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P24297

- RUBR_PYRFU

UniProt

P24297 - RUBR_PYRFU

Protein

Rubredoxin

Gene

rub

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
  1. 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

    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

    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 – 64
    Turni7 – 93
    Beta strandi12 – 143
    Turni15 – 173
    Helixi20 – 223
    Helixi30 – 323
    Turni40 – 423
    Helixi46 – 483
    Beta strandi49 – 524

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    OMAiLPEDWIC.

    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

    MAKWVCKICG YIYDEDAGDP DNGISPGTKF EELPDDWVCP ICGAPKSEFE   50
    KLED 54
    Length:54
    Mass (Da):6,027
    Last modified:January 23, 2007 - v2
    Checksum:i7181BBB4A3E8B1A8
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF156097 Genomic DNA. Translation: AAF03228.1 .
    AE009950 Genomic DNA. Translation: AAL81406.1 .
    PIRi T44570. RUPF.
    RefSeqi NP_579011.1. NC_003413.1.
    WP_011012426.1. NC_003413.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1BQ8 X-ray 1.10 A 1-54 [» ]
    1BQ9 X-ray 1.20 A 1-54 [» ]
    1BRF X-ray 0.95 A 2-54 [» ]
    1CAA X-ray 1.80 A 2-54 [» ]
    1CAD X-ray 1.80 A 2-54 [» ]
    1IU5 X-ray 1.50 A 2-54 [» ]
    1IU6 neutron diffraction 1.60 A 2-54 [» ]
    1QCV NMR - A 2-54 [» ]
    1RWD NMR - A 2-54 [» ]
    1VCX neutron diffraction 1.50 A 2-54 [» ]
    1ZRP NMR - A 2-54 [» ]
    2PVX X-ray 1.04 A/B/C/D/E/F/G/H 1-54 [» ]
    3KYU X-ray 1.10 A 1-54 [» ]
    3KYV X-ray 1.10 A 1-54 [» ]
    3KYW X-ray 1.10 A 1-54 [» ]
    3KYX Other 1.68 A 1-54 [» ]
    3KYY X-ray 1.10 A 1-54 [» ]
    3RYG neutron diffraction 1.75 A 1-54 [» ]
    3RZ6 neutron diffraction 1.75 A 1-54 [» ]
    3RZT neutron diffraction 1.75 A 1-54 [» ]
    3SS2 neutron diffraction 1.75 A 1-54 [» ]
    4AR3 neutron diffraction 1.05 A 1-54 [» ]
    4AR4 neutron diffraction 1.38 A 1-54 [» ]
    4AR5 X-ray 1.00 A 1-54 [» ]
    4AR6 X-ray 0.92 A 1-54 [» ]
    4K9F neutron diffraction 1.75 A 1-54 [» ]
    ProteinModelPortali P24297.
    SMRi P24297. Positions 1-54.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 186497.PF1282.

    Proteomic databases

    PRIDEi P24297.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL81406 ; AAL81406 ; PF1282 .
    GeneIDi 1469155.
    KEGGi pfu:PF1282.

    Phylogenomic databases

    eggNOGi COG1773.
    HOGENOMi HOG000223371.
    OMAi LPEDWIC.

    Miscellaneous databases

    EvolutionaryTracei P24297.

    Family and domain databases

    Gene3Di 2.20.28.10. 1 hit.
    InterProi IPR024922. Rubredoxin.
    IPR024934. Rubredoxin-like_dom.
    IPR004039. Rubredoxin-type_fold.
    IPR024935. Rubredoxin_dom.
    IPR018527. Rubredoxin_Fe_BS.
    [Graphical view ]
    Pfami PF00301. Rubredoxin. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000071. Rubredoxin. 1 hit.
    PRINTSi PR00163. RUBREDOXIN.
    PROSITEi PS00202. RUBREDOXIN. 1 hit.
    PS50903. RUBREDOXIN_LIKE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 110 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