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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE PEROXIDASE 3 (SELENOCYSTEINE TO GLYCINE MUTANT)
 
Authors :  E. S. Pilka, K. Guo, O. Gileadi, A. Rojkowa, F. Von Delft, A. C. W. Pike, K. L. Kavanagh, C. Johannson, M. Sundstrom, C. H. Arrowsmith, J. Weige A. M. Edwards, U. Oppermann, Structural Genomics Consortium (Sgc
Date :  29 Aug 07  (Deposition) - 11 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Biol. Unit 3:  A (2x),B (2x)
Keywords :  Glutathione, Peroxidase, Plasma, Structural Genomics Consortium, Sgc, Oxidoreductase, Secreted, Selenium, Selenocysteine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. S. Pilka, K. Guo, O. Gileadi, A. Rojkowa, F. Von Delft, A. C. W. Pike, K. L. Kavanagh, C. Johannson, M. Sundstrom, C. H. Arrowsmith, J. Weigelt, A. M. Edwards, U. Oppermann
Crystal Structure Of Human Glutathione Peroxidase 3 (Selenocysteine To Glycine Mutant).
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUTATHIONE PEROXIDASE 3
    ChainsA, B
    EC Number1.11.1.9
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-CTHF
    Expression System StrainROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 25-223
    GeneGPX3, GPXP
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGSHPX-3, GPX-3, PLASMA GLUTATHIONE PEROXIDASE, GSHPX-P, EXTRACELLULAR GLUTATHIONE PEROXIDASE, GPX-P

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)A 
Biological Unit 2 (2x) B
Biological Unit 3 (2x)A (2x)B (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2NA2Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:73 , GLY A:74 , LEU A:75 , TRP A:181 , ASN A:182BINDING SITE FOR RESIDUE CL A 1
2AC2SOFTWAREGLY B:73 , GLY B:74 , LEU B:75 , TRP B:181 , ASN B:182BINDING SITE FOR RESIDUE CL B 2
3AC3SOFTWARESER A:166 , LEU A:169 , HOH A:300 , HOH A:412 , HOH A:413 , HOH A:417BINDING SITE FOR RESIDUE NA A 237
4AC4SOFTWARESER B:166 , LEU B:169 , HOH B:257 , HOH B:381 , HOH B:382 , HOH B:411BINDING SITE FOR RESIDUE NA B 237

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R37)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:123 -Pro A:124
2Glu A:172 -Pro A:173
3Arg B:123 -Pro B:124
4Glu B:172 -Pro B:173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020943F128LGPX3_HUMANPolymorphism8177445A/BF128L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020943F128LGPX3_HUMANPolymorphism8177445AF128L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020943F128LGPX3_HUMANPolymorphism8177445BF128L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020943F128LGPX3_HUMANPolymorphism8177445A/BF128L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTATHIONE_PEROXID_1PS00460 Glutathione peroxidases active site.GPX3_HUMAN61-76
 
  2A:61-76
B:61-76
2GLUTATHIONE_PEROXID_2PS00763 Glutathione peroxidases signature 2.GPX3_HUMAN97-104
 
  2A:97-104
B:97-104
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTATHIONE_PEROXID_1PS00460 Glutathione peroxidases active site.GPX3_HUMAN61-76
 
  2A:61-76
-
2GLUTATHIONE_PEROXID_2PS00763 Glutathione peroxidases signature 2.GPX3_HUMAN97-104
 
  2A:97-104
-
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTATHIONE_PEROXID_1PS00460 Glutathione peroxidases active site.GPX3_HUMAN61-76
 
  2-
B:61-76
2GLUTATHIONE_PEROXID_2PS00763 Glutathione peroxidases signature 2.GPX3_HUMAN97-104
 
  2-
B:97-104
Biological Unit 3 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTATHIONE_PEROXID_1PS00460 Glutathione peroxidases active site.GPX3_HUMAN61-76
 
  4A:61-76
B:61-76
2GLUTATHIONE_PEROXID_2PS00763 Glutathione peroxidases signature 2.GPX3_HUMAN97-104
 
  4A:97-104
B:97-104

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003888251aENSE00002107942chr5:150400124-150400302179GPX3_HUMAN1-29290--
1.4aENST000003888254aENSE00001504051chr5:150404901-150405054154GPX3_HUMAN30-81522A:38-81
B:36-81
44
46
1.5cENST000003888255cENSE00001504050chr5:150406461-150406578118GPX3_HUMAN81-120402A:81-120
B:81-120
40
40
1.6cENST000003888256cENSE00001702811chr5:150406993-150407092100GPX3_HUMAN120-153342A:120-153
B:120-153
34
34
1.7dENST000003888257dENSE00001504048chr5:150407470-1504085541085GPX3_HUMAN154-226732A:154-226
B:154-223
73
70

