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(-) Description

Title :  URE2P IN COMPLEX WITH S-HEXYLGLUTATHIONE
 
Authors :  L. Bousset, H. Belrhali, R. Melki, S. Morera
Date :  19 Sep 01  (Deposition) - 21 Dec 01  (Release) - 21 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nitrate Assimilation, Structural Genomics, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Bousset, H. Belrhali, R. Melki, S. Morera
Crystal Structures Of The Yeast Prion Ure2P Functional Region In Complex With Glutathione And Related Compounds.
Biochemistry V. 40 13564 2001
PubMed-ID: 11695904  |  Reference-DOI: 10.1021/BI011007B
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URE2 PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GSH1Ligand/IonGLUTATHIONE
2GTX1Ligand/IonS-HEXYLGLUTATHIONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:6 , HOH A:9 , HOH A:12 , HOH A:27 , HOH A:62 , ALA A:122 , PRO A:123 , ASN A:124 , PHE A:146 , ARG A:164 , VAL A:165 , PRO A:166 , GLU A:180 , SER A:181 , LEU A:231 , SER B:221BINDING SITE FOR RESIDUE GTX A 355
2AC2SOFTWARESER A:221 , HOH B:7 , HOH B:13 , HOH B:26 , ALA B:122 , ASN B:124 , PHE B:146 , ARG B:164 , VAL B:165 , GLU B:180 , SER B:181BINDING SITE FOR RESIDUE GSH B 356

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K0A)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:165 -Pro A:166
2Val B:165 -Pro B:166

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K0A)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GST_NTERPS50404 Soluble glutathione S-transferase N-terminal domain profile.URE2_YEAST112-196
 		  2A:112-196
B:112-196
2GST_CTERPS50405 Soluble glutathione S-transferase C-terminal domain profile.URE2_YEAST205-354
 		  2A:205-354
B:205-352

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNL229C1YNL229C.1XIV:220202-2191381065URE2_YEAST1-3543542A:100-354 (gaps)
B:109-352 (gaps)		255
244

(-) 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:234
 aligned with URE2_YEAST | P23202 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:255
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349     
           URE2_YEAST   100 SRITKFFQEQPLEGYTLFSHRSAPNGFKVAIVLSELGFHYNTIFLDFNLGEHRAPEFVSVNPNARVPALIDHGMDNLSIWESGAILLHLVNKYYKETGNPLLWSDDLADQSQINAWLFFQTSGHAPMIGQALHFRYFHSQKIASAVERYTDEVRRVYGVVEMALAERREALVMELDTENAAAYSAGTTPMSQSRFFDYPVWLVGDKLTIADLAFVPWNNVVDRIGINIKIEFPEVYKWTKHMMRRPAVIKALRGE 354
               SCOP domains d1k0aa2 A:100-200 Yeast prion protein ure2p, nitrogen regulation fragment                            d1k0aa1 A:201-354 Yeast prion protein ure2p, nitrogen regulation fragment                                                                                  SCOP domains
               CATH domains 1k0aA01 A:100-196 Glutaredoxin                                                                   1k0aA02 A:197-352  [code=1.20.1050.10, no name defined]                                                                                                     -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.......eeeee...hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh......eeee.hhh.eeeehhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.---------------------............hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------GST_NTER  PDB: A:112-196 UniProt: 112-196                                            --------GST_CTER  PDB: A:205-354 UniProt: 205-354                                                                                                              PROSITE
               Transcript 1 Exon 1.1  PDB: A:100-354 (gaps) UniProt: 1-354 [INCOMPLETE]                                                                                                                                                                                                     Transcript 1
                 1k0a A 100 SRITKFFQEQPLEGYTLFSHRSAPNGFKVAIVLSELGFHYNTIFLDFNLGEHRAPEFVSVNPNARVPALIDHGMDNLSIWESGAILLHLVNKYYKETGNPLLWSDDLADQSQINAWLFFQTSGHAPMIGQALHFRYFHSQKIASAVERYTDEVRRVYGVVEMALAERREALVME---------------------FDYPVWLVGDKLTIADLAFVPWNNVVDRIGINIKIEFPEVYKWTKHMMRRPAVIKALRGE 354
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269   |     -         -     | 299       309       319       329       339       349     
                                                                                                                                                                                                       273                   295                                                           


