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(-) Description

Title :  CRYSTAL STRUCTURE OF SODA-2 (BA5696) FROM BACILLUS ANTHRACIS AT 1.8A RESOLUTION.
 
Authors :  I. W. Boucher, V. M. Levdikov, E. V. Blagova, M. J. Fogg, J. A. Brannigan, A. J. Wilkinson, K. S. Wilson
Date :  14 Oct 04  (Deposition) - 19 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Soda-2; Superoxide Dismutase; Bacillus Anthracis; Ba5696; Spine, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. W. Boucher, A. K. Kalliomaa, V. M. Levdikov, E. V. Blagova, M. J. Fogg, J. A. Brannigan, K. S. Wilson, A. J. Wilkinson
Structures Of Two Superoxide Dismutases From Bacillus Anthracis Reveal A Novel Active Centre.
Acta Crystallogr. , Sect. F V. 61 621 2005
PubMed-ID: 16511113  |  Reference-DOI: 10.1107/S1744309105017380
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE
    Chains: A, B
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET-YSBLIC
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: SODA2, SODA-2
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 1392
    Synonym: SODA-2

 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
1MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:28 , HIS A:83 , ASP A:165 , HIS A:169 , HOH A:388BINDING SITE FOR RESIDUE MN A 209
2AC2SOFTWAREHIS B:28 , HIS B:83 , ASP B:165 , HIS B:169 , HOH B:212BINDING SITE FOR RESIDUE MN B 209

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:17 -Pro A:18
2Glu B:17 -Pro B:18

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM2_BACAN165-172
 		  2A:165-172
B:165-172

(-) Exons   (0, 0)

(no "Exon" information available for 1XRE)

(-) 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:201
 aligned with SODM2_BACAN | Q81JK8 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:201
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202 
          SODM2_BACAN     3 SFQLPKLSYDYDELEPYIDSNTLSIHHGKHHATYVNNLNAALENYSELHNKSLEELLCNLETLPKEIVTAVRNNGGGHYCHSLFWEVMSPRGGGEPNGDVAKVIDYYFNTFDNLKDQLSKAAISRFGSGYGWLVLDGEELSVMSTPNQDTPLQEGKIPLLVIDVWEHAYYLKYQNRRPEFVTNWWHTVNWDRVNEKYLQAI 203
               SCOP domains d1xrea1 A:3-92 automated matches                                                          d1xrea2 A:93-203 automated matches                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xre A   3 SFQLPKLSYDYDELEPYIDSNTLSIHHGKHHATYVNNLNAALENYSELHNKSLEELLCNLETLPKEIVTAVRNNGGGHYCHSLFWEVMSPRGGGEPNGDVAKVIDYYFNTFDNLKDQLSKAAISRFGSGYGWLVLDGEELSVMSTPNQDTPLQEGKIPLLVIDVWEHAYYLKYQNRRPEFVTNWWHTVNWDRVNEKYLQAI 203
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202 


Chain B from PDB  Type:PROTEIN  Length:201
 aligned with SODM2_BACAN | Q81JK8 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:201
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202 
          SODM2_BACAN     3 SFQLPKLSYDYDELEPYIDSNTLSIHHGKHHATYVNNLNAALENYSELHNKSLEELLCNLETLPKEIVTAVRNNGGGHYCHSLFWEVMSPRGGGEPNGDVAKVIDYYFNTFDNLKDQLSKAAISRFGSGYGWLVLDGEELSVMSTPNQDTPLQEGKIPLLVIDVWEHAYYLKYQNRRPEFVTNWWHTVNWDRVNEKYLQAI 203
               SCOP domains d1xreb1 B:3-92 automated matches                                                          d1xreb2 B:93-203 automated matches                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xre B   3 SFQLPKLSYDYDELEPYIDSNTLSIHHGKHHATYVNNLNAALENYSELHNKSLEELLCNLETLPKEIVTAVRNNGGGHYCHSLFWEVMSPRGGGEPNGDVAKVIDYYFNTFDNLKDQLSKAAISRFGSGYGWLVLDGEELSVMSTPNQDTPLQEGKIPLLVIDVWEHAYYLKYQNRRPEFVTNWWHTVNWDRVNEKYLQAI 203
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202
   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 alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SODM2_BACAN | Q81JK8)
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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