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(-) Description

Title :  CRYSTAL STRUCTURE OF MANGANESE SUPEROXIDE DISMUTASES FROM BACILLUS HALODENITRIFICANS
 
Authors :  J. Liao, M. Y. Liu, T. Chang, M. Li, J. Legall, L. L. Gui, J. P. Zhang, T. Jiang, D. C. Liang, W. R. Chang
Date :  13 Aug 01  (Deposition) - 14 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Manganese Superoxide Dismutase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Liao, M. Y. Liu, T. Chang, M. Li, J. Le Gall, L. L. Gui, J. P. Zhang, T. Jiang, D. C. Liang, W. R. Chang
Three-Dimensional Structure Of Manganese Superoxide Dismutase From Bacillus Halodenitrificans, A Component Of The So-Called "Green Protein".
J. Struct. Biol. V. 139 171 2002
PubMed-ID: 12457847  |  Reference-DOI: 10.1016/S0006-291X(02)00436-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANGANESE SUPEROXIDE DISMUTASE
    ChainsA
    EC Number1.15.1.1
    FragmentGREEN PROTEIN
    Organism ScientificVIRGIBACILLUS HALODENITRIFICANS
    Organism Taxid1482
    Other DetailsCYTOPLASM

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1MN1Ligand/IonMANGANESE (II) ION
2ZN1Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:27 , HIS A:82 , ASP A:164 , HIS A:168BINDING SITE FOR RESIDUE MN A 204
2AC2SOFTWAREHIS A:46 , ASP A:180 , HOH A:206 , HOH A:207BINDING SITE FOR RESIDUE ZN A 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JR9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JR9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JR9)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM_VIRHA164-171  1A:164-171
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM_VIRHA164-171  2A:164-171

(-) Exons   (0, 0)

(no "Exon" information available for 1JR9)

(-) 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:201
 aligned with SODM_VIRHA | Q7SIC3 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:201
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201 
           SODM_VIRHA     2 KFELPELPYAYDALEPTIDKETMNIHHTKHHNTYVTKLNGALEGHEDLKNKSLNDLISNLDAVPENIRTAVRNNGGGHANHSLFWKLMSPNGGGKPTGEVADKINDKYGSFEKFQEEFAAAAAGRFGSGWAWLVVNNGEIEIMSTPIQDNPLMEGKKPILGLDVWEHAYYLKYQNKRPDYISAFWNVVNWDEVAAQYSQAA 202
               SCOP domains d1jr9a1 A:2-91 Mn superoxide dismutase (MnSOD)                                            d1jr9a2 A:92-202 Mn superoxide dismutase (MnSOD)                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..........eeee...hhhhhh.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jr9 A   2 KFELPELPYAYDALEPTIDKETMNIHHTKHHNTYVTKLNGALEGHEDLKNKSLNDLISNLDAVPENIRTAVRNNGGGHANHSLFWKLMSPNGGGKPTGEVADKINDKYGSFEKFQEEFAAAAAGRFGSGWAWLVVNNGEIEIMSTPIQDNPLMEGKKPILGLDVWEHAYYLKYQNKRPDYISAFWNVVNWDEVAAQYSQAA 202
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201 

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1JR9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1JR9)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (SODM_VIRHA | Q7SIC3)
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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