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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE FLUOROACETATE DEHALOGENASE D104 MUTANT FROM BURKHOLDERIA SP. FA1 IN COMPLEX WITH FLUOROACETATE
 
Authors :  R. Omi, K. Hirotsu
Date :  19 Jun 11  (Deposition) - 20 Jun 12  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dehalogease, Fluoroacetate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nakayama, T. Kamachi, K. Jitsumori, R. Omi, K. Hirotsu, N. Esaki, T. Kurihara, K. Yoshizawa
Substrate Specificity Of Fluoroacetate Dehalogenase: An Insight From Crystallographic Analysis, Fluorescence Spectroscopy, And Theoretical Computations
Chemistry V. 18 8392 2012
PubMed-ID: 22674735  |  Reference-DOI: 10.1002/CHEM.201103369

(-) Compounds

Molecule 1 - FLUOROACETATE DEHALOGENASE
    Chains: A, B
    EC Number: 3.8.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FAC-DEX
    Mutation: YES
    Organism Scientific: BURKHOLDERIA SP.
    Organism Taxid: 36773
    Strain: FA1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1FAH3Ligand/IonFLUOROACETIC ACID
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:104 , ARG A:105 , ARG A:108 , ILE A:129 , HIS A:149 , TRP A:150 , TYR A:212 , HIS A:271 , HOH A:544BINDING SITE FOR RESIDUE FAH A 501
2AC2SOFTWARETYR A:77 , PHE A:79 , ASP A:211 , ASP A:219BINDING SITE FOR RESIDUE MG A 503
3AC3SOFTWAREALA B:104 , ARG B:105 , ARG B:108 , ILE B:129 , HIS B:149 , TRP B:150 , TYR B:212 , HIS B:271 , HOH B:440BINDING SITE FOR RESIDUE FAH B 501
4AC4SOFTWAREHIS B:111 , ASP B:223 , LEU B:227 , ARG B:258 , HOH B:358 , HOH B:459 , HOH B:496BINDING SITE FOR RESIDUE FAH B 502
5AC5SOFTWARETYR B:77 , PHE B:79 , ASP B:211 , ASP B:219BINDING SITE FOR RESIDUE MG B 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B12)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:34 -Pro A:35
2Ala A:157 -Pro A:158
3Phe B:34 -Pro B:35
4Ala B:157 -Pro B:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B12)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B12)

(-) Exons   (0, 0)

(no "Exon" information available for 3B12)

(-) 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:294
 aligned with DEHA_BURSP | Q1JU72 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:294
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290    
           DEHA_BURSP     1 MFEGFERRLVDVGDVTINCVVGGSGPALLLLHGFPQNLHMWARVAPLLANEYTVVCADLRGYGGSSKPVGAPDHANYSFRAMASDQRELMRTLGFERFHLVGHDRGGRTGHRMALDHPDSVLSLAVLDIIPTYVMFEEVDRFVARAYWHWYFLQQPAPYPEKVIGADPDTFYEGCLFGWGATGADGFDPEQLEEYRKQWRDPAAIHGSCCDYRAGGTIDFELDHGDLGRQVQCPALVFSGSAGLMHSLFEMQVVWAPRLANMRFASLPGGHFFVDRFPDDTARILREFLSDARS 294
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee....eeeeeeee...eeeee.....hhhhhhhhhhhhh...eeeee................hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee...hhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee..hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3b12 A   1 MFEGFERRLVDVGDVTINCVVGGSGPALLLLHGFPQNLHMWARVAPLLANEYTVVCADLRGYGGSSKPVGAPDHANYSFRAMASDQRELMRTLGFERFHLVGHARGGRTGHRMALDHPDSVLSLAVLDIIPTYVMFEEVDRFVARAYWHWYFLQQPAPYPEKVIGADPDTFYEGCLFGWGATGADGFDPEQLEEYRKQWRDPAAIHGSCCDYRAGGTIDFELDHGDLGRQVQCPALVFSGSAGLMHSLFEMQVVWAPRLANMRFASLPGGHFFVDRFPDDTARILREFLSDARS 294
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290    


Chain B from PDB  Type:PROTEIN  Length:294
 aligned with DEHA_BURSP | Q1JU72 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:294
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290    
           DEHA_BURSP     1 MFEGFERRLVDVGDVTINCVVGGSGPALLLLHGFPQNLHMWARVAPLLANEYTVVCADLRGYGGSSKPVGAPDHANYSFRAMASDQRELMRTLGFERFHLVGHDRGGRTGHRMALDHPDSVLSLAVLDIIPTYVMFEEVDRFVARAYWHWYFLQQPAPYPEKVIGADPDTFYEGCLFGWGATGADGFDPEQLEEYRKQWRDPAAIHGSCCDYRAGGTIDFELDHGDLGRQVQCPALVFSGSAGLMHSLFEMQVVWAPRLANMRFASLPGGHFFVDRFPDDTARILREFLSDARS 294
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee....eeeeeeee...eeeee.....hhhhhhhhhhhhh...eeeee................hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee...hhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee..hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3b12 B   1 MFEGFERRLVDVGDVTINCVVGGSGPALLLLHGFPQNLHMWARVAPLLANEYTVVCADLRGYGGSSKPVGAPDHANYSFRAMASDQRELMRTLGFERFHLVGHARGGRTGHRMALDHPDSVLSLAVLDIIPTYVMFEEVDRFVARAYWHWYFLQQPAPYPEKVIGADPDTFYEGCLFGWGATGADGFDPEQLEEYRKQWRDPAAIHGSCCDYRAGGTIDFELDHGDLGRQVQCPALVFSGSAGLMHSLFEMQVVWAPRLANMRFASLPGGHFFVDRFPDDTARILREFLSDARS 294
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   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  (0, 0)

(no "SCOP Domain" information available for 3B12)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3B12)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B12)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DEHA_BURSP | Q1JU72)
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:0018785    haloacetate dehalogenase activity    Catalysis of the reaction: haloacetate + H2O = glycolate + halide.
    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/Biological 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
    FAH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:157 - Pro A:158   [ RasMol ]  
    Ala B:157 - Pro B:158   [ RasMol ]  
    Phe A:34 - Pro A:35   [ RasMol ]  
    Phe B:34 - Pro B:35   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  3b12
    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
  DEHA_BURSP | Q1JU72
    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)
  3.8.1.3
    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
  DEHA_BURSP | Q1JU72
    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
        DEHA_BURSP | Q1JU72: 1y37

(-) Related Entries Specified in the PDB File

1y37