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(-) Description

Title :  STRUCTURE OF SUPEROXIDE REDUCTASE BOUND TO FERROCYANIDE AND ACTIVE SITE EXPANSION UPON X-RAY INDUCED PHOTOREDUCTION
 
Authors :  V. Adam, A. Royant, V. Niviere, F. P. Molina-Heredia, D. Bourgeois
Date :  19 May 04  (Deposition) - 27 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ferrocyanide, Microspectrophotometry, Redox States, Photoreduction, Dinuclear Iron Cluster, Oxidoreductase, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Adam, A. Royant, V. Niviere, F. P. Molina-Heredia, D. Bourgeois
Structure Of Superoxide Reductase Bound To Ferrocyanide And Active Site Expansion Upon X-Ray Induced Photoreduction
Structure V. 12 1729 2004
PubMed-ID: 15341736  |  Reference-DOI: 10.1016/J.STR.2004.07.013

(-) Compounds

Molecule 1 - DESULFOFERRODOXIN
    Chains: A, B
    EC Number: 1.15.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: DH5 ALPHA
    Expression System Taxid: 562
    Expression System Vector: PMLE47A
    Mutation: YES
    Organism Common: DESULFOARCULUS BAARSII
    Organism Scientific: DESULFOVIBRIO BAARSII
    Organism Taxid: 887
    Synonym: SUPEROXIDE REDUCTASE, DFX, SOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2FC62Ligand/IonHEXACYANOFERRATE(3-)
3FE4Ligand/IonFE (III) ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:10 , CYS A:13 , ASN A:15 , CYS A:29 , CYS A:30 , GLY B:25BINDING SITE FOR RESIDUE FE A1127
2AC2SOFTWARECYS A:88 , THR A:90 , HOH A:2019 , CYS B:88 , THR B:90 , HOH B:2013BINDING SITE FOR RESIDUE CA A1128
3AC3SOFTWAREHIS A:49 , HIS A:69 , HIS A:75 , CYS A:116 , HIS A:119 , FC6 A:1130BINDING SITE FOR RESIDUE FE A1129
4AC4SOFTWAREGLY A:25 , CYS B:10 , CYS B:13 , CYS B:29 , CYS B:30BINDING SITE FOR RESIDUE FE B1127
5AC5SOFTWAREHIS B:49 , HIS B:69 , HIS B:75 , CYS B:116 , HIS B:119 , FC6 B:1129BINDING SITE FOR RESIDUE FE B1128
6AC6SOFTWAREALA A:45 , LYS A:48 , HIS A:49 , HIS A:69 , HIS A:75 , HIS A:119 , FE A:1129 , HOH A:2083BINDING SITE FOR RESIDUE FC6 A1130
7AC7SOFTWAREALA B:45 , LYS B:48 , HIS B:49 , HIS B:69 , HIS B:75 , HIS B:119 , FE B:1128 , HOH B:2078BINDING SITE FOR RESIDUE FC6 B1129

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:10 -A:29
2A:10 -A:29
3A:13 -A:30
4B:10 -B:29
5B:13 -B:30

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:64 -Gly A:65
2Val B:64 -Gly B:65

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VZH)

(-) 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:125
 aligned with DFX_DESB2 | Q46495 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:125
                                    11        21        31        41        51        61        71        81        91       101       111       121     
            DFX_DESB2     2 PERLQVYKCEVCGNIVEVLNGGIGELVCCNQDMKLMSENTVDAAKEKHVPVIEKIDGGYKVKVGAVAHPMEEKHYIQWIELLADDKCYTQFLKPGQAPEAVFLIEAAKVVAREYCNIHGHWKAEN 126
               SCOP domains d1vzha2 A:2-37                      d1vzha1 A:38-126 Desulfoferrodoxin C-terminal domain                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee......eeeeee.....eee..ee.ee........hhhhhheeeeee..eeeeee............eeeeeeee..eeeeee.......eeeee......eeeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vzh A   2 PERLQVYKCEVCGNIVEVLNGGIGELVCCNQDMKLMSENTVDAAKAKHVPVIEKIDGGYKVKVGAVAHPMEEKHYIQWIELLADDKCYTQFLKPGQAPEAVFLIEAAKVVAREYCNIHGHWKAEN 126
                                    11        21        31        41        51        61        71        81        91       101       111       121     


Chain B from PDB  Type:PROTEIN  Length:125
 aligned with DFX_DESB2 | Q46495 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:125
                                    11        21        31        41        51        61        71        81        91       101       111       121     
            DFX_DESB2     2 PERLQVYKCEVCGNIVEVLNGGIGELVCCNQDMKLMSENTVDAAKEKHVPVIEKIDGGYKVKVGAVAHPMEEKHYIQWIELLADDKCYTQFLKPGQAPEAVFLIEAAKVVAREYCNIHGHWKAEN 126
               SCOP domains d1vzhb2 B:2-37                      d1vzhb1 B:38-126 Desulfoferrodoxin C-terminal domain                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Desulfoferrod_N-1vzhB01 B:2-37      ---Desulfoferrodox-1vzhB03 B:41-125                                                     - Pfam domains (1)
           Pfam domains (2) Desulfoferrod_N-1vzhB02 B:2-37      ---Desulfoferrodox-1vzhB04 B:41-125                                                     - Pfam domains (2)
         Sec.struct. author .....eee......eeeeee......ee..ee.ee........hhhhhheeeeee..eeeeee............eeeeeee...eeeeee.......eeeee......eeeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vzh B   2 PERLQVYKCEVCGNIVEVLNGGIGELVCCNQDMKLMSENTVDAAKAKHVPVIEKIDGGYKVKVGAVAHPMEEKHYIQWIELLADDKCYTQFLKPGQAPEAVFLIEAAKVVAREYCNIHGHWKAEN 126
                                    11        21        31        41        51        61        71        81        91       101       111       121
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VZH)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Rubredoxin (46)
(-)
Clan: SOR (12)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DFX_DESB2 | Q46495)
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: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.
    GO:0019430    removal of superoxide radicals    Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.

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  DFX_DESB2 | Q46495
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  1.15.1.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        DFX_DESB2 | Q46495: 1vzg 1vzi 2ji1 2ji2 2ji3

(-) Related Entries Specified in the PDB File

1vzg STRUCTURE OF SUPEROXIDE REDUCTASE BOUND TO FERROCYANIDE AND ACTIVE SITE EXPANSION UPON X-RAY INDUCED PHOTOREDUCTION
1vzi STRUCTURE OF SUPEROXIDE REDUCTASE BOUND TO FERROCYANIDE AND ACTIVE SITE EXPANSION UPON X-RAY INDUCED PHOTOREDUCTION