Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  X-RAY STRUCTURE OF E114A MUTANT OF SUPEROXIDE REDUCTASE FROM DESULFOARCULUS BAARSII IN THE NATIVE, REDUCED FORM
 
Authors :  G. Katona, P. Carpentier, V. Niviere, P. Amara, V. Adam, J. Ohana, N. Tsanov, D. Bourgeois
Date :  24 Feb 07  (Deposition) - 01 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Oxidoreductase, Raman Spectroscopy, Superoxide Reductase, Intermediate Trapping, Microspectrophotometry, Detoxification, Electron Transport, Iron, Transport, Redox States, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Katona, P. Carpentier, V. Niviere, P. Amara, V. Adam, J. Ohana, N. Tsanov, D. Bourgeois
Raman-Assisted Crystallography Reveals End-On Peroxide Intermediates In A Nonheme Iron Enzyme
Science V. 316 449 2007
PubMed-ID: 17446401  |  Reference-DOI: 10.1126/SCIENCE.1138885

(-) Compounds

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

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
3FE4Ligand/IonFE (III) ION
2FE24Ligand/IonFE (II) ION
4NO34Ligand/IonNITRATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
3FE-1Ligand/IonFE (III) ION
2FE22Ligand/IonFE (II) ION
4NO32Ligand/IonNITRATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
3FE-1Ligand/IonFE (III) ION
2FE22Ligand/IonFE (II) ION
4NO32Ligand/IonNITRATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:10 , CYS A:13 , CYS A:29 , CYS A:30BINDING SITE FOR RESIDUE FE A1000
02AC2SOFTWARELYS A:48 , HIS A:49 , HIS A:69 , PRO A:70 , HIS A:75 , HIS A:119 , FE2 A:2000 , HOH A:2147BINDING SITE FOR RESIDUE NO3 A1127
03AC3SOFTWAREHIS A:49 , HIS A:69 , HIS A:75 , CYS A:116 , HIS A:119 , NO3 A:1127BINDING SITE FOR RESIDUE FE2 A2000
04AC4SOFTWARECYS B:10 , CYS B:13 , CYS B:29 , CYS B:30BINDING SITE FOR RESIDUE FE B1001
05AC5SOFTWARELYS B:48 , HIS B:49 , HIS B:69 , HIS B:75 , HIS B:119 , FE2 B:1129 , HOH B:2173 , HOH B:2174BINDING SITE FOR RESIDUE NO3 B1127
06AC6SOFTWAREGLU A:18 , HOH A:2026 , GLU B:18 , HOH B:2138 , HOH B:2141BINDING SITE FOR RESIDUE CA B1128
07AC7SOFTWAREHIS B:49 , HIS B:69 , HIS B:75 , CYS B:116 , HIS B:119 , NO3 B:1127BINDING SITE FOR RESIDUE FE2 B1129
08AC8SOFTWARECYS C:10 , CYS C:13 , CYS C:29 , CYS C:30BINDING SITE FOR RESIDUE FE C1002
09AC9SOFTWARELYS C:48 , HIS C:49 , HIS C:69 , PRO C:70 , HIS C:75 , HIS C:119 , FE2 C:1131 , HOH C:2127BINDING SITE FOR RESIDUE NO3 C1127
10BC1SOFTWAREGLU C:18 , HOH C:2029 , HOH C:2104 , HOH C:2107 , HOH D:2030 , HOH D:2097BINDING SITE FOR RESIDUE CA C1128
11BC2SOFTWAREASP A:33 , HOH A:2036 , GLU C:26 , ASP C:33 , HOH C:2055 , HOH C:2056BINDING SITE FOR RESIDUE CA C1129
12BC3SOFTWAREASP A:33 , HOH A:2050 , GLU C:26 , HOH C:2037 , HOH C:2038 , HOH C:2041BINDING SITE FOR RESIDUE CA C1130
13BC4SOFTWAREHIS C:49 , HIS C:69 , HIS C:75 , CYS C:116 , HIS C:119 , NO3 C:1127BINDING SITE FOR RESIDUE FE2 C1131
14BC5SOFTWARECYS D:10 , CYS D:13 , CYS D:29 , CYS D:30BINDING SITE FOR RESIDUE FE D1003
15BC6SOFTWARELYS D:48 , HIS D:49 , HIS D:69 , PRO D:70 , HIS D:75 , HIS D:119 , FE2 D:1128 , HOH D:2120BINDING SITE FOR RESIDUE NO3 D1127
16BC7SOFTWAREHIS D:49 , HIS D:69 , HIS D:75 , CYS D:116 , HIS D:119 , NO3 D:1127BINDING SITE FOR RESIDUE FE2 D1128

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JI2)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Val A:64 -Gly A:65
2Val B:64 -Gly B:65
3Val C:64 -Gly C:65
4Val D:64 -Gly D:65

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JI2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JI2)

(-) Exons   (0, 0)

(no "Exon" information available for 2JI2)

