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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST MONOTHIOL GLUTAREDOXIN GRX6
 
Authors :  M. Luo, Y. -L. Jiang, X. -X. Ma, Y. -X. He, Y. -J. Tang, J. Yu, R. -G. Zhang, Y Z. Zhou
Date :  21 Dec 09  (Deposition) - 07 Apr 10  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  C-Terminal Domain Of Grx6, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Luo, Y. -L. Jiang, X. -X. Ma, Y. -J. Tang, Y. -X. He, J. Yu, R. -G. Zhang, Y. Chen, C. -Z. Zhou
Structural And Biochemical Characterization Of Yeast Monothiol Glutaredoxin Grx6
J. Mol. Biol. V. 398 614 2010
PubMed-ID: 20347849  |  Reference-DOI: 10.1016/J.JMB.2010.03.029

(-) Compounds

Molecule 1 - MONOTHIOL GLUTAREDOXIN-6
    ChainsA
    EC Number1.8.1.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System StrainROSETTA (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentGRX6 C-TERMINAL GRX DOMAIN, UNP RESIDUES 113-231
    GeneGRX6, YDL010W, D2890
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainS288C
    SynonymMONOTHIOL GLUTAREDOXIN GRX6

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GSH1Ligand/IonGLUTATHIONE
2MSE1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:8 , LYS A:133 , CYS A:136 , TYR A:138 , GLN A:171 , THR A:182 , VAL A:183 , PRO A:184 , GLY A:195 , ASN A:196 , GLU A:197 , HOH A:252 , HOH A:256 , HOH A:277 , HOH A:313 , HOH A:322 , HOH A:326BINDING SITE FOR RESIDUE GSH A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L4N)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:153 -Pro A:154
2Val A:183 -Pro A:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L4N)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTAREDOXIN_2PS51354 Glutaredoxin domain profile.GLRX6_YEAST116-219  1A:116-219

(-) Exons   (0, 0)

(no "Exon" information available for 3L4N)

(-) 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    
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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:113
 aligned with GLRX6_YEAST | Q12438 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:113
                                   122       132       142       152       162       172       182       192       202       212       222   
          GLRX6_YEAST   113 FNVQKEYSLILDLSPIIIFSKSTCSYSKGMKELLENEYQFIPNYYIIELDKHGHGEELQEYIKLVTGRGTVPNLLVNGVSRGGNEEIKKLHTQGKLLESLQVWSDGKFSVEQR 225
               SCOP domains d3l4na_ A: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------Glutaredoxin-3l4nA01 A:128-193                                    -------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eeeee...hhhhhhhhhhhhhheeee...eeee.hhh.hhhhhhhhhhhhhh.....eeee..ee..hhhhhhhhhhh.hhhhhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---GLUTAREDOXIN_2  PDB: A:116-219 UniProt: 116-219                                                         ------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3l4n A 113 FNVQKEYSLILDLSPIIIFSKSTCSYSKGmKELLENEYQFIPNYYIIELDKHGHGEELQEYIKLVTGRGTVPNLLVNGVSRGGNEEIKKLHTQGKLLESLQVWSDGKFSVEQR 225
                                   122       132       142       152       162       172       182       192       202       212       222   
                                                       142-MSE                                                                               

   Legend:   → Mismatch (orange background)
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  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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L4N)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GLRX6_YEAST | Q12438)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    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:0004362    glutathione-disulfide reductase activity    Catalysis of the reaction: 2 glutathione + NADP+ = glutathione disulfide + NADPH + H+.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
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.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0005801    cis-Golgi network    The network of interconnected tubular and cisternal structures located at the convex side of the Golgi apparatus, which abuts the endoplasmic reticulum.
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0000324    fungal-type vacuole    A vacuole that has both lytic and storage functions. The fungal vacuole is a large, membrane-bounded organelle that functions as a reservoir for the storage of small molecules (including polyphosphate, amino acids, several divalent cations (e.g. calcium), other ions, and other small molecules) as well as being the primary compartment for degradation. It is an acidic compartment, containing an ensemble of acid hydrolases. At least in S. cerevisiae, there are indications that the morphology of the vacuole is variable and correlated with the cell cycle, with logarithmically growing cells having a multilobed, reticulated vacuole, while stationary phase cells contain a single large structure.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLRX6_YEAST | Q124385j3r

(-) Related Entries Specified in the PDB File

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