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(-) Description

Title :  MANGANESE SUPEROXIDE DISMUTASE (MN-SOD) FROM DEINOCOCCUS RADIODURANS
 
Authors :  R. Dennis, E. Micossi, J. Mccarthy, E. Moe, E. Gordon, G. Leonard, S. Mcsweeney
Date :  03 Feb 06  (Deposition) - 13 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Manganese Superoxide Dismutase, Deinococcus Radiodurans, Radiation Resistance, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Dennis, E. Micossi, J. Mccarthy, E. Moe, E. Gordon, G. Leonard, S. Mcsweeney
Structure Of The Manganese Superoxide Dismutase From Deinococcus Radiodurans In Two Crystal Forms.
Acta Crystallogr. , Sect. F V. 62 325 2006
PubMed-ID: 16582477  |  Reference-DOI: 10.1107/S1744309106008402

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [MN]
    Atcc: 13939
    Chains: A, B
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector: GATEWAY PDEST17
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 243230
    Strain: R1
    Synonym: MNSOD

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:26 , HIS A:80 , ASP A:172 , HIS A:176 , HOH A:2198BINDING SITE FOR RESIDUE MN A1211
2AC2SOFTWAREHIS B:26 , HIS B:80 , ASP B:172 , HIS B:176 , HOH B:2167BINDING SITE FOR RESIDUE MN B1211

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CE4)

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CE4)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM_DEIRA173-180
 		  2A:172-179
B:172-179
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM_DEIRA173-180
 		  1A:172-179
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM_DEIRA173-180
 		  1-
B:172-179

(-) Exons   (0, 0)

(no "Exon" information available for 2CE4)

(-) 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:203
 aligned with SODM_DEIRA | Q9RUV2 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
           SODM_DEIRA     2 AYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQGQGQNGANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK 211
               SCOP domains d2ce4a1 A:1-87 automated matches                                                       --      ---d2ce4a2 A:99-210 automated matches                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhh-......hhhhhh.........hhhhhhhhhhhhhhhhhhhhh...------....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeee...hhhhhhhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ce4 A   1 AYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALE-TEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQ------ANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK 210
                                    10        20        30        40  | |   50        60        70        80        |-     | 100       110       120       130       140       150       160       170       180       190       200       210
                                                                     43 |                                          89     96                                                                                                                  
                                                                       45                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:206
 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 d2ce4b1 B:-1-87 automated matches                                                       -----------d2ce4b2 B:99-210 automated matches                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....-----....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeee...hhhhhhhhhh...eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ce4 B  -1 LAYTLPQLPYAYDALEPHIDARTMEIHHTKHHQTYVDNANKALEGTEFADLPVEQLIQQLDRVPADKKGALRNNAGGHANHSMFWQIMGQG-----ANQPSGELLDAINSAFGSFDAFKQKFEDAAKTRFGSGWAWLVVKDGKLDVVSTANQDNPLMGEAIAGVSGTPILGVDVWEHAYYLNYQNRRPDYLAAFWNVVNWDEVSKRYAAAK 210
                            ||       9        19        29        39        49        59        69        79        89|     | 99       109       119       129       139       149       159       169       179       189       199       209 
                           -1|                                                                                       90    96                                                                                                                  
                             1
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CE4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CE4)

(-) Gene Ontology  (6, 6)

Asymmetric 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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  1.15.1.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        SODM_DEIRA | Q9RUV2: 1y67 2aw9 2cdy 3kky

(-) Related Entries Specified in the PDB File

1y67 CRYSTAL STRUCTURE OF MANGANESE SUPEROXIDE DISMUTASE FROMDEINOCOCCUS RADIODURANS
2cdy MANGANESE SUPEROXIDE DISMUTASE (MN-SOD) FROM DEINOCOCCUS RADIODURANS