Chain B from PDB  Type:PROTEIN  Length:223
 aligned with URE2_YEAST | P23202 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:244
                                   118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348    
           URE2_YEAST   109 QPLEGYTLFSHRSAPNGFKVAIVLSELGFHYNTIFLDFNLGEHRAPEFVSVNPNARVPALIDHGMDNLSIWESGAILLHLVNKYYKETGNPLLWSDDLADQSQINAWLFFQTSGHAPMIGQALHFRYFHSQKIASAVERYTDEVRRVYGVVEMALAERREALVMELDTENAAAYSAGTTPMSQSRFFDYPVWLVGDKLTIADLAFVPWNNVVDRIGINIKIEFPEVYKWTKHMMRRPAVIKALR 352
               SCOP domains d1k0ab2 B:109-200 Yeast prion protein ure2p, nitrogen regulation fragment                   d1k0ab1 B:201-352 Yeast prion protein ure2p, nitrogen regulation fragment                                                                                SCOP domains
               CATH domains 1k0aB01 B:109-196 Glutaredoxin                                                          1k0aB02 B:197-351  [code=1.20.1050.10, no name defined]                                                                                                    - CATH domains
           Pfam domains (1) ---GST_N-1k0aB03 B:112-190                                                        --------------------------------GST_C-1k0aB01 B:223-345                                                                                                    ------- Pfam domains (1)
           Pfam domains (2) ---GST_N-1k0aB04 B:112-190                                                        --------------------------------GST_C-1k0aB02 B:223-345                                                                                                    ------- Pfam domains (2)
         Sec.struct. author .....eeeee...hhhhhhhhhhhhhh...eeeee.........hhhhhh........eeee.hhh.eeeehhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh---------------------............hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---GST_NTER  PDB: B:112-196 UniProt: 112-196                                            --------GST_CTER  PDB: B:205-352 UniProt: 205-354                                                                                                            PROSITE
               Transcript 1 Exon 1.1  PDB: B:109-352 (gaps) UniProt: 1-354 [INCOMPLETE]                                                                                                                                                                                          Transcript 1
                 1k0a B 109 QPLEGYTLFSHRSAPNGFKVAIVLSELGFHYNTIFLDFNLGEHRAPEFVSVNPNARVPALIDHGMDNLSIWESGAILLHLVNKYYKETGNPLLWSDDLADQSQINAWLFFQTSGHAPMIGQALHFRYFHSQKIASAVERYTDEVRRVYGVVEMALAERREALVME---------------------FDYPVWLVGDKLTIADLAFVPWNNVVDRIGINIKIEFPEVYKWTKHMMRRPAVIKALR 352
                                   118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268    |    -         -      |298       308       318       328       338       348    
                                                                                                                                                                                              273                   295
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: GST_C (118)
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (URE2_YEAST | P23202)
molecular function
    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: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:0051219    phosphoprotein binding    Interacting selectively and non-covalently with a phosphorylated protein.
    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:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
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:0051220    cytoplasmic sequestering of protein    The selective interaction of a protein with specific molecules in the cytoplasm, thereby inhibiting its transport into other areas of the cell.
    GO:0042994    cytoplasmic sequestering of transcription factor    The selective interaction of a transcription factor with specific molecules in the cytoplasm, thereby inhibiting its translocation into the nucleus.
    GO:0006749    glutathione metabolic process    The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
    GO:1903507    negative regulation of nucleic acid-templated transcription    Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
    GO:0042128    nitrate assimilation    The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.
    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:0032447    protein urmylation    Covalent attachment of the ubiquitin-like protein URM1 to another protein.
    GO:0006808    regulation of nitrogen utilization    Any process that modulates the frequency, rate or extent of nitrogen utilization.
    GO:0010044    response to aluminum ion    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 an aluminum ion stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        URE2_YEAST | P23202: 1g6w 1g6y 1hqo 1jzr 1k0b 1k0c 1k0d

(-) Related Entries Specified in the PDB File

1g6w URE2P STRUCTURE
1jzr URE2P IN COMPLEX WITH GLUTATHIONE
1k0b URE2P IN COMPLEX WITH GLUTATHIONE
1k0c URE2P IN COMPLEX WITH S-P-NITROBENZYLGLUTATHIONE
1k0d URE2P IN COMPLEX WITH GLUTATHIONE