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(-) Description

Title :  CRYSTAL STRUCTURE OF A MANGANESE SUPEROXIDE DISMUTASES FROM CAENORHABDITIS ELEGANS
 
Authors :  C. H. Trinh, T. Hunter, E. E. Stewart, S. E. V. Phillips, G. J. Hunter
Date :  03 Jun 08  (Deposition) - 09 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A,C  (2x)
Keywords :  Alpha Hairpin N Domain, Alpha/Beta C Domain, Oxidoreductase, Manganese, Metal-Binding, Mitochondrion, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. H. Trinh, T. Hunter, E. E. Stewart, S. E. Phillips, G. J. Hunter
Purification, Crystallization And X-Ray Structures Of The Two Manganese Superoxide Dismutases From Caenorhabditis Elegans
Acta Crystallogr. , Sect. F V. 64 1110 2008
PubMed-ID: 19052361  |  Reference-DOI: 10.1107/S1744309108037056

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [MN] 2
    ChainsA, C
    EC Number1.15.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTRC-99A
    Expression System StrainOX326A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSOD-3, C08A9.1
    Organism CommonNEMATODE
    Organism ScientificCAENORHABDITIS ELEGANS
    Organism Taxid6239

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AC
Biological Unit 1 (2x)AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1MLI1Ligand/IonMALONATE ION
2MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MLI2Ligand/IonMALONATE ION
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS C:26 , HIS C:74 , ASP C:155 , HIS C:159BINDING SITE FOR RESIDUE MN C 195
2AC2SOFTWAREHIS A:26 , HIS A:74 , ASP A:155 , HIS A:159BINDING SITE FOR RESIDUE MN A 195
3AC3SOFTWAREASN A:167BINDING SITE FOR RESIDUE MLI A 196

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DC5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:15 -Pro A:16
2Glu C:15 -Pro C:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DC5)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM2_CAEEL179-186
 
  2A:155-162
C:155-162
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM2_CAEEL179-186
 
  4A:155-162
C:155-162

(-) Exons   (0, 0)

(no "Exon" information available for 3DC5)

(-) 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:194
 aligned with SODM2_CAEEL | P41977 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:194
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214    
          SODM2_CAEEL    25 KHTLPDLPFDYADLEPVISHEIMQLHHQKHHATYVNNLNQIEEKLHEAVSKGNLKEAIALQPALKFNGGGHINHSIFWTNLAKDGGEPSKELMDTIKRDFGSLDNLQKRLSDITIAVQGSGWGWLGYCKKDKILKIATCANQDPLEGMVPLFGIDVWEHAYYLQYKNVRPDYVHAIWKIANWKNISERFANARQ 218
               SCOP domains d3dc5a1 A:1-85 automated matches                                                     d3dc5a2 A:86-194 automated matches                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dc5 A   1 KHTLPDLPFDYADLEPVISHEIMQLHHQKHHATYVNNLNQIEEKLHEAVSKGNLKEAIALQPALKFNGGGHINHSIFWTNLAKDGGEPSKELMDTIKRDFGSLDNLQKRLSDITIAVQGSGWGWLGYCKKDKILKIATCANQDPLEGMVPLFGIDVWEHAYYLQYKNVRPDYVHAIWKIANWKNISERFANARQ 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    

Chain C from PDB  Type:PROTEIN  Length:195
 aligned with SODM2_CAEEL | P41977 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:195
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213     
          SODM2_CAEEL    24 SKHTLPDLPFDYADLEPVISHEIMQLHHQKHHATYVNNLNQIEEKLHEAVSKGNLKEAIALQPALKFNGGGHINHSIFWTNLAKDGGEPSKELMDTIKRDFGSLDNLQKRLSDITIAVQGSGWGWLGYCKKDKILKIATCANQDPLEGMVPLFGIDVWEHAYYLQYKNVRPDYVHAIWKIANWKNISERFANARQ 218
               SCOP domains d3dc5c1 C:0-85 automated matches                                                      d3dc5c2 C:86-194 automated matches                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dc5 C   0 MKHTLPDLPFDYADLEPVISHEIMQLHHQKHHATYVNNLNQIEEKLHEAVSKGNLKEAIALQPALKFNGGGHINHSIFWTNLAKDGGEPSKELMDTIKRDFGSLDNLQKRLSDITIAVQGSGWGWLGYCKKDKILKIATCANQDPLEGMVPLFGIDVWEHAYYLQYKNVRPDYVHAIWKIANWKNISERFANARQ 194
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189     

   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 Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DC5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DC5)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (SODM2_CAEEL | P41977)
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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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.
cellular component
    GO:0097249    mitochondrial respiratory chain supercomplex    A set of respiratory enzyme complexes of the mitochondrial inner membrane (including, for example, Complex II, Complex III, Complex IV, or F1-F0 ATPase) arranged to form a large supercomplex.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SODM2_CAEEL | P419774x9q 5ag2

(-) Related Entries Specified in the PDB File

3dc6