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P29603

- FER_PYRFU

UniProt

P29603 - FER_PYRFU

Protein

Ferredoxin

Gene

fdxA

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
  1. Functioni

    Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.

    Cofactori

    Binds 1 4Fe-4S cluster which readily converts to a stable 3Fe-4S form.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi12 – 121Iron-sulfur (4Fe-4S)
    Metal bindingi15 – 151Iron-sulfur (4Fe-4S)
    Metal bindingi18 – 181Iron-sulfur (4Fe-4S)
    Metal bindingi57 – 571Iron-sulfur (4Fe-4S)

    GO - Molecular functioni

    1. 3 iron, 4 sulfur cluster binding Source: UniProtKB-KW
    2. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
    3. electron carrier activity Source: InterPro
    4. iron ion binding Source: InterPro

    GO - Biological processi

    1. oxidation-reduction process Source: UniProtKB-KW

    Keywords - Biological processi

    Electron transport, Transport

    Keywords - Ligandi

    3Fe-4S, 4Fe-4S, Iron, Iron-sulfur, Metal-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ferredoxin
    Gene namesi
    Name:fdxA
    Ordered Locus Names:PF1909
    OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
    Taxonomic identifieri186497 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
    ProteomesiUP000001013: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi15 – 151D → C: No effect on the efficiency of electron transfer. 4 Publications
    Mutagenesisi15 – 151D → S: The efficiency of electron transfer is compromised. 4 Publications
    Mutagenesisi34 – 341A → C: The mixed spin cluster is converted into a homogeneous spin cluster (S=3/2). 3 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed
    Chaini2 – 6766FerredoxinPRO_0000159199Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi22 ↔ 492 Publications

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    PRIDEiP29603.

    Interactioni

    Subunit structurei

    Homodimer.Curated

    Protein-protein interaction databases

    STRINGi186497.PF1909.

    Structurei

    Secondary structure

    1
    67
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 75
    Turni9 – 113
    Helixi17 – 215
    Turni23 – 253
    Beta strandi26 – 283
    Beta strandi34 – 374
    Helixi44 – 5613
    Beta strandi62 – 665

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1SIZX-ray2.25A/C2-67[»]
    1SJ1X-ray1.50A/B2-67[»]
    2Z8QX-ray1.70A/B2-67[»]
    3PNIX-ray2.80A/B2-67[»]
    4DHVX-ray1.95A/B2-67[»]
    ProteinModelPortaliP29603.
    SMRiP29603. Positions 2-67.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP29603.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini3 – 31294Fe-4S ferredoxin-type 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini36 – 67324Fe-4S ferredoxin-type 2PROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 2 4Fe-4S ferredoxin-type domains.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiCOG1141.
    HOGENOMiHOG000044619.
    KOiK05337.
    OMAiANIYRSC.

    Family and domain databases

    InterProiIPR001080. 3Fe4S_ferredoxin.
    IPR017896. 4Fe4S_Fe-S-bd.
    [Graphical view]
    PRINTSiPR00352. 3FE4SFRDOXIN.
    PROSITEiPS51379. 4FE4S_FER_2. 2 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P29603-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAWKVSVDQD TCIGDAICAS LCPDVFEMND EGKAQPKVEV IEDEELYNCA   50
    KEAMEACPVS AITIEEA 67
    Length:67
    Mass (Da):7,298
    Last modified:January 23, 2007 - v2
    Checksum:iAF9B062690B34420
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X79502 Genomic DNA. Translation: CAA56040.1.
    AE009950 Genomic DNA. Translation: AAL82033.1.
    PIRiA44203.
    RefSeqiNP_579638.1. NC_003413.1.
    WP_011013049.1. NC_003413.1.

    Genome annotation databases

    EnsemblBacteriaiAAL82033; AAL82033; PF1909.
    GeneIDi1469789.
    KEGGipfu:PF1909.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X79502 Genomic DNA. Translation: CAA56040.1 .
    AE009950 Genomic DNA. Translation: AAL82033.1 .
    PIRi A44203.
    RefSeqi NP_579638.1. NC_003413.1.
    WP_011013049.1. NC_003413.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1SIZ X-ray 2.25 A/C 2-67 [» ]
    1SJ1 X-ray 1.50 A/B 2-67 [» ]
    2Z8Q X-ray 1.70 A/B 2-67 [» ]
    3PNI X-ray 2.80 A/B 2-67 [» ]
    4DHV X-ray 1.95 A/B 2-67 [» ]
    ProteinModelPortali P29603.
    SMRi P29603. Positions 2-67.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 186497.PF1909.

    Proteomic databases

    PRIDEi P29603.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL82033 ; AAL82033 ; PF1909 .
    GeneIDi 1469789.
    KEGGi pfu:PF1909.

    Phylogenomic databases

    eggNOGi COG1141.
    HOGENOMi HOG000044619.
    KOi K05337.
    OMAi ANIYRSC.

    Miscellaneous databases

    EvolutionaryTracei P29603.

