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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NITROGEN REGULATION FRAGMENT OF THE YEAST PRION PROTEIN URE2P
 
Authors :  T. C. Umland, K. L. Taylor, S. Rhee, R. B. Wickner, D. R. Davies
Date :  18 Dec 00  (Deposition) - 14 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glutathione S-Transferase Superfamily Fold, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. C. Umland, K. L. Taylor, S. Rhee, R. B. Wickner, D. R. Davies
The Crystal Structure Of The Nitrogen Regulation Fragment Of The Yeast Prion Protein Ure2P.
Proc. Natl. Acad. Sci. Usa V. 98 1459 2001
PubMed-ID: 11171973  |  Reference-DOI: 10.1073/PNAS.041607898
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URE2 PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPFLAG
    Expression System StrainB834(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentNITROGEN REGULATION FRAGMENT
    GeneURE2
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1HQO)

(-) SS Bonds  (0, 0)

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

(-) 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 1HQO)

(-) 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:205-354

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNL229C1YNL229C.1XIV:220202-2191381065URE2_YEAST1-3543542A:106-354 (gaps)
B:110-354 (gaps)
249
245

(-) 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:227
 aligned with URE2_YEAST | P23202 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:249
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345         
           URE2_YEAST   106 FQEQPLEGYTLFSHRSAPNGFKVAIVLSELGFHYNTIFLDFNLGEHRAPEFVSVNPNARVPALIDHGMDNLSIWESGAILLHLVNKYYKETGNPLLWSDDLADQSQINAWLFFQTSGHAPMIGQALHFRYFHSQKIASAVERYTDEVRRVYGVVEMALAERREALVMELDTENAAAYSAGTTPMSQSRFFDYPVWLVGDKLTIADLAFVPWNNVVDRIGINIKIEFPEVYKWTKHMMRRPAVIKALRGE 354
               SCOP domains d1hqoa2 A:106-200 Yeast prion protein ure2p, nitrogen regulation fragment                      d1hqoa1 A:201-354 Yeast prion protein ure2p, nitrogen regulation fragmen                      t                                                            SCOP domains
               CATH domains 1hqoA01 A:106-196 Glutaredoxin                                                             1hqoA02 A:197-349  [code=1.20.1050.10, no name defined]                                                                                                  ----- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhhh..eeeee.........hhhhhhhh......eeee.hhh.eee.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...----------------------............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:106-354 (gaps) UniProt: 1-354 [INCOMPLETE]                                                                                                                                                                                               Transcript 1
                 1hqo A 106 FQEQPLEGYTLFSHRSAPNGFKVAIVLSELGFHYNTIFLDFNLGEHRAPEFVSVNPNARVPALIDHGmDNLSIWESGAILLHLVNKYYKETGNPLLWSDDLADQSQINAWLFFQTSGHAPmIGQALHFRYFHSQKIASAVERYTDEVRRVYGVVEmALAERREALVm----------------------FDYPVWLVGDKLTIADLAFVPWNNVVDRIGINIKIEFPEVYKWTKHmmRRPAVIKALRGE 354
                                   115       125       135       145       155       165       175       185       195       205       215       225|      235       245       255     | 265      |  -         -       295       305       315       325       335     ||345         
                                                                                             173-MSE                                              226-MSE                            261-MSE    272-MSE                295                                           341-MSE         
                                                                                                                                                                                                                                                                      342-MSE        

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

    Alignment length:245
                                   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   110 PLEGYTLFSHRSAPNGFKVAIVLSELGFHYNTIFLDFNLGEHRAPEFVSVNPNARVPALIDHGMDNLSIWESGAILLHLVNKYYKETGNPLLWSDDLADQSQINAWLFFQTSGHAPMIGQALHFRYFHSQKIASAVERYTDEVRRVYGVVEMALAERREALVMELDTENAAAYSAGTTPMSQSRFFDYPVWLVGDKLTIADLAFVPWNNVVDRIGINIKIEFPEVYKWTKHMMRRPAVIKALRGE 354
               SCOP domains d1hqob2 B:110-200 Yeast prion protein ure2p, nitrogen regulation fragment                  d1hqob1 B:201-354 Yeast prion protein ure2p, nitrogen regulation fragmen                      t                                                            SCOP domains
               CATH domains 1hqoB01 B:110-196 Glutaredoxin                                                         1hqoB02 B:197-349  [code=1.20.1050.10, no name defined]                                                                                                  ----- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhhhhhhhh..eeee............hhhhhh......eeee.hhh.eee.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...----------------------............hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GST_NTER  PDB: B:112-196 UniProt: 112-196                                            --------GST_CTER  PDB: B:205-354 UniProt: 205-354                                                                                                              PROSITE
               Transcript 1 Exon 1.1  PDB: B:110-354 (gaps) UniProt: 1-354 [INCOMPLETE]                                                                                                                                                                                           Transcript 1
                 1hqo B 110 PLEGYTLFSHRSAPNGFKVAIVLSELGFHYNTIFLDFNLGEHRAPEFVSVNPNARVPALIDHGmDNLSIWESGAILLHLVNKYYKETGNPLLWSDDLADQSQINAWLFFQTSGHAPmIGQALHFRYFHSQKIASAVERYTDEVRRVYGVVEmALAERREALVm----------------------FDYPVWLVGDKLTIADLAFVPWNNVVDRIGINIKIEFPEVYKWTKHmmRRPAVIKALRGE 354
                                   119       129       139       149       159       169   |   179       189       199       209       219      |229       239       249       259 |     269  |      -         -     | 299       309       319       329       339 ||    349     
                                                                                         173-MSE                                              226-MSE                            261-MSE    272-MSE                295                                           341-MSE         
                                                                                                                                                                                                                                                                  342-MSE        

   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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HQO)

(-) 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 | P232021g6w 1g6y 1jzr 1k0a 1k0b 1k0c 1k0d

(-) Related Entries Specified in the PDB File

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