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(-) Description

Title :  CRYSTAL STRUCTURE OF YHI9, THE YEAST MEMBER OF THE PHENAZINE BIOSYNTHESIS PHZF ENZYME SUPERFAMILY.
 
Authors :  D. Liger, S. Quevillon-Cheruel, I. Sorel, M. Bremang, K. Blondeau, I. Aboulfath, J. Janin, H. Van Tilbeurgh, N. Leulliot, Paris-Sud Yeast Structural Genomics (Ysg)
Date :  20 Jan 05  (Deposition) - 02 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Phzf Enzyme Superfamily, Double Hot-Dog, Structural Genomics, Paris-Sud Yeast Structural Genomics, Ysg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Liger, S. Quevillon-Cheruel, I. Sorel, M. Bremang, K. Blondeau, I. Aboulfath, J. Janin, H. Van Tilbeurgh, N. Leulliot
Crystal Structure Of Yhi9, The Yeast Member Of The Phenazine Biosynthesis Phzf Enzyme Superfamily
Proteins V. 60 778 2005
PubMed-ID: 16021630  |  Reference-DOI: 10.1002/PROT.20548
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL 32.6 KDA PROTEIN IN DAP2-SLT2 INTERGENIC REGION
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET9
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: YHI9

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1YM5)

(-) Sites  (0, 0)

(no "Site" information available for 1YM5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YM5)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YM5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YM5)

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YHR029C1YHR029C.1VIII:168554-167670885YHI9_YEAST1-2942941A:2-294293

(-) 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:294
 aligned with YHI9_YEAST | P38765 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:294
                                                                                                                                                                                                                                                                                                                              294 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291  | 
           YHI9_YEAST     2 TLMVPFKQVDVFTEKPFMGNPVAVINFLEIDENEVSQEELQAIANWTNLSETTFLFKPSDKKYDYKLRIFTPRSELPFAGHPTIGSCKAFLEFTKNTTATSLVQECKIGAVPITINEGLISFKAPMADYESISSEMIADYEKAIGLKFIKPPALLHTGPEWIVALVEDAETCFNANPNFAMLAHQTKQNDHVGIILAGPKKEAAIKNSYEMRAFAPVINVYEDPVCGSGSVALARYLQEVYKFEKTTDITISEGGRLKRNGLMLASIKKEADNSTSYYIAGHATTVIDGKIKV-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1ym5A01 A:2-125,A:284-295 Diaminopimelate Epimerase; Chain A, domain 1                                                      --------------------------------------------------------------------------------------------------------------------------------------------------------------1ym5A01      CATH domains
               Pfam domains --------PhzC-PhzF-1ym5A01 A:10-290                                                                                                                                                                                                                                                               ----- Pfam domains
         Sec.struct. author .eeeeeeeeee........eeeeeee....hhhhhhhhhhhhhhhhhh...eeeee........eeeeee....ee..hhhhhhhhhhhhhhhh......eeeeee..eeeeeeee..eeeee....eeee.hhhhhhhhhhhhh.......eeee...eeeeee..hhhhhhhh..hhhhhhhhhhhhh..eeeeeee........eeeeeeeehhhheeee..hhhhhhhhhhhhhhhhh....eeeeeee.hhhh..eeeeeeeee.....eeeeeee.eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-294 UniProt: 1-294 [INCOMPLETE]                                                                                                                                                                                                                                                   - Transcript 1
                 1ym5 A   2 TLMVPFKQVDVFTEKPFMGNPVAVINFLEIDENEVSQEELQAIANWTNLSETTFLFKPSDKKYDYKLRIFTPRSELPFAGHPTIGSCKAFLEFTKNTTATSLVQECKIGAVPITINEGLISFKAPMADYESISSEMIADYEKAIGLKFIKPPALLHTGPEWIVALVEDAETCFNANPNFAMLAHQTKQNDHVGIILAGPKKEAAIKNSYEMRAFAPVINVYEDPVCGSGSVALARYLQEVYKFEKTTDITISEGGRLKRNGLMLASIKKEADNSTSYYIAGHATTVIDGKIKVH 295
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
   Legend:   → Mismatch (orange background)
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  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 1YM5)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: DAP_epimerase (14)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (YHI9_YEAST | P38765)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0030968    endoplasmic reticulum unfolded protein response    The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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 Related Entries

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