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(-) Description

Title :  CRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE IN THE REDUCED STATE AT 2.0 ANGSTROMS RESOLUTION
 
Authors :  A. P. Yeh, Y. Hu, F. E. Jenney Jr. , M. W. W. Adams, D. C. Rees
Date :  04 Jan 00  (Deposition) - 10 May 00  (Release) - 04 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Non-Heme Mononuclear 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, C, D
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: SOR

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1FE24Ligand/IonFE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:16 , HIS A:41 , HIS A:47 , CYS A:111 , HIS A:114BINDING SITE FOR RESIDUE FE2 A 401
2AC2SOFTWAREHIS B:16 , HIS B:41 , HIS B:47 , CYS B:111 , HIS B:114BINDING SITE FOR RESIDUE FE2 B 402
3AC3SOFTWAREHIS C:16 , HIS C:41 , HIS C:47 , CYS C:111 , HIS C:114BINDING SITE FOR RESIDUE FE2 C 403
4AC4SOFTWAREHIS D:16 , HIS D:41 , HIS D:47 , CYS D:111 , HIS D:114BINDING SITE FOR RESIDUE FE2 D 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DQK)

(-) 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: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 d1dqka_ A: Superoxide reductase (SOR)                                                                                        SCOP domains
               CATH domains 1dqkA00 A:1-124  [code=2.60.40.730, no name defined]                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.ee..........eeeeeeee..eeeeeeee.............eeeeeeeeee......eeeeeeee...............ee..eeeeeee....eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dqk 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 d1dqkb_ B: Superoxide reductase (SOR)                                                                                        SCOP domains
               CATH domains 1dqkB00 B:1-124  [code=2.60.40.730, no name defined]                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.ee..........eeeeeeee..eeeeeeee.............eeeeeeeeee......eeeeeeee...............ee..eeeeeee....eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dqk B   1 MISETIRSGDWKGEKHVPVIEYEREGELVKVKVQVGKEIPHPNTTEHHIRYIELYFLPEGENFVYQVGRVEFTAHGESVNGPNTSDVYTEPIAYFVLKTKKKGKLYALSYCNIHGLWENEVTLE 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    


Chain C 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 d1dqkc_ C: Superoxide reductase (SOR)                                                                                        SCOP domains
               CATH domains 1dqkC00 C:1-124  [code=2.60.40.730, no name defined]                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.ee..........eeeeeeee..eeeeeeee.............eeeeeeeeee......eeeeeeee...............ee..eeeeeee....eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dqk C   1 MISETIRSGDWKGEKHVPVIEYEREGELVKVKVQVGKEIPHPNTTEHHIRYIELYFLPEGENFVYQVGRVEFTAHGESVNGPNTSDVYTEPIAYFVLKTKKKGKLYALSYCNIHGLWENEVTLE 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    


Chain D 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 d1dqkd_ D: Superoxide reductase (SOR)                                                                                        SCOP domains
               CATH domains 1dqkD00 D:1-124  [code=2.60.40.730, no name defined]                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.ee..........eeeeeeee..eeeeeeee.............eeeeeeeeee......eeeeeeee...............ee..eeeeeee....eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dqk D   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, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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

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

UniProtKB/Swiss-Prot
        SOR_PYRFU | P82385: 1do6 1dqi

(-) Related Entries Specified in the PDB File

1do6 1DO6 CONTAINS THE STRUCTURE OF SUPEROXIDE REDUCTASE IN THE OXIDIZED STATE DETERMINED AT 2.0 ANGSTROMS RESOLUTION.
1dqi 1DQI CONTAINS THE STRUCTURE OF SUPEROXIDE REDUCTASE IN THE OXIDIZED STATE DETERMINED AT 1.7 ANGSTROMS RESOLUTION.