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(-) Description

Title :  CRYSTAL STRUCTURE OF THE [FE3S4]-FERREDOXIN FROM THE HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS FURIOSUS
 
Authors :  M. S. Nielsen, P. Harris, H. E. M. Christensen
Date :  02 Mar 04  (Deposition) - 25 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Thermostability, Iron-Sulfur Clusters, Dimer, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Nielsen, P. Harris, B. L. Ooi, H. E. M. Christensen
The 1. 5 A Resolution Crystal Structure Of [Fe3S4]-Ferredoxin From The Hyperthermophilic Archaeon Pyrococcus Furiosus
Biochemistry V. 43 5188 2004
PubMed-ID: 15122884  |  Reference-DOI: 10.1021/BI049942X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FERREDOXIN
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FDXA, PF1909
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
13CO4Ligand/IonCOBALT (III) ION
2F3S2Ligand/IonFE3-S4 CLUSTER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:104 , ILE C:12BINDING SITE FOR RESIDUE 3CO A 74
2AC2SOFTWAREILE A:12 , HOH C:87BINDING SITE FOR RESIDUE 3CO C 75
3AC3SOFTWARECYS A:11 , ILE A:12 , ASP A:14 , ALA A:15 , ILE A:16 , CYS A:17 , ALA A:33 , CYS A:56BINDING SITE FOR RESIDUE F3S A 70
4AC4SOFTWARECYS C:11 , ILE C:12 , ASP C:14 , ALA C:15 , ILE C:16 , CYS C:17 , ALA C:33 , CYS C:56BINDING SITE FOR RESIDUE F3S C 71

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:21 -A:48
2C:21 -C:48

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SIZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SIZ)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
14FE4S_FER_2PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.FER_PYRFU3-31
 
36-67
 		  4A:2-30
C:2-30
A:35-66
C:35-66

(-) Exons   (0, 0)

(no "Exon" information available for 1SIZ)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:66
 aligned with FER_PYRFU | P29603 from UniProtKB/Swiss-Prot  Length:67

    Alignment length:66
                                    11        21        31        41        51        61      
             FER_PYRFU    2 AWKVSVDQDTCIGDAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA 67
               SCOP domains d1siza_ A: Fe3S4-ferredoxin PF1909                                 SCOP domains
               CATH domains 1sizA00 A:1-66  [code=3.30.70.20, no name defined]                 CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee........hhhhhhh...eee.....eee......hhhhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -4FE4S_FER_2  PDB: A:2-30     ----4FE4S_FER_2  PDB: A:35-66        PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  1siz A  1 AWKVSVDQDTCIGDAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA 66
                                    10        20        30        40        50        60      


Chain C from PDB  Type:PROTEIN  Length:66
 aligned with FER_PYRFU | P29603 from UniProtKB/Swiss-Prot  Length:67

    Alignment length:66
                                    11        21        31        41        51        61      
             FER_PYRFU    2 AWKVSVDQDTCIGDAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA 67
               SCOP domains d1sizc_ C: Fe3S4-ferredoxin PF1909                                 SCOP domains
               CATH domains 1sizC00 C:1-66  [code=3.30.70.20, no name defined]                 CATH domains
           Pfam domains (1) -----Fer4_13-1sizC01 C:6-63                                    --- Pfam domains (1)
           Pfam domains (2) -----Fer4_13-1sizC02 C:6-63                                    --- Pfam domains (2)
         Sec.struct. author .eeeee........hhhhhhh...eee.....eee......hhhhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -4FE4S_FER_2  PDB: C:2-30     ----4FE4S_FER_2  PDB: C:35-66        PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  1siz C  1 AWKVSVDQDTCIGDAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA 66
                                    10        20        30        40        50        60
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: 4Fe-4S (51)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (FER_PYRFU | P29603)
molecular function
    GO:0051538    3 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        FER_PYRFU | P29603: 1sj1 2z8q 3pni 4dhv

(-) Related Entries Specified in the PDB File

1sj1 THE 1.5 A RESOLUTION CRYSTAL STRUCTURE OF [FE3S4]- FERREDOXIN FROM THE HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS FURIOSUS