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(-) Description

Title :  CRYSTAL STRUCTURE OF GRX1 IN GLUTATHIONYLATED FORM
 
Authors :  J. Yu, C. Z. Zhou
Date :  24 Jan 08  (Deposition) - 09 Dec 08  (Release) - 09 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Glutathionylated Form, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Yu, N. N. Zhang, P. D. Yin, P. X. Cui, C. Z. Zhou
Glutathionylation-Triggered Conformational Changes Of Glutaredoxin Grx1 From The Yeast Saccharomyces Cerevisiae.
Proteins V. 72 1077 2008
PubMed-ID: 18473363  |  Reference-DOI: 10.1002/PROT.22096
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAREDOXIN-1
    Chains: A
    EC Number: 1.20.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GRX1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Strain: S288C
    Synonym: GLUTATHIONE-DEPENDENT OXIDOREDUCTASE 1

 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
1GSH1Ligand/IonGLUTATHIONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:24 , TYR A:26 , CYS A:27 , TYR A:29 , GLN A:63 , THR A:74 , PRO A:76 , GLY A:87 , ASN A:88 , ASP A:89 , HOH A:2013 , HOH A:2019 , HOH A:2036 , HOH A:2037 , HOH A:2039 , HOH A:2041BINDING SITE FOR RESIDUE GSH A 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C1S)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:75 -Pro A:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C1S)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTAREDOXIN_2PS51354 Glutaredoxin domain profile.GLRX1_YEAST7-110  1A:7-108
2GLUTAREDOXIN_1PS00195 Glutaredoxin active site.GLRX1_YEAST21-37  1A:21-37

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YCL035C1YCL035C.1III:61173-60841333GLRX1_YEAST1-1101101A:2-108107

(-) 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:107
 aligned with GLRX1_YEAST | P25373 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:107
                                    11        21        31        41        51        61        71        81        91       101       
          GLRX1_YEAST     2 VSQETIKHVKDLIAENEIFVASKTYCPYCHAALNTLFEKLKVPRSKVLVLQLNDMKEGADIQAALYEINGQRTVPNIYINGKHIGGNDDLQELRETGELEELLEPIL 108
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh....hhh.eeeee.hhh.hhhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhh.hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----GLUTAREDOXIN_2  PDB: A:7-108 UniProt: 7-110                                                            PROSITE (1)
                PROSITE (2) -------------------GLUTAREDOXIN_1   ----------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:2-108 UniProt: 1-110 [INCOMPLETE]                                                          Transcript 1
                 3c1s A   2 VSQETIKHVKDLIAENEIFVASKTYCPYCHAALNTLFEKLKVPRSKVLVLQLNDMKEGADIQAALYEINGQRTVPNIYINGKHIGGNDDLQELRETGELEELLEPIL 108
                                    11        21        31        41        51        61        71        81        91       101
   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  (0, 0)

(no "SCOP Domain" information available for 3C1S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3C1S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C1S)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GLRX1_YEAST | P25373)
molecular function
    GO:0015036    disulfide oxidoreductase activity    Catalysis of the reaction: substrate with reduced sulfide groups = substrate with oxidized disulfide bonds.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0004602    glutathione peroxidase activity    Catalysis of the reaction: 2 glutathione + hydrogen peroxide = oxidized glutathione + 2 H2O.
    GO:0004364    glutathione transferase activity    Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group.
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    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:0034599    cellular response to oxidative stress    Any process that results in a change in state or activity of a cell (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: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:0010731    protein glutathionylation    The protein modification process in which a glutathione molecule is added to a protein amino acid through a disulfide linkage.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLRX1_YEAST | P25373: 2jac 2jad 3c1r

(-) Related Entries Specified in the PDB File

3c1r