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(-) Description

Title :  CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE YN9A PROTEIN, NEW YORK STRUCTURAL GENOMICS CONSORTIUM
 
Authors :  Y. Patskovsky, S. C. Almo, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  04 Jan 05  (Deposition) - 18 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aldose_1_epimerase, Sugar Metabolism, Predicted, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, S. C. Almo
Crystal Structure Of The Yeast Aldose_1_epimerase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL 37.9 KDA PROTEIN IN BIO3-HXT17 INTERGENIC REGION
    Chains: A, B
    EC Number: 5.1.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET
    Gene: YN9A
    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  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 1YGA)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:89 -B:295
2A:295 -B:89

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:64 -Arg A:65
2Thr A:236 -Pro A:237
3Gly B:64 -Arg B:65
4Thr B:236 -Pro B:237

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDOSE_1_EPIMERASEPS00545 Aldose 1-epimerase putative active site.YN9A_YEAST172-181
 		  2A:172-181
B:172-181

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNR071C1YNR071C.1XIV:771469-7704411029YN9A_YEAST1-3423422A:7-342
B:7-342		336
336

(-) 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:336
 aligned with YN9A_YEAST | P53757 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:336
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336      
           YN9A_YEAST     7 DNKYGVITIGDEKKFQATIAPLGATLVDLKVNGQSVVQGYSNVQDYLTDGNMMGATVGRYANRIAKGVFSLDDGPHKLTVNNCGNTNHSSISSLNLKQYKASPVENPSKGVYVVEFKLLDDHTQPNPNEFPGDLEVTVKYTLNVAEMTLDMEYQAQLVRGDATPINMTNHSYFNLNKVKSEKSIRGTEVKVCSNKSLEVTEGALLPTGKIIERNIATFDSTKPTVLHEDTPVFDCTFIIDANKDLKTTDSVSVNKLVPVFKAYHPESHIKFEVSTTEPTVHLYTGDNLCGKFVPRSGFAVQQGRYVDAINRDEWRGCVLLKRGEVYTSKTQYKFDI 342
               SCOP domains d1ygaa_ A: automated matches                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee...eeeeee....eeeeeee..ee......hhhhhh........ee.....ee...eeee..eeee........ee.hhhhhhhhh..ee...eeee..eeeeeeeeee............eeeeeeeeeee....eeeeeeeeeeee..eee...ee.................eeeee...eeeee......eeeeeee...........eee.......eeeee..................eeeeeee......eeeeee...eeeee...............eeeee...hhhhhhhhhh..eee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------ALDOSE_1_E----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:7-342 UniProt: 1-342 [INCOMPLETE]                                                                                                                                                                                                                                                                                               Transcript 1
                 1yga A   7 DNKYGVITIGDEKKFQATIAPLGATLVDLKVNGQSVVQGYSNVQDYLTDGNMMGATVGRYANRIAKGVFSLDDGPHKLTVNNCGNTNHSSISSLNLKQYKASPVENPSKGVYVVEFKLLDDHTQPNPNEFPGDLEVTVKYTLNVAEMTLDMEYQAQLVRGDATPINMTNHSYFNLNKVKSEKSIRGTEVKVCSNKSLEVTEGALLPTGKIIERNIATFDSTKPTVLHEDTPVFDCTFIIDANKDLKTTDSVSVNKLVPVFKAYHPESHIKFEVSTTEPTVHLYTGDNLCGKFVPRSGFAVQQGRYVDAINRDEWRGCVLLKRGEVYTSKTQYKFDI 342
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336      


Chain B from PDB  Type:PROTEIN  Length:336
 aligned with YN9A_YEAST | P53757 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:336
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336      
           YN9A_YEAST     7 DNKYGVITIGDEKKFQATIAPLGATLVDLKVNGQSVVQGYSNVQDYLTDGNMMGATVGRYANRIAKGVFSLDDGPHKLTVNNCGNTNHSSISSLNLKQYKASPVENPSKGVYVVEFKLLDDHTQPNPNEFPGDLEVTVKYTLNVAEMTLDMEYQAQLVRGDATPINMTNHSYFNLNKVKSEKSIRGTEVKVCSNKSLEVTEGALLPTGKIIERNIATFDSTKPTVLHEDTPVFDCTFIIDANKDLKTTDSVSVNKLVPVFKAYHPESHIKFEVSTTEPTVHLYTGDNLCGKFVPRSGFAVQQGRYVDAINRDEWRGCVLLKRGEVYTSKTQYKFDI 342
               SCOP domains d1ygab_ B: automated matches                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----Aldose_epim-1ygaB01 B:11-339                                                                                                                                                                                                                                                                                                             --- Pfam domains (1)
           Pfam domains (2) ----Aldose_epim-1ygaB02 B:11-339                                                                                                                                                                                                                                                                                                             --- Pfam domains (2)
         Sec.struct. author ......eeeee...eeeeee....eeeeeee..ee......hhhhhh........ee.....ee...eeee..eeee........ee.hhhhhhhhh..ee...eeee..eeeeeeeeee............eeeeeeeeeee....eeeeeeeeeeee..eee...ee......hhhhhh.....eeeee...eeeee......eeeeeee...........eee.......eeeee..........hhhhhh..eeeeeee......eeeeee...eeeee...............eeeee...hhhhhhhhhh..eee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------ALDOSE_1_E----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:7-342 UniProt: 1-342 [INCOMPLETE]                                                                                                                                                                                                                                                                                               Transcript 1
                 1yga B   7 DNKYGVITIGDEKKFQATIAPLGATLVDLKVNGQSVVQGYSNVQDYLTDGNMMGATVGRYANRIAKGVFSLDDGPHKLTVNNCGNTNHSSISSLNLKQYKASPVENPSKGVYVVEFKLLDDHTQPNPNEFPGDLEVTVKYTLNVAEMTLDMEYQAQLVRGDATPINMTNHSYFNLNKVKSEKSIRGTEVKVCSNKSLEVTEGALLPTGKIIERNIATFDSTKPTVLHEDTPVFDCTFIIDANKDLKTTDSVSVNKLVPVFKAYHPESHIKFEVSTTEPTVHLYTGDNLCGKFVPRSGFAVQQGRYVDAINRDEWRGCVLLKRGEVYTSKTQYKFDI 342
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YGA)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Gal_mutarotase (81)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (YN9A_YEAST | P53757)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    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:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
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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    Gly A:64 - Arg A:65   [ RasMol ]  
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