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(-) Description

Title :  THE 1.6 A STRUCTURE OF FE-SUPEROXIDE DISMUTASE FROM THE THERMOPHILIC CYANOBACTERIUM THERMOSYNECHOCOCCUS ELONGATUS : CORRELATION OF EPR AND STRUCTURAL CHARACTERISTICS
 
Authors :  S. M. Yoshida, D. Cascio, M. R. Sawaya, T. O. Yeates, C. A. Kerfeld
Date :  03 Oct 02  (Deposition) - 29 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Iron Speroxide Dismutase, Thermophile, Reactive Oxygen Species, Cyanobacteria, Thermosynechococcus, Thermosynechococcus Elongatus, Superoxide Dismutase, Sod, Fesod, Iron(Iii) Superoxide Dismutase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. A. Kerfeld, S. Yoshida, K. T. Tran, T. O. Yeates, D. Cascio, H. Bottin, C. Berthomieu, M. Sugiura, A. Boussac
The 1. 6 A Resolution Structure Of Fe-Superoxide Dismutase From The Thermophilic Cyanobacterium Thermosynechococcus Elongatus.
J. Biol. Inorg. Chem. V. 8 707 2003
PubMed-ID: 12827458  |  Reference-DOI: 10.1007/S00775-003-0469-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IRON (III) SUPEROXIDE DISMUTASE
    Chains: A, B
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMOSYNECHOCOCCUS ELONGATUS
    Organism Taxid: 146786

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:27 , HIS A:79 , ASP A:161 , HIS A:165 , HOH A:3001BINDING SITE FOR RESIDUE FE A 200
2AC2SOFTWAREHIS B:27 , HIS B:79 , ASP B:161 , HIS B:165 , HOH B:3085BINDING SITE FOR RESIDUE FE B 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MY6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MY6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MY6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MY6)

(-) Exons   (0, 0)

(no "Exon" information available for 1MY6)

(-) 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:198
 aligned with Q8DIR2_THEEB | Q8DIR2 from UniProtKB/TrEMBL  Length:200

    Alignment length:198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
         Q8DIR2_THEEB     2 AFVQEPLPFDPGALEPYGMSAKTLEFHYGKHHKGYVDNLNKLTQDTELADKSLEDVIRTTYGDAAKVGIFNNAAQVWNHTFFWNSLKPGGGGVPTGDVAARINSAFGSYDEFKAQFKNAAATQFGSGWAWLVLEAGTLKVTKTANAENPLVHGQVPLLTIDVWEHAYYLDYQNRRPDFIDNFLNQLVNWDFVAKNLAA 199
               SCOP domains d1my6a1 A:1-88 Fe superoxide dismutase (FeSOD)                                          d1my6a2 A:89-198 Fe superoxide dismutase (FeSOD)                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1my6 A   1 AFVQEPLPFDPGALEPYGMSAKTLEFHYGKHHKGYVDNLNKLTQDTELADKSLEDVIRTTYGDAAKVGIFNNAAQVWNHTFFWNSLKPGGGGVPTGDVAARINSAFGSYDEFKAQFKNAAATQFGSGWAWLVLEAGTLKVTKTANAENPLVHGQVPLLTIDVWEHAYYLDYQNRRPDFIDNFLNQLVNWDFVAKNLAA 198
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        


Chain B from PDB  Type:PROTEIN  Length:198
 aligned with Q8DIR2_THEEB | Q8DIR2 from UniProtKB/TrEMBL  Length:200

    Alignment length:198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
         Q8DIR2_THEEB     2 AFVQEPLPFDPGALEPYGMSAKTLEFHYGKHHKGYVDNLNKLTQDTELADKSLEDVIRTTYGDAAKVGIFNNAAQVWNHTFFWNSLKPGGGGVPTGDVAARINSAFGSYDEFKAQFKNAAATQFGSGWAWLVLEAGTLKVTKTANAENPLVHGQVPLLTIDVWEHAYYLDYQNRRPDFIDNFLNQLVNWDFVAKNLAA 199
               SCOP domains d1my6b1 B:1-88 Fe superoxide dismutase (FeSOD)                                          d1my6b2 B:89-198 Fe superoxide dismutase (FeSOD)                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Sod_Fe_N-1my6B03 B:1-87                                                                ----Sod_Fe_C-1my6B01 B:92-196                                                                                -- Pfam domains (1)
           Pfam domains (2) Sod_Fe_N-1my6B04 B:1-87                                                                ----Sod_Fe_C-1my6B02 B:92-196                                                                                -- Pfam domains (2)
         Sec.struct. author .............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1my6 B   1 AFVQEPLPFDPGALEPYGMSAKTLEFHYGKHHKGYVDNLNKLTQDTELADKSLEDVIRTTYGDAAKVGIFNNAAQVWNHTFFWNSLKPGGGGVPTGDVAARINSAFGSYDEFKAQFKNAAATQFGSGWAWLVLEAGTLKVTKTANAENPLVHGQVPLLTIDVWEHAYYLDYQNRRPDFIDNFLNQLVNWDFVAKNLAA 198
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1MY6)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Sod_Fe_C] (46)
(-)
Clan: no clan defined [family: Sod_Fe_N] (46)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8DIR2_THEEB | Q8DIR2)
molecular function
    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:0004784    superoxide dismutase activity    Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
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:0006801    superoxide metabolic process    The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.

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 Related Entries

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