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(-) Description

Title :  CRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE IN THE OXIDIZED STATE AT 2.0 ANGSTROM RESOLUTION
 
Authors :  A. P. Yeh, Y. Hu, F. E. Jenney Junior, M. W. Adams, D. C. Rees
Date :  19 Dec 99  (Deposition) - 24 Mar 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Non-Heme Iron Protein, Immunoglobulin-Like (Ig) Beta Barrel Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Yeh, Y. Hu, F. E. Jenney Jr. , M. W. Adams, D. C. Rees
Structures Of The Superoxide Reductase From Pyrococcus Furiosus In The Oxidized And Reduced States.
Biochemistry V. 39 2499 2000
PubMed-ID: 10704199  |  Reference-DOI: 10.1021/BI992428K
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUPEROXIDE REDUCTASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: SOR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:14 , HIS A:16 , HIS A:41 , HIS A:47 , CYS A:111 , HIS A:114BINDING SITE FOR RESIDUE FE A 200
2AC2SOFTWARELYS B:15 , HIS B:16 , HIS B:41 , HIS B:47 , CYS B:111 , HIS B:114BINDING SITE FOR RESIDUE FE B 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DO6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DO6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DO6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DO6)

(-) Exons   (0, 0)

(no "Exon" information available for 1DO6)

(-) Sequences/Alignments

Asymmetric 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:124
 aligned with SOR_PYRFU | P82385 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:124
                                    10        20        30        40        50        60        70        80        90       100       110       120    
            SOR_PYRFU     1 MISETIRSGDWKGEKHVPVIEYEREGELVKVKVQVGKEIPHPNTTEHHIRYIELYFLPEGENFVYQVGRVEFTAHGESVNGPNTSDVYTEPIAYFVLKTKKKGKLYALSYCNIHGLWENEVTLE 124
               SCOP domains d1do6a_ A: Superoxide reductase (SOR)                                                                                        SCOP domains
               CATH domains 1do6A00 A:1-124  [code=2.60.40.730, no name defined]                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.ee...........eeeeeee..eeeeeee..............eeeeeeeeee......eeeeeee....................eeeeeee....eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1do6 A   1 MISETIRSGDWKGEKHVPVIEYEREGELVKVKVQVGKEIPHPNTTEHHIRYIELYFLPEGENFVYQVGRVEFTAHGESVNGPNTSDVYTEPIAYFVLKTKKKGKLYALSYCNIHGLWENEVTLE 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    


Chain B from PDB  Type:PROTEIN  Length:124
 aligned with SOR_PYRFU | P82385 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:124
                                    10        20        30        40        50        60        70        80        90       100       110       120    
            SOR_PYRFU     1 MISETIRSGDWKGEKHVPVIEYEREGELVKVKVQVGKEIPHPNTTEHHIRYIELYFLPEGENFVYQVGRVEFTAHGESVNGPNTSDVYTEPIAYFVLKTKKKGKLYALSYCNIHGLWENEVTLE 124
               SCOP domains d1do6b_ B: Superoxide reductase (SOR)                                                                                        SCOP domains
               CATH domains 1do6B00 B:1-124  [code=2.60.40.730, no name defined]                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.ee...........eeeeeee..eeeeeee..............eeeeeeeeee......eeeeeee....................eeeeeee....eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1do6 B   1 MISETIRSGDWKGEKHVPVIEYEREGELVKVKVQVGKEIPHPNTTEHHIRYIELYFLPEGENFVYQVGRVEFTAHGESVNGPNTSDVYTEPIAYFVLKTKKKGKLYALSYCNIHGLWENEVTLE 124
                                    10        20        30        40        50        60        70        80        90       100       110       120
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DO6)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SOR_PYRFU | P82385)
molecular function
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0050605    superoxide reductase activity    Catalysis of the reaction: superoxide + reduced rubredoxin + 2 H+ = H2O2 + rubredoxin.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    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

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UniProtKB/Swiss-Prot
        SOR_PYRFU | P82385: 1dqi 1dqk

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