Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A META-CLEAVAGE PRODUCT HYDROLASE (CUMD) COMPLEXED WITH (S)-2-METHYLBUTYRATE
 
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 :  1.70
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: IPI140
    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, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SMB1Ligand/Ion2-METHYLBUTANOIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SMB2Ligand/Ion2-METHYLBUTANOIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:34 , ALA A:103 , PHE A:104 , TRP A:143 , HIS A:252 , HOH A:1341BINDING SITE FOR RESIDUE SMB A 1300

(-) SS Bonds  (0, 0)

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

(-) 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 1UKA)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UKA)

(-) 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 d1ukaa_ A: Meta-cleavage product hydrolase CumD                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1ukaA00 A:3-273  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------Abhydrolase_1-1ukaA01 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.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uka 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)
    → 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, 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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    SMB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:193 - Pro A:194   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1uka
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  P96965_PSEFL | P96965
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.7.1.9
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  P96965_PSEFL | P96965
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        P96965_PSEFL | P96965: 1iun 1iuo 1iup 1uk6 1uk7 1uk8 1uk9 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
1uk6 THE SAME PROTEIN COMPLEXED WITH PROPIONATE
1uk7 THE SAME PROTEIN COMPLEXED WITH N-BUTYRATE
1uk8 THE SAME PROTEIN COMPLEXED WITH N-VALERATE
1uk9 THE SAME PROTEIN COMPLEXED WITH ISOVALERATE
1ukb THE SAME PROTEIN COMPLEXED WITH BENZOATE