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(-) Description

Title :  X-RAY 3D STRUCTURE OF P.LEIOGNATHI CU,ZN SOD MUTANT V29G
 
Authors :  M. E. Stroppolo, A. Pesce, M. D'Orazio, P. O'Neill, D. Bordo, C. Rosano, M. Milani, A. Battistoni, M. Bolognesi, A. Desideri
Date :  28 Mar 01  (Deposition) - 09 May 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Prokaryotic Superoxide Dismutase, Subunit Interaction, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Stroppolo, A. Pesce, M. D'Orazio, P. O'Neill, D. Bordo, C. Rosano, M. Milani, A. Battistoni, M. Bolognesi, A. Desideri
Single Mutations At The Subunit Interface Modulate Copper Reactivity In Photobacterium Leiognathi Cu, Zn Superoxide Dismutase.
J. Mol. Biol. V. 308 555 2001
PubMed-ID: 11327787  |  Reference-DOI: 10.1006/JMBI.2001.4606
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CU,ZN SUPEROXIDE DISMUTASE
    Chains: A
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: PHOTOBACTERIUM LEIOGNATHI
    Organism Taxid: 658

 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
1CU1Ligand/IonCOPPER (II) ION
2ZN1Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:70 , HIS A:79 , HIS A:88 , ASP A:91BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREHIS A:45 , HIS A:47 , HIS A:70 , HIS A:125BINDING SITE FOR RESIDUE CU A 202

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:52 -A:147

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Met A:134 -Pro A:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_CU_ZN_1PS00087 Copper/Zinc superoxide dismutase signature 1.SODC_PHOLE65-75  1A:43-53
2SOD_CU_ZN_2PS00332 Copper/Zinc superoxide dismutase signature 2.SODC_PHOLE161-172  1A:139-150
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_CU_ZN_1PS00087 Copper/Zinc superoxide dismutase signature 1.SODC_PHOLE65-75  2A:43-53
2SOD_CU_ZN_2PS00332 Copper/Zinc superoxide dismutase signature 2.SODC_PHOLE161-172  2A:139-150

(-) Exons   (0, 0)

(no "Exon" information available for 1IBF)

(-) 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:151
 aligned with SODC_PHOLE | P00446 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:151
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172 
           SODC_PHOLE    23 QDLTVKMTDLQTGKPVGTIELSQNKYGVVFTPELADLTPGMHGFHIHQNGSCASSEKDGKVVLGGAAGGHYDPEHTNKHGFPWTDDNHKGDLPALFVSANGLATNPVLAPRLTLKELKGHAIMIHAGGDNHSDMPKALGGGGARVACGVIQ 173
               SCOP domains d1ibfa_ A: Cu,Zn superoxide dismutase, SOD                                                                                                              SCOP domains
               CATH domains 1ibfA00 A:1-151  [code=2.60.40.200, no name defined]                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....eeeeeeeeee..eeeeeeee.....eee.eeee.......eee..eee.hhhhh..........................eee.........eee....hhhhh..eeeee..........hhhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------SOD_CU_ZN_1-------------------------------------------------------------------------------------SOD_CU_ZN_2 - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ibf A   1 QDLTVKMTDLQTGKPVGTIELSQNKYGVGFIPELADLTPGMHGFHIHQNGSCASSEKDGKVVLGGAAGGHYDPEHTNKHGFPWTDDNHKGDLPALFVSANGLATNPVLAPRLTLKELKGHAIMIHAGGDNHSDMPKALGGGGARVACGVIQ 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (SODC_PHOLE | P00446)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    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:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    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:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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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
        SODC_PHOLE | P00446: 1bzo 1ib5 1ibb 1ibd 1ibh 1oaj 1oal 1yai

(-) Related Entries Specified in the PDB File

1bzo P.LEIOGNATHI CU,ZN SOD WILD TYPE
1ib5 P.LEIOGNATHI CU,ZN SOD W83Y MUTATION
1ibb P.LEIOGNATHI CU,ZN SOD W83F MUTATION
1ibd P.LEIOGNATHI CU,ZN SOD V29A MUTATION
1ibh P.LEIOGNATHI CU,ZN SOD M41I MUTATION