    Family and domain databases

    InterProi IPR001080. 3Fe4S_ferredoxin.
    IPR017896. 4Fe4S_Fe-S-bd.
    [Graphical view ]
    PRINTSi PR00352. 3FE4SFRDOXIN.
    PROSITEi PS51379. 4FE4S_FER_2. 2 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Cloning, expression, and molecular characterization of the gene encoding an extremely thermostable [4Fe-4S] ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus."
      Heltzel A., Smith E.T., Zhou Z.H., Blamey J.M., Adams M.W.W.
      J. Bacteriol. 176:4790-4793(1994) [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. "Site-directed mutations of the 4Fe-ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus: role of the cluster-coordinating aspartate in physiological electron transfer reactions."
      Zhou Z.H., Adams M.W.W.
      Biochemistry 36:10892-10900(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF ASP-15, CIRCULAR DICHROISM ANALYSIS, EPR SPECTROSCOPY.
    4. "Spectroscopic evidence for a new type of [Fe3S4] cluster in a mutant form of Pyrococcus furiosus ferredoxin."
      Duderstadt R.E., Brereton P.S., Adams M.W.W., Johnson M.K.
      J. Am. Chem. Soc. 120:8525-8526(1998)
      Cited for: MUTAGENESIS OF ALA-34, MAGNETIC CIRCULAR DICHROISM, EPR SPECTROSCOPY, RESONANCE RAMAN SPECTROSCOPY OF (3FE--4S) FORM.
    5. "Effect of serinate ligation at each of the iron sites of the [Fe4S4] cluster of Pyrococcus furiosus ferredoxin on the redox, spectroscopic, and biological properties."
      Brereton P.S., Duderstadt R.E., Staples C.R., Johnson M.K., Adams M.W.W.
      Biochemistry 38:10594-10605(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF CYSTEINE RESIDUES, MAGNETIC CIRCULAR DICHROISM, EPR SPECTROSCOPY, RESONANCE RAMAN SPECTROSCOPY.
    6. "A pure S=3/2 [Fe4S4]+ cluster in the A33Y variant of Pyrococcus furiosus ferredoxin."
      Duderstadt R.E., Brereton P.S., Adams M.W.W., Johnson M.K.
      FEBS Lett. 454:21-26(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF ALA-34, MAGNETIC CIRCULAR DICHROISM, EPR SPECTROSCOPY, RESONANCE RAMAN SPECTROSCOPY.
    7. "Proton NMR investigation of the oxidized three-iron clusters in the ferredoxins from the hyperthermophilic archae Pyrococcus furiosus and Thermococcus litoralis."
      Busse S.C., la Mar G.N., Yu L.P., Howard J.B., Smith E.T., Zhou Z.H., Adams M.W.W.
      Biochemistry 31:11952-11962(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR.
    8. "Solution 1H NMR determination of secondary structure for the three-iron form of ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus."
      Teng Q., Zhou Z.H., Smith E.T., Busse S.C., Howard J.B., Adams M.W.W., La Mar G.N.
      Biochemistry 33:6316-6326(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 3FE--4S FORM.
    9. "1H NMR investigation of the electronic and molecular structure of the four-iron cluster ferredoxin from the hyperthermophile Pyrococcus furiosus. Identification of Asp 14 as a cluster ligand in each of the four redox states."
      Calzolai L., Gorst C.M., Zhou Z.H., Teng Q., Adams M.W.W., La Mar G.N.
      Biochemistry 34:11373-11384(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR.
    10. "1H NMR investigation of the paramagnetic cluster environment in Pyrococcus furiosus three-iron ferredoxin: sequence-specific assignment of ligated cysteines independent of tertiary structure."
      Gorst C.M., Yeh Y.-H., Teng Q., Calzolai L., Zhou Z.H., Adams M.W.W., La Mar G.N.
      Biochemistry 34:600-610(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 3FE--4S FORM.
    11. "Participation of the disulfide bridge in the redox cycle of the ferredoxin from the hyperthermophile Pyrococcus furiosus: 1H nuclear magnetic resonance time resolution of the four redox states at ambient temperature."
      Gorst C.M., Zhou Z.H., Teng Q., Howard J.B., Adams M.W.W., La Mar G.N.
      Biochemistry 34:8788-8795(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR, DISULFIDE BOND.
    12. "Role of cluster-ligated aspartate in gating electron transfer in the four-iron ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus."
      Calzolai L., Zhou Z.H., Adams M.W.W., La Mar G.N.
      J. Am. Chem. Soc. 118:2513-2514(1996)
      Cited for: STRUCTURE BY NMR, MUTAGENESIS OF ASP-15.
    13. "Solution NMR study of the electronic structure and magnetic properties of cluster ligation mutants of the four-iron ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus."
      Calzolai L., Gorst C.M., Bren K.L., Zhou Z.H., Adams M.W.W., La Mar G.N.
      J. Am. Chem. Soc. 119:9341-9350(1997)
      Cited for: STRUCTURE BY NMR, MUTAGENESIS OF ASP-15.
    14. "Solution NMR characterization of the thermodynamics of the disulfide bond orientational isomerism and its effect of cluster electronic properties for the hyperthermostable three-iron cluster ferredoxin from the archaeon Pyrococcus furiosus."
      Webba da Silva M., Sham S., Gorst C.M., Calzolai L., Brereton P.S., Adams M.W.W., La Mar G.N.
      Biochemistry 40:12575-12583(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 3FE--4S FORM.
    15. "The 1.5 A resolution crystal structure of [Fe3S4]-ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus."
      Nielsen M.S., Harris P., Ooi B.L., Christensen H.E.
      Biochemistry 43:5188-5194(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR CLUSTER, SUBUNIT.

    Entry informationi

    Entry nameiFER_PYRFU
    AccessioniPrimary (citable) accession number: P29603
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1993
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 111 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, 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