(-) 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:191
 aligned with GPX3_HUMAN | P22352 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:191
                                                                                                                                                                                                                      226  
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217        |- 
           GPX3_HUMAN    38 GTIYEYGALTIDGEEYIPFKQYAGKYVLFVNVASYUGLTGQYIELNALQEELAPFGLVILGFPCNQFGKQEPGENSEILPTLKYVRPGGGFVPNFQLFEKGDVNGEKEQKFYTFLKNSCPPTSELLGTSDRLFWEPMKVHDIRWNFEKFLVGPDGIPIMRWHHRTTVSNVKMDILSYMRRQAALGVKRK--   -
               SCOP domains d2r37a_ A: automated matches                                                                                                                                                                    SCOP domains
               CATH domains 2r37A00 A:38-228 Glutaredoxin                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.eee......eee.hhhh..eeeeeee.......hhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..........ee...........hhhhhhhhhhh........hhhhh...............eeee.....eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------L---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------GLUTATHIONE_PERO--------------------GLUTATHI---------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4a  PDB: A:38-81 UniProt: 30-81      --------------------------------------Exon 1.6c  PDB: A:120-153         Exon 1.7d  PDB: A:154-226 UniProt: 154-226                               -- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.5c  PDB: A:81-120 UniProt: 81-120------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2r37 A  38 GTIYEYGALTIDGEEYIPFKQYAGKYVLFVNVASYGGLTGQYIELNALQEELAPFGLVILGFPCNQFGKQEPGENSEILPTLKYVRPGGGFVPNFQLFEKGDVNGEKEQKFYTFLKNSCPPTSELLGTSDRLFWEPMKVHDIRWNFEKFLVGPDGIPIMRWHHRTTVSNVKMDILSYMRRQAALGVAENLY 228
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227 

Chain B from PDB  Type:PROTEIN  Length:188
 aligned with GPX3_HUMAN | P22352 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:188
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215        
           GPX3_HUMAN    36 ISGTIYEYGALTIDGEEYIPFKQYAGKYVLFVNVASYUGLTGQYIELNALQEELAPFGLVILGFPCNQFGKQEPGENSEILPTLKYVRPGGGFVPNFQLFEKGDVNGEKEQKFYTFLKNSCPPTSELLGTSDRLFWEPMKVHDIRWNFEKFLVGPDGIPIMRWHHRTTVSNVKMDILSYMRRQAALGV 223
               SCOP domains d2r37b_ B: automated matches                                                                                                                                                                 SCOP domains
               CATH domains 2r37B00 B:36-223 Glutaredoxin                                                                                                                                                                CATH domains
           Pfam domains (1) ----GSHPx-2r37B01 B:40-153                                                                                            ---------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----GSHPx-2r37B02 B:40-153                                                                                            ---------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhh.eee......eee.hhhh..eeeeeee.......hhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..........ee...........hhhhhhhhhhh........hhhhh...............eeee.....eeeee....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------L----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------GLUTATHIONE_PERO--------------------GLUTATHI----------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4a  PDB: B:36-81 UniProt: 30-81        --------------------------------------Exon 1.6c  PDB: B:120-153         Exon 1.7d  PDB: B:154-223 UniProt: 154-226 [INCOMPLETE]                Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.5c  PDB: B:81-120 UniProt: 81-120------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2r37 B  36 ISGTIYEYGALTIDGEEYIPFKQYAGKYVLFVNVASYGGLTGQYIELNALQEELAPFGLVILGFPCNQFGKQEPGENSEILPTLKYVRPGGGFVPNFQLFEKGDVNGEKEQKFYTFLKNSCPPTSELLGTSDRLFWEPMKVHDIRWNFEKFLVGPDGIPIMRWHHRTTVSNVKMDILSYMRRQAALGV 223
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215        

   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 Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GPX3_HUMAN | P22352)
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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008430    selenium binding    Interacting selectively and non-covalently with selenium (Se).
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
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:0042744    hydrogen peroxide catabolic process    The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
    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:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0006982    response to lipid hydroperoxide    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 a lipid hydroperoxide stimulus. Lipid hydroperoxide is the highly reactive primary oxygenated products of polyunsaturated fatty acids.
    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.
    GO:0000302    response to reactive oxygen species    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 a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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2i3y CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE PEROXIDASE 5