54[»]
3SS2neutron diffraction1.75A1-54[»]
4AR3neutron diffraction1.05A1-54[»]
4AR4neutron diffraction1.38A1-54[»]
4AR5X-ray1.00A1-54[»]
4AR6X-ray0.92A1-54[»]
4K9Fneutron diffraction1.75A1-54[»]
ProteinModelPortaliP24297.
SMRiP24297. Positions 1-54.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP24297.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini2 – 5251Rubredoxin-likePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1773.
HOGENOMiHOG000223371.
OMAiSKDMFEP.

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.

Sequence processingi: The displayed sequence is further processed into a mature form.

P24297-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKWVCKICG YIYDEDAGDP DNGISPGTKF EELPDDWVCP ICGAPKSEFE

KLED
Length:54
Mass (Da):6,027
Last modified:January 23, 2007 - v2
Checksum:i7181BBB4A3E8B1A8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF156097 Genomic DNA. Translation: AAF03228.1.
AE009950 Genomic DNA. Translation: AAL81406.1.
PIRiT44570. RUPF.
RefSeqiNP_579011.1. NC_003413.1.
WP_011012426.1. NC_003413.1.

Genome annotation databases

EnsemblBacteriaiAAL81406; AAL81406; PF1282.
GeneIDi1469155.
KEGGipfu:PF1282.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF156097 Genomic DNA. Translation: AAF03228.1.
AE009950 Genomic DNA. Translation: AAL81406.1.
PIRiT44570. RUPF.
RefSeqiNP_579011.1. NC_003413.1.
WP_011012426.1. NC_003413.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BQ8X-ray1.10A1-54[»]
1BQ9X-ray1.20A1-54[»]
1BRFX-ray0.95A2-54[»]
1CAAX-ray1.80A2-54[»]
1CADX-ray1.80A2-54[»]
1IU5X-ray1.50A2-54[»]
1IU6neutron diffraction1.60A2-54[»]
1QCVNMR-A2-54[»]
1RWDNMR-A2-54[»]
1VCXneutron diffraction1.50A2-54[»]
1ZRPNMR-A2-54[»]
2PVXX-ray1.04A/B/C/D/E/F/G/H1-54[»]
3KYUX-ray1.10A1-54[»]
3KYVX-ray1.10A1-54[»]
3KYWX-ray1.10A1-54[»]
3KYXOther1.68A1-54[»]
3KYYX-ray1.10A1-54[»]
3RYGneutron diffraction1.75A1-54[»]
3RZ6neutron diffraction1.75A1-54[»]
3RZTneutron diffraction1.75A1-54[»]
3SS2neutron diffraction1.75A1-54[»]
4AR3neutron diffraction1.05A1-54[»]
4AR4neutron diffraction1.38A1-54[»]
4AR5X-ray1.00A1-54[»]
4AR6X-ray0.92A1-54[»]
4K9Fneutron diffraction1.75A1-54[»]
ProteinModelPortaliP24297.
SMRiP24297. Positions 1-54.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi186497.PF1282.

Proteomic databases

PRIDEiP24297.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL81406; AAL81406; PF1282.
GeneIDi1469155.
KEGGipfu:PF1282.

Phylogenomic databases

eggNOGiCOG1773.
HOGENOMiHOG000223371.
OMAiSKDMFEP.

Miscellaneous databases

EvolutionaryTraceiP24297.

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. "Anaerobic microbes: oxygen detoxification without superoxide dismutase."
    Jenney F.E. Jr., Verhagen M.F.J.M., Cui X., Adams M.W.W.
    Science 286:306-309(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
  2. "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences."
    Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T.
    Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
  3. "Determinants of protein hyperthermostability: purification and amino acid sequence of rubredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus and secondary structure of the zinc adduct by NMR."
    Blake P.R., Park J.-B., Bryant F.O., Aono S., Magnuson J.K., Eccleston E., Howard J.B., Summers M.F., Adams M.W.W.
    Biochemistry 30:10885-10895(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-54.
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
  4. "X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus."
    Day M.W., Hsu B.T., Joshua-Tor L., Park J.-B., Zhou Z.H., Adams M.W.W., Rees D.C.
    Protein Sci. 1:1494-1507(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
  5. "Solution-state structure by NMR of zinc-substituted rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus."
    Blake P.R., Park J.-B., Zhou Z.H., Hare D.R., Adams M.W.W., Summers M.F.
    Protein Sci. 1:1508-1521(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR.
  6. "Comparison of the X-ray structure of native rubredoxin from Pyrococcus furiosus with the NMR structure of the zinc-substituted protein."
    Blake P.R., Day M.W., Hsu B.T., Joshua-Tor L., Park J.-B., Hare D.R., Adams M.W.W., Rees D.C., Summers M.F.
    Protein Sci. 1:1522-1525(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: COMPARISON OF NMR STRUCTURE WITH X-RAY STRUCTURE.
  7. "Crystal structure of rubredoxin from Pyrococcus furiosus at 0.95-A resolution, and the structures of N-terminal methionine and formylmethionine variants of Pf Rd. Contributions of N-terminal interactions to thermostability."
    Bau R., Rees D.C., Kurtz D.M. Jr., Scott R.A., Huang H., Adams M.W.W., Eidsness M.K.
    J. Biol. Inorg. Chem. 3:484-493(1998)
    Cited for: X-RAY CRYSTALLOGRAPHY (1.1 ANGSTROMS).
  8. "Contribution of surface salt bridges to protein stability."
    Strop P., Mayo S.L.
    Biochemistry 39:1251-1255(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR.

Entry informationi

Entry nameiRUBR_PYRFU
AccessioniPrimary (citable) accession number: P24297
Secondary accession number(s): Q9UWP6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: January 23, 2007
Last modified: January 7, 2015
This is version 112 of the entry and version 2 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

External Data

Dasty 3

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 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.