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(-) Description

Title :  CRYSTAL STRUCTURE OF A META-CLEAVAGE PRODUCT HYDROLASE (CUMD) COMPLEXED WITH PROPIONATE
 
Authors :  S. Fushinobu, S. -Y. Jun, M. Hidaka, H. Nojiri, H. Yamane, H. Shoun, T. Omori, T. Wakagi
Date :  19 Aug 03  (Deposition) - 14 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Aromatic Compounds, Cumene, Isopropylbenzene, Meta-Cleavage Compound Hydrolase, Polychlorinated Biphenyl Degradation, Pseudomonas Fluorescens Ip01, Alpha/Beta-Hydrolase, Substrate Specificity, Cumene Degradation, Pcb, Beta- Ketolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Fushinobu, S. -Y. Jun, M. Hidaka, H. Nojiri, H. Yamane, H. Shoun, T. Omori, T. Wakagi
A Series Of Crystal Structures Of A Meta-Cleavage Product Hydrolase From Pseudomonas Fluorescens Ip01 (Cumd) Complexed With Various Cleavage Products
Biosci. Biotechnol. Biochem. V. 69 491 2005
PubMed-ID: 15784976  |  Reference-DOI: 10.1271/BBB.69.491
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-HYDROXY-6-OXO-7-METHYLOCTA-2,4-DIENOATE HYDROLASE
    Chains: A
    EC Number: 3.7.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PIP140
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CUMD
    Mutation: YES
    Organism Scientific: PSEUDOMONAS FLUORESCENS
    Organism Taxid: 294
    Synonym: META-CLEAVAGE PRODUCT HYDROLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PPI2Ligand/IonPROPANOIC ACID
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1PPI4Ligand/IonPROPANOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:34 , ALA A:103 , PHE A:104 , LEU A:139 , HIS A:252BINDING SITE FOR RESIDUE PPI A 1300
2AC2SOFTWAREARG A:222 , GLY A:236 , ALA A:242 , LEU A:244 , VAL A:246 , PHE A:247 , GLY A:248 , HOH A:1314BINDING SITE FOR RESIDUE PPI A 1301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UK6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:193 -Pro A:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UK6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UK6)

(-) Exons   (0, 0)

(no "Exon" information available for 1UK6)

(-) 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:271
 aligned with P96965_PSEFL | P96965 from UniProtKB/TrEMBL  Length:282

    Alignment length:271
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272 
         P96965_PSEFL     3 NLEIGKSILAAGVLTNYHDVGEGQPVILIHGSGPGVSAYANWRLTIPALSKFYRVIAPDMVGFGFTDRPENYNYSKDSWVDHIIGIMDALEIEKAHIVGNSFGGGLAIATALRYSERVDRMVLMGAAGTRFDVTEGLNAVWGYTPSIENMRNLLDIFAYDRSLVTDELARLRYEASIQPGFQESFSSMFPEPRQRWIDALASSDEDIKTLPNETLIIHGREDQVVPLSSSLRLGELIDRAQLHVFGRCGHWTQIEQTDRFNRLVVEFFNEA 273
               SCOP domains d1uk6a_ A: Meta-cleavage product hydrolase CumD                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1uk6A00 A:3-273  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------Abhydrolase_1-1uk6A01 A:55-268                                                                                                                                                                                        ----- Pfam domains
         Sec.struct. author .....eeeee..eeeeeeee....eeeee.......hhhhhhh.hhhhhh...eeeee................hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee.........hhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhh.hhhhhh.....eeeeee......hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uk6 A   3 NLEIGKSILAAGVLTNYHDVGEGQPVILIHGSGPGVSAYANWRLTIPALSKFYRVIAPDMVGFGFTDRPENYNYSKDSWVDHIIGIMDALEIEKAHIVGNAFGGGLAIATALRYSERVDRMVLMGAAGTRFDVTEGLNAVWGYTPSIENMRNLLDIFAYDRSLVTDELARLRYEASIQPGFQESFSSMFPEPRQRWIDALASSDEDIKTLPNETLIIHGREDQVVPLSSSLRLGELIDRAQLHVFGRCGHWTQIEQTDRFNRLVVEFFNEA 273
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (P96965_PSEFL | P96965)
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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.

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  1uk6
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  P96965_PSEFL | P96965
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  3.7.1.9
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 Related Entries

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

UniProtKB/TrEMBL
        P96965_PSEFL | P96965: 1iun 1iuo 1iup 1uk7 1uk8 1uk9 1uka 1ukb 2d0d

(-) Related Entries Specified in the PDB File

1iun THE SAME PROTEIN WITH A HEXAGONAL SPACE GROUP
1iuo THE SAME PROTEIN COMPLEXED WITH ACETATE
1iup THE SAME PROTEIN COMPLEXED WITH ISOBUTYRATE
1uk7 THE SAME PROTEIN COMPLEXED WITH N-BUTYRATE
1uk8 THE SAME PROTEIN COMPLEXED WITH N-VALERATE
1uk9 THE SAME PROTEIN COMPLEXED WITH ISOVALERATE
1uka THE SAME PROTEIN COMPLEXED WITH (S)-2-METHYLBUTYRATE
1ukb THE SAME PROTEIN COMPLEXED WITH BENZOATE