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(-) Description

Title :  YERSINIA PSEUDOTUBERCULOSIS SUPEROXIDE DISMUTASE C
 
Authors :  A. K. Basak, M. L. Duffield, C. E. Naylor, J. Huyet, R. W. Titball
Date :  26 Oct 09  (Deposition) - 03 Nov 10  (Release) - 03 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Huyet, C. E. Naylor, R. W. Titball, H. Bullifent, N. Walker, H. E. Jones, M. L. Duffied, A. K. Basak
Crystal Structure Of The Yersinia Pseudotuberculosis Superoxide Dismutase (Sodc)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [CU-ZN]
    Chains: A, B
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: STAR
    Expression System Vector Type: PLASMID
    Organism Scientific: YERSINIA PSEUDOTUBERCULOSIS
    Organism Taxid: 633
    Strain: IP32953
    Synonym: SUPEROXIDE DISMUTASE C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3ZN7Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:79 , HIS A:88 , HIS A:97 , ASP A:100BINDING SITE FOR RESIDUE ZN A1162
02AC2SOFTWAREHIS B:79 , HIS B:88 , HIS B:97 , ASP B:100BINDING SITE FOR RESIDUE ZN B1162
03AC3SOFTWAREHIS A:130 , HOH A:2090 , HOH A:2091 , HOH A:2092BINDING SITE FOR RESIDUE ZN A1163
04AC4SOFTWAREHIS A:144 , HIS B:144 , HOH B:2118 , HOH B:2119BINDING SITE FOR RESIDUE ZN B1163
05AC5SOFTWAREASN A:4 , ASP A:5 , HOH A:2093 , HOH A:2094 , HIS B:130BINDING SITE FOR RESIDUE ZN A1164
06AC6SOFTWAREHIS A:54 , HIS A:56 , HIS A:79 , HIS A:135BINDING SITE FOR RESIDUE ZN A1165
07AC7SOFTWAREHIS B:54 , HIS B:56 , HIS B:79 , HIS B:135BINDING SITE FOR RESIDUE ZN B1164
08AC8SOFTWAREASN A:140 , THR B:29 , HIS B:42 , THR B:113 , PRO B:115 , GOL B:1167 , HOH B:2120 , HOH B:2121 , HOH B:2122BINDING SITE FOR RESIDUE MES B1165
09AC9SOFTWARELEU B:46 , PRO B:48 , ALA B:108 , HOH B:2123BINDING SITE FOR RESIDUE GOL B1166
10BC1SOFTWARELYS B:6 , THR B:31 , LEU B:38 , MES B:1165 , HOH B:2122BINDING SITE FOR RESIDUE GOL B1167

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:61 -A:157
2B:61 -B:157

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:144 -Pro A:145
2His B:144 -Pro B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WWO)

(-) Exons   (0, 0)

(no "Exon" information available for 2WWO)

(-) 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:158
 aligned with Q66ED7_YERPS | Q66ED7 from UniProtKB/TrEMBL  Length:189

    Alignment length:158
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181        
         Q66ED7_YERPS    32 NDKASMTVKINESLPQGNGKALGTVTVTETAYGLLFTPHLTGLAPGIHGFHLHEKPSCAPGMKDGKAVPALAAGGHLDPNKTGVHLGPYNDKGHLGDLPGLVVNADGTATYPVLAPRLKSLSEVKQHALMIHAGGDNYSDHPMPLGGGGARMACGVIE 189
               SCOP domains d2wwoa_ A: automated matches                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....eeeeeeeeeeeee..eeeeeeee.....eee.eeee.......eee..eee.hhhhh..........................eee.........eee....hhhhh...eeeee..........hhhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wwo A   4 NDKASMTVKINESLPQGNGKALGTVTVTETAYGLLFTPHLTGLAPGIHGFHLHEKPSCAPGMKDGKAVPALAAGGHLDPNKTGVHLGPYNDKGHLGDLPGLVVNADGTATYPVLAPRLKSLSEVKQHALMIHAGGDNYSDHPMPLGGGGARMACGVIE 161
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153        


Chain B from PDB  Type:PROTEIN  Length:157
 aligned with Q66ED7_YERPS | Q66ED7 from UniProtKB/TrEMBL  Length:189

    Alignment length:157
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       
         Q66ED7_YERPS    33 DKASMTVKINESLPQGNGKALGTVTVTETAYGLLFTPHLTGLAPGIHGFHLHEKPSCAPGMKDGKAVPALAAGGHLDPNKTGVHLGPYNDKGHLGDLPGLVVNADGTATYPVLAPRLKSLSEVKQHALMIHAGGDNYSDHPMPLGGGGARMACGVIE 189
               SCOP domains d2wwob_ B: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Sod_Cu-2wwoB01 B:5-160                                                                                                                                      - Pfam domains (1)
           Pfam domains (2) Sod_Cu-2wwoB02 B:5-160                                                                                                                                      - Pfam domains (2)
         Sec.struct. author ...eeeeeeeee....eeeeeeeeeeeee..eeeeeeee.....eee.eeee.......eee..eee.hhhhh..........................eee.........eee....hhhhh...eeeee..........hhhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wwo B   5 DKASMTVKINESLPQGNGKALGTVTVTETAYGLLFTPHLTGLAPGIHGFHLHEKPSCAPGMKDGKAVPALAAGGHLDPNKTGVHLGPYNDKGHLGDLPGLVVNADGTATYPVLAPRLKSLSEVKQHALMIHAGGDNYSDHPMPLGGGGARMACGVIE 161
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0 ; only for superseded entry 2WN0: 1,2)

(no "CATH Domain" information available for 2WWO, only for superseded entry 2WN0 replaced by 2WWO)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Sod_Cu] (71)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q66ED7_YERPS | Q66ED7)
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/TrEMBL
        Q66ED7_YERPS | Q66ED7: 2wwn

(-) Related Entries Specified in the PDB File

2wwn YERSINIA PSEUDOTUBERCULOSIS SUPEROXIDE DISMUTASE C WITH BOUND AZIDE