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 ARTHROBACTER SP. STRAIN SU 4-HYDROXYBENZOYL COA THIOESTERASE MUTANT T77A COMPLEXED WITH 4-HYDROXYPHENACYL COA
 
Authors :  H. M. Holden, J. B. Thoden, F. Song, Z. Zhuang, M. Trujillo, D. Dunaway-M
Date :  15 Mar 11  (Deposition) - 28 Mar 12  (Release) - 19 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Thioesterase, Hotdog-Fold, Hydrolase, 4-Hydroxybenzoyl-Coa (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Song, J. B. Thoden, Z. Zhuang, J. Latham, M. Trujillo, H. M. Holden, D. Dunaway-Mariano
The Catalytic Mechanism Of The Hotdog-Fold Enzyme Superfamily 4-Hydroxybenzoyl-Coa Thioesterase From Arthrobacter Sp. Strain Su.
Biochemistry V. 51 7000 2012
PubMed-ID: 22873756  |  Reference-DOI: 10.1021/BI301059M

(-) Compounds

Molecule 1 - 4-HYDROXYBENZOYL-COA THIOESTERASE
    Chains: A, B
    EC Number: 3.1.2.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: FCBC, FCBC1
    Mutation: YES
    Organism Scientific: ARTHROBACTER SP.
    Organism Taxid: 1667
    Synonym: 4-HBA-COA THIOESTERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
14CO2Ligand/Ion4-HYDROXYPHENACYL COENZYME A
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
14CO4Ligand/Ion4-HYDROXYPHENACYL COENZYME A

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:15 , GLU A:73 , MET A:74 , ALA A:77 , GLU A:78 , MET A:90 , GLY A:93 , HIS A:117 , GLY A:119 , SER A:120 , THR A:121 , THR A:122 , ARG A:147 , PRO A:148 , ARG A:150 , HOH A:513 , HOH A:519 , HOH A:654 , HOH A:947 , GLN B:58 , VAL B:63 , HIS B:64 , GLY B:65 , PHE B:100 , PHE B:101 , ARG B:102 , PRO B:103 , HOH B:500BINDING SITE FOR RESIDUE 4CO A 152
2AC2SOFTWAREGLN A:58 , VAL A:63 , HIS A:64 , GLY A:65 , PHE A:100 , PHE A:101 , ARG A:102 , PRO A:103 , HOH A:503 , HOH A:509 , LEU B:15 , GLU B:73 , MET B:74 , ALA B:77 , GLU B:78 , MET B:90 , VAL B:92 , GLY B:93 , HIS B:117 , GLY B:119 , SER B:120 , THR B:121 , THR B:122 , ARG B:147 , PRO B:148 , ARG B:150 , HOH B:516 , HOH B:560 , HOH B:624 , HOH B:683 , HOH B:689 , HOH B:699 , HOH B:997BINDING SITE FOR RESIDUE 4CO B 152

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R3F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3R3F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R3F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R3F)

(-) Exons   (0, 0)

(no "Exon" information available for 3R3F)

(-) 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:140
 aligned with 4HBT_ARTSP | Q04416 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:140
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151
           4HBT_ARTSP    12 GGNLPDVASHYPVAYEQTLDGTVGFVIDEMTPERATASVEVTDTLRQRWGLVHGGAYCALAEMLATEATVAVVHEKGMMAVGQSNHTSFFRPVKEGHVRAEAVRIHAGSTTWFWDVSLRDDAGRLCAVSSMSIAVRPRRD 151
               SCOP domains d3r3fa_ A: automated matches                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhh.eeeee...eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r3f A  12 GGNLPDVASHYPVAYEQTLDGTVGFVIDEMTPERATASVEVTDTLRQRWGLVHGGAYCALAEMLAAEATVAVVHEKGMMAVGQSNHTSFFRPVKEGHVRAEAVRIHAGSTTWFWDVSLRDDAGRLCAVSSMSIAVRPRRD 151
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151


Chain B from PDB  Type:PROTEIN  Length:140
 aligned with 4HBT_ARTSP | Q04416 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:140
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151
           4HBT_ARTSP    12 GGNLPDVASHYPVAYEQTLDGTVGFVIDEMTPERATASVEVTDTLRQRWGLVHGGAYCALAEMLATEATVAVVHEKGMMAVGQSNHTSFFRPVKEGHVRAEAVRIHAGSTTWFWDVSLRDDAGRLCAVSSMSIAVRPRRD 151
               SCOP domains d3r3fb_ B: automated matches                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhh.eeeee...eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r3f B  12 GGNLPDVASHYPVAYEQTLDGTVGFVIDEMTPERATASVEVTDTLRQRWGLVHGGAYCALAEMLAAEATVAVVHEKGMMAVGQSNHTSFFRPVKEGHVRAEAVRIHAGSTTWFWDVSLRDDAGRLCAVSSMSIAVRPRRD 151
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R3F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3R3F)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (4HBT_ARTSP | Q04416)
molecular function
    GO:0018739    4-hydroxybenzoyl-CoA thioesterase activity    Catalysis of the reaction: 4-hydroxybenzoyl-CoA + H(2)O = 4-hydroxybenzoate + CoA + H(+).
    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
    4CO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3r3f)
 
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
  3r3f
    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
  4HBT_ARTSP | Q04416
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.2.23
    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
  4HBT_ARTSP | Q04416
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        4HBT_ARTSP | Q04416: 1q4s 1q4t 1q4u 3r32 3r34 3r35 3r36 3r37 3r3a 3r3b 3r3c 3r3d 3tea

(-) Related Entries Specified in the PDB File

3r32 E73A MUTANT IN COMPLEX WITH 4-HYDROXYPHENACYL COA
3r34 E73D MUTANT IN COMPLEX WITH COENZYME A
3r35 E73D MUTANT IN COMPLEX WITH 4-HYDROXYPHENACYL COA
3r36 E73Q MUTANT IN COMPLEX WITH 4-HYDROXYBENZOIC ACID
3r37 E73Q MUTANT IN COMPLEX WITH 4-HYDROXYPHENACYL COA
3r3a Q58A MUTANT IN COMPLEX WITH 4-HYDROXYBENZOIC ACID AND COA
3r3b Q58A MUTANT IN COMPLEX WITH 4-HYDROXYPHENACYL COA
3r3c H64A MUTANT IN COMPLEX WITH 4-HYDROXYPHENACYL COA
3r3d T77S MUTANT IN COMPLEX WITH 4-HYDROXYPHENACYL COA