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

    Alignment length:126
                                    10        20        30        40        50        60        70        80        90       100       110       120      
            DFX_DESB2     1 MPERLQVYKCEVCGNIVEVLNGGIGELVCCNQDMKLMSENTVDAAKEKHVPVIEKIDGGYKVKVGAVAHPMEEKHYIQWIELLADDKCYTQFLKPGQAPEAVFLIEAAKVVAREYCNIHGHWKAEN 126
               SCOP domains d2ji2a2 A:1-37 automated matches     d2ji2a1 A:38-126 automated matches                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee......eeeeee......ee..ee.ee........hhhhhheeeeee..eeeeee............eeeeeeee..eeeeee.......eeeee......eeeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ji2 A   1 MPERLQVYKCEVCGNIVEVLNGGIGELVCCNQDMKLMSENTVDAAKEKHVPVIEKIDGGYKVKVGAVAHPMEEKHYIQWIELLADDKCYTQFLKPGQAPEAVFLIEAAKVVARAYCNIHGHWKAEN 126
                                    10        20        30        40        50        60        70        80        90       100       110       120      


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 d2ji2b2 B:2-37 automated matches    d2ji2b1 B:38-126 automated matches                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee......eeeeee......ee..ee.ee........hhhhhheeeeee..eeeeee............eeeeeeee..eeeeee.......eeeee......eeeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ji2 B   2 PERLQVYKCEVCGNIVEVLNGGIGELVCCNQDMKLMSENTVDAAKEKHVPVIEKIDGGYKVKVGAVAHPMEEKHYIQWIELLADDKCYTQFLKPGQAPEAVFLIEAAKVVARAYCNIHGHWKAEN 126
                                    11        21        31        41        51        61        71        81        91       101       111       121     


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

    Alignment length:126
                                    10        20        30        40        50        60        70        80        90       100       110       120      
            DFX_DESB2     1 MPERLQVYKCEVCGNIVEVLNGGIGELVCCNQDMKLMSENTVDAAKEKHVPVIEKIDGGYKVKVGAVAHPMEEKHYIQWIELLADDKCYTQFLKPGQAPEAVFLIEAAKVVAREYCNIHGHWKAEN 126
               SCOP domains d2ji2c2 C:1-37 automated matches     d2ji2c1 C:38-126 automated matches                                                        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
                 2ji2 C   1 MPERLQVYKCEVCGNIVEVLNGGIGELVCCNQDMKLMSENTVDAAKEKHVPVIEKIDGGYKVKVGAVAHPMEEKHYIQWIELLADDKCYTQFLKPGQAPEAVFLIEAAKVVARAYCNIHGHWKAEN 126
                                    10        20        30        40        50        60        70        80        90       100       110       120      


Chain D 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 d2ji2d2 D:2-37 automated matches    d2ji2d1 D:38-126 automated matches                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Desulfoferrod_N-2ji2D01 D:2-37      ---Desulfoferrodox-2ji2D05 D:41-125                                                     - Pfam domains (1)
           Pfam domains (2) Desulfoferrod_N-2ji2D02 D:2-37      ---Desulfoferrodox-2ji2D06 D:41-125                                                     - Pfam domains (2)
           Pfam domains (3) Desulfoferrod_N-2ji2D03 D:2-37      ---Desulfoferrodox-2ji2D07 D:41-125                                                     - Pfam domains (3)
           Pfam domains (4) Desulfoferrod_N-2ji2D04 D:2-37      ---Desulfoferrodox-2ji2D08 D:41-125                                                     - Pfam domains (4)
         Sec.struct. author .....eee......eeeeee......ee..ee.ee........hhhhhheeeeee..eeeeee............eeeeeeee..eeeeee.......eeeee......eeeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ji2 D   2 PERLQVYKCEVCGNIVEVLNGGIGELVCCNQDMKLMSENTVDAAKEKHVPVIEKIDGGYKVKVGAVAHPMEEKHYIQWIELLADDKCYTQFLKPGQAPEAVFLIEAAKVVARAYCNIHGHWKAEN 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, 8)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JI2)

(-) Pfam Domains  (2, 8)

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

(-) Gene Ontology  (7, 7)

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

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NO3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val A:64 - Gly A:65   [ RasMol ]  
    Val B:64 - Gly B:65   [ RasMol ]  
    Val C:64 - Gly C:65   [ RasMol ]  
    Val D:64 - Gly D:65   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2ji2
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DFX_DESB2 | Q46495
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.15.1.2
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DFX_DESB2 | Q46495
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DFX_DESB2 | Q46495: 1vzg 1vzh 1vzi 2ji1 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
1vzh 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
2ji1 X-RAY STRUCTURE OF WILD-TYPE SUPEROXIDE REDUCTASE FROM DESULFOARCULUS BAARSII
2ji3 X-RAY STRUCTURE OF THE IRON-PEROXIDE INTERMEDIATE OF SUPEROXIDE REDUCTASE (E114A MUTANT) FROM DESULFOARCULUS BAARSII