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(-) Description

Title :  COMBINING CRYSTALLOGRAPHY AND MOLECULAR DYNAMICS: THE CASE OF SCHISTOSOMA MANSONI PHOSPHOLIPID GLUTATHIONE PEROXIDASE
 
Authors :  D. Dimastrogiovanni, M. Anselmi, A. E. Miele, G. Boumis, F. Angelucci, A. Di Nola, M. Brunori, A. Bellelli
Date :  24 Apr 09  (Deposition) - 08 Sep 09  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Selenium, Oxidoreductase, Selenocysteine, Schistosomiasis, Lipid Gsh Peroxidase, Molecular Dynamics Simulations, Ros Detoxification Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Dimastrogiovanni, M. Anselmi, A. E. Miele, G. Boumis, L. Petersson, F. Angelucci, A. D. Nola, M. Brunori, A. Bellelli
Combining Crystallography And Molecular Dynamics: The Case Of Schistosoma Mansoni Phospholipid Glutathione Peroxidase.
Proteins V. 78 259 2010
PubMed-ID: 19714775  |  Reference-DOI: 10.1002/PROT.22536

(-) Compounds

Molecule 1 - GLUTATHIONE PEROXIDASE
    Chains: A
    EC Number: 1.11.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: SCHISTOSOMA MANSONI
    Organism Taxid: 6183
    Synonym: PHOSPHOLIPID-HYDROPEROXIDE GLUTATHIONE PEROXIDASE, GPX

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1POP1Ligand/IonPYROPHOSPHATE 2-

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:59 , GLY A:124 , THR A:125 , ASN A:129 , ILE A:130 , LYS A:131 , SER A:135 , ARG A:148 , TYR A:149 , SER A:150 , PRO A:151 , HOH A:2140BINDING SITE FOR RESIDUE POP A1170

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WGR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTATHIONE_PEROXID_1PS00460 Glutathione peroxidases active site.GPX1_SCHMA31-46  1A:31-46
2GLUTATHIONE_PEROXID_2PS00763 Glutathione peroxidases signature 2.GPX1_SCHMA68-75  1A:68-75

(-) Exons   (0, 0)

(no "Exon" information available for 2WGR)

(-) 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:163
 aligned with GPX1_SCHMA | Q00277 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:163
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166   
           GPX1_SCHMA     7 SWNSIYEFTVKDINGVDVSLEKYRGHVCLIVNVACKUGATDKNYRQLQEMHTRLVGKGLRILAFPCNQFGGQEPWAEAEIKKFVTEKYGVQFDMFSKIKVNGSDADDLYKFLKSRQHGTLTNNIKWNFSKFLVDRQGQPVKRYSPTTAPYDIEGDIMELLEKK 169
               SCOP domains d2wgra_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----GSHPx-2wgrA01 A:11-119                                                                                       -------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eee.....eee.hhhh..eeeeeee.....hhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhh...ee...........hhhhhhhhhhh.............eeee.....eeeee....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------GLUTATHIONE_PERO---------------------GLUTATHI---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wgr A   7 SWNSIYEFTVKDINGVDVSLEKYRGHVCLIVNVACKSGATDKNYRQLQEMHTRLVGKGLRILAFPCNQFGGQEPWAEAEIKKFVTEKYGVQFDMFSKIKVNGSDADDLYKFLKSRQHGTLTNNIKWNFSKFLVDRQGQPVKRYSPTTAPYDIEGDIMELLEKK 169
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166
   Legend:   → Mismatch (orange background)
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GPX1_SCHMA | Q00277)
molecular function
    GO:0004602    glutathione peroxidase activity    Catalysis of the reaction: 2 glutathione + hydrogen peroxide = oxidized glutathione + 2 H2O.
    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:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
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:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.

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  2wgr
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  GPX1_SCHMA | Q00277
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 Related Entries

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

UniProtKB/Swiss-Prot
        GPX1_SCHMA | Q00277: 2v1m

(-) Related Entries Specified in the PDB File

2v1m CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI GLUTATHIONE PEROXIDASE