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(-) Description

Title :  SUPEROXIDE DISMUTASE WITH MANGANESE FROM DEINOCOCCUS RADIODURANS
 
Authors :  S. Tanaka, M. R. Sawaya, S. Chan, L. J. Perry
Date :  31 Aug 05  (Deposition) - 22 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Tanaka, M. R. Sawaya, S. Chan, L. J. Perry
Crystal Structure Of Manganese Superoxide Dismutase From Deinococcus Radiodurans
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [MN]
    Chains: A, B
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)GOLD
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SODA
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Synonym: MNSOD

 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:27 , HIS A:81 , ASP A:173 , HIS A:177 , HOH A:236BINDING SITE FOR RESIDUE MN A 229
2AC2SOFTWAREHIS B:27 , HIS B:81 , ASP B:173 , HIS B:177 , HOH B:240BINDING SITE FOR RESIDUE MN B 229

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AW9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:16 -Pro A:17
2Glu B:16 -Pro B:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AW9)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM_DEIRA173-180
 		  2A:173-180
B:173-180

(-) Exons   (0, 0)

(no "Exon" information available for 2AW9)

(-) 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:210
 aligned with SODM_DEIRA | Q9RUV2 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:213
                                                                                                                                                                                                                                            211  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210|  
           SODM_DEIRA     1 MAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQGQNGANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK--   -
               SCOP domains d2aw9a1 A:1-89 Mn superoxide dismutase (MnSOD)                                           --------d2aw9a2 A:98-213 Mn superoxide dismutase (MnSOD)                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh......---....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee...hhhhhhhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aw9 A   1 AAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQG---ANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAKLV 213
                                    10        20        30        40        50        60        70        80        90  |   |100       110       120       130       140       150       160       170       180       190       200       210   
                                                                                                                       93  97                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:208
 aligned with SODM_DEIRA | Q9RUV2 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
           SODM_DEIRA     1 MAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQGQNGANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK 211
               SCOP domains d2aw9b1 B:1-89 Mn superoxide dismutase (MnSOD)                                           --------d2aw9b2 B:98-211 Mn superoxide dismutase (MnSOD)                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh......---....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeee...hhhhhhhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aw9 B   1 AAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQG---ANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK 211
                                    10        20        30        40        50        60        70        80        90  |   |100       110       120       130       140       150       160       170       180       190       200       210 
                                                                                                                       93  97
   Legend:   → Mismatch (orange background)
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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 2AW9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AW9)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SODM_DEIRA | Q9RUV2)
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

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

UniProtKB/Swiss-Prot
        SODM_DEIRA | Q9RUV2: 1y67 2cdy 2ce4 3kky

(-) Related Entries Specified in the PDB File

1y67 THE SAME PROTEIN WITHOUT MANGANESE.