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(-) Description

Title :  THE CRYSTAL STRUCTURE OF YDCE, A 4-OXALOCROTONATE TAUTOMERASE HOMOLOGUE FROM ESCHERICHIA COLI, CONFIRMS THE STRUCTURAL BASIS FOR OLIGOMER DIVERSITY
 
Authors :  J. Almrud, A. Kern, S. Wang, R. Czerwinski, W. Johnson, A. Murzin, M. Hackert, C. Whitman
Date :  30 Apr 02  (Deposition) - 10 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tautomerase, Isomerase, Hypothetical Protein, Complete Proteo (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Almrud, A. Kern, S. Wang, R. Czerwinski, W. Johnson, A. Murzin, M. Hackert, C. Whitman
The Crystal Structure Of Ydce, A 4-Oxalocrotonate Tautomerase Homologue From Escherichia Coli, Confirms The Structural Basis For Oligomer Diversity
Biochemistry V. 41 12010 2002
PubMed-ID: 12356301  |  Reference-DOI: 10.1021/BI020271H

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YDCE
    Chains: A, B
    EC Number: 5.3.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A+
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Other Details: INACTIVATED BY HEPES AND BENZOIC ACID
    Strain: K12
    Synonym: YDCE, B1461

 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
1BEZ1Ligand/IonBENZOIC ACID
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:7 , PHE A:8 , ARG A:10 , TRP A:51 , TYR A:72 , HOH A:2149 , HOH A:2150 , PRO B:1 , SER B:38BINDING SITE FOR RESIDUE BEZ A1077
2AC2SOFTWAREPRO A:1 , SER A:38 , TYR A:72 , MET A:74 , CYS B:7 , PHE B:8 , ARG B:10 , TRP B:51 , TYR B:72 , HOH B:2151 , HOH B:2152 , HOH B:2153 , HOH B:2154BINDING SITE FOR RESIDUE EPE B1077

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GYX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GYX)

(-) 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:76
 aligned with PPTA_ECOLI | P31992 from UniProtKB/Swiss-Prot  Length:77

    Alignment length:76
                                    11        21        31        41        51        61        71      
            PPTA_ECOLI    2 PHIDIKCFPRELDEQQKAALAADITDVIIRHLNSKDSSISIALQQIQPESWQAIWDAEIAPQMEALIKKPGYSMNA 77
               SCOP domains d1gyxa_ A: 4-oxalocrotonate tautomerase homologue YdcE                       SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhhhhhhhh.hhhhheeeeee.hhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  1gyx A  1 PHIDIKCFPRELDEQQKAALAADITDVIIRHLNSKDSSISIALQQIQPESWQAIWDAEIAPQMEALIKKPGYSMNA 76
                                    10        20        30        40        50        60        70      


Chain B from PDB  Type:PROTEIN  Length:76
 aligned with PPTA_ECOLI | P31992 from UniProtKB/Swiss-Prot  Length:77

    Alignment length:76
                                    11        21        31        41        51        61        71      
            PPTA_ECOLI    2 PHIDIKCFPRELDEQQKAALAADITDVIIRHLNSKDSSISIALQQIQPESWQAIWDAEIAPQMEALIKKPGYSMNA 77
               SCOP domains d1gyxb_ B: 4-oxalocrotonate tautomerase homologue YdcE                       SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhhhhhhhh.hhhhheeeeee.hhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                  1gyx B  1 PHIDIKCFPRELDEQQKAALAADITDVIIRHLNSKDSSISIALQQIQPESWQAIWDAEIAPQMEALIKKPGYSMNA 76
                                    10        20        30        40        50        60        70
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PPTA_ECOLI | P31992)
molecular function
    GO:0016862    intramolecular oxidoreductase activity, interconverting keto- and enol-groups    Catalysis of an oxidation-reduction (redox) reaction in which the hydrogen donor and acceptor, which is a keto- or an enol-group, are the same molecule, and no oxidized product appears.
    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.
biological process
    GO:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PPTA_ECOLI | P31992: 1gyj 1gyy

(-) Related Entries Specified in the PDB File

1gyj THE CRYSTAL STRUCTURE OF YDCE, A 4- OXALOCROTONATE TAUTOMERASE HOMOLOGUE FROM ESCHERICHIA COLI, CONFIRMS THE STRUCTURAL BASIS FOR OLIGOMER DIVERSITY
1gyy THE CRYSTAL STRUCTURE OF YDCE, A 4- OXALOCROTONATE TAUTOMERASE HOMOLOGUE FROM ESCHERICHIA COLI, CONFIRMS THE STRUCTURAL BASIS FOR OLIGOMER DIVERSITY