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(-) Description

Title :  CRYSTAL STRUCTURE OF SUPEROXIDE DISMUTASE FROM HELICOBACTER PYLORI
 
Authors :  L. Esposito, A. Seydel, R. Aiello, G. Sorrentino, L. Cendron, G. Zanotti, A. Zagari
Date :  29 Feb 08  (Deposition) - 10 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Esposito, A. Seydel, R. Aiello, G. Sorrentino, L. Cendron, G. Zanotti, A. Zagari
The Crystal Structure Of The Superoxide Dismutase From Helicobacter Pylori Reveals A Structured C-Terminal Extension
Biochim. Biophys. Acta V. 1784 1601 2008
PubMed-ID: 18502213  |  Reference-DOI: 10.1016/J.BBAPAP.2008.04.024
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE
    ChainsA, B
    EC Number1.15.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-28B
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSOD
    Organism CommonCAMPYLOBACTER PYLORI
    Organism ScientificHELICOBACTER PYLORI
    Organism Taxid210
    StrainCCUG17874

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:26 , HIS A:73 , ASP A:156 , HIS A:160BINDING SITE FOR RESIDUE FE A 500
2AC2SOFTWAREHIS B:26 , HIS B:73 , ASP B:156 , HIS B:160BINDING SITE FOR RESIDUE FE B 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CEI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_HELPY156-163
 
  2A:156-163
B:156-163

(-) Exons   (0, 0)

(no "Exon" information available for 3CEI)

(-) 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:213
 aligned with B1VJF0_HELPX | B1VJF0 from UniProtKB/TrEMBL  Length:213

    Alignment length:213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   
         B1VJF0_HELPX     1 MFTLRELPFAKDSMGDFLSPVAFDFHHGKHHQTYVNNLNNLIKGTDFEKSSLFAILTKSSGGVFNNAAQIYNHDFYWDCLSPKATALSDELKGALEKDFGSLEKFKEDFIKSATTLFGSGWNWAAYNLDTQKIEIIQTSNAQTPVTDKKVPLLVVDVWEHAYYIDHKNARPVYLEKFYGHINWHFVSQCYEWAKKEGLGSVDYYINELVHKKL 213
               SCOP domains d3ceia1 A:1-84 automated matches                                                    d3ceia2 A:85-213 automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cei A   1 MFTLRELPFAKDSMGDFLSPVAFDFHHGKHHQTYVNNLNNLIKGTDFEKSSLFAILTKSSGGVFNNAAQIYNHDFYWDCLSPKATALSDELKGALEKDFGSLEKFKEDFIKSATTLFGSGWNWAAYNLDTQKIEIIQTSNAQTPVTDKKVPLLVVDVWEHAYYIDHKNARPVYLEKFYGHINWHFVSQCYEWAKKEGLGSVDYYINELVHKKL 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

Chain A from PDB  Type:PROTEIN  Length:213
 aligned with SODF_HELPY | P43312 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   
           SODF_HELPY     1 MFTLRELPFAKDSMGDFLSPVAFDFHHGKHHQTYVNNLNNLIKGTDFEKSSLFDILTKSSGGVFNNAAQIYNHDFYWDCLSPKATALSDELKGALEKDFGSLEKFKEDFIKSATTLFGSGWNWAAYNLDTQKIEIIQTSNAQTPVTDKKVPLLVVDVWEHAYYIDHKNARPVYLEKFYGHINWHFVSQCYEWAKKEGLGSVDYYINELVHKKA 213
               SCOP domains d3ceia1 A:1-84 automated matches                                                    d3ceia2 A:85-213 automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cei A   1 MFTLRELPFAKDSMGDFLSPVAFDFHHGKHHQTYVNNLNNLIKGTDFEKSSLFAILTKSSGGVFNNAAQIYNHDFYWDCLSPKATALSDELKGALEKDFGSLEKFKEDFIKSATTLFGSGWNWAAYNLDTQKIEIIQTSNAQTPVTDKKVPLLVVDVWEHAYYIDHKNARPVYLEKFYGHINWHFVSQCYEWAKKEGLGSVDYYINELVHKKL 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

Chain B from PDB  Type:PROTEIN  Length:210
 aligned with B1VJF0_HELPX | B1VJF0 from UniProtKB/TrEMBL  Length:213

    Alignment length:210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
         B1VJF0_HELPX     1 MFTLRELPFAKDSMGDFLSPVAFDFHHGKHHQTYVNNLNNLIKGTDFEKSSLFAILTKSSGGVFNNAAQIYNHDFYWDCLSPKATALSDELKGALEKDFGSLEKFKEDFIKSATTLFGSGWNWAAYNLDTQKIEIIQTSNAQTPVTDKKVPLLVVDVWEHAYYIDHKNARPVYLEKFYGHINWHFVSQCYEWAKKEGLGSVDYYINELVH 210
               SCOP domains d3ceib1 B:1-84 automated matches                                                    d3ceib2 B:85-210 automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee...hhhhh.eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cei B   1 MFTLRELPFAKDSMGDFLSPVAFDFHHGKHHQTYVNNLNNLIKGTDFEKSSLFAILTKSSGGVFNNAAQIYNHDFYWDCLSPKATALSDELKGALEKDFGSLEKFKEDFIKSATTLFGSGWNWAAYNLDTQKIEIIQTSNAQTPVTDKKVPLLVVDVWEHAYYIDHKNARPVYLEKFYGHINWHFVSQCYEWAKKEGLGSVDYYINELVH 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:210
 aligned with SODF_HELPY | P43312 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
           SODF_HELPY     1 MFTLRELPFAKDSMGDFLSPVAFDFHHGKHHQTYVNNLNNLIKGTDFEKSSLFDILTKSSGGVFNNAAQIYNHDFYWDCLSPKATALSDELKGALEKDFGSLEKFKEDFIKSATTLFGSGWNWAAYNLDTQKIEIIQTSNAQTPVTDKKVPLLVVDVWEHAYYIDHKNARPVYLEKFYGHINWHFVSQCYEWAKKEGLGSVDYYINELVH 210
               SCOP domains d3ceib1 B:1-84 automated matches                                                    d3ceib2 B:85-210 automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee...hhhhh.eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ----------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cei B   1 MFTLRELPFAKDSMGDFLSPVAFDFHHGKHHQTYVNNLNNLIKGTDFEKSSLFAILTKSSGGVFNNAAQIYNHDFYWDCLSPKATALSDELKGALEKDFGSLEKFKEDFIKSATTLFGSGWNWAAYNLDTQKIEIIQTSNAQTPVTDKKVPLLVVDVWEHAYYIDHKNARPVYLEKFYGHINWHFVSQCYEWAKKEGLGSVDYYINELVH 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B1VJF0_HELPX | B1VJF0)
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.

Chain A,B   (SODF_HELPY | P43312)
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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