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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FLUOROACETATE DEHALOGENASE RPA1163 - ASP110ASN/BROMOACETATE
 
Authors :  P. W. Y. Chan, A. F. Yakunin, E. A. Edwards, E. F. Pai
Date :  16 Mar 11  (Deposition) - 04 May 11  (Release) - 01 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Facd, Defluorinase, Alpha/Beta Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. W. Chan, A. F. Yakunin, E. A. Edwards, E. F. Pai
Mapping The Reaction Coordinates Of Enzymatic Defluorination.
J. Am. Chem. Soc. V. 133 7461 2011
PubMed-ID: 21510690  |  Reference-DOI: 10.1021/JA200277D

(-) Compounds

Molecule 1 - FLUOROACETATE DEHALOGENASE
    Chains: A, B
    EC Number: 3.8.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV-L
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RPA1163
    Mutation: YES
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS
    Organism Taxid: 1076
    Strain: CGA009

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1BXA1Ligand/IonBROMOACETIC ACID
2CA1Ligand/IonCALCIUM ION
3CL5Ligand/IonCHLORIDE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:110 , ARG A:111 , ARG A:114 , HIS A:155 , TRP A:156 , TRP A:185 , TYR A:219 , ILE A:253 , HOH A:330BINDING SITE FOR RESIDUE BXA A 305
2AC2SOFTWAREGLN A:98 , HOH A:315 , HOH A:496 , HOH B:335BINDING SITE FOR RESIDUE CA A 306
3AC3SOFTWAREASN A:110 , ARG A:114BINDING SITE FOR RESIDUE CL A 307
4AC4SOFTWAREARG A:114 , LEU A:136 , HOH A:379BINDING SITE FOR RESIDUE CL A 308
5AC5SOFTWAREALA A:286 , PRO A:287 , ASP A:288 , GLN A:289BINDING SITE FOR RESIDUE CL A 309
6AC6SOFTWAREALA B:286 , ASP B:288 , GLN B:289BINDING SITE FOR RESIDUE CL B 305
7AC7SOFTWAREASN B:110 , ARG B:114BINDING SITE FOR RESIDUE CL B 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R3X)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:40 -Pro A:41
2Ala A:163 -Pro A:164
3Phe B:40 -Pro B:41
4Ala B:163 -Pro B:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R3X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R3X)

(-) Exons   (0, 0)

(no "Exon" information available for 3R3X)

(-) 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:293
 aligned with DEHA_RHOPA | Q6NAM1 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:297
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       
           DEHA_RHOPA     4 LADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAPKLAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHVHFALAGHDRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALKIYHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHYRIAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGASGIAQSAATPLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFSA 300
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee......eeeeeee...eeeee.....hhhhhh.hhhhhh...eeeee................hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee...hhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhh.hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee.....----hhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r3x A   4 LADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAPKLAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHVHFALAGHNRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALKIYHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHYRIAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGASGIA----TPLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFSA 300
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253|    | 263       273       283       293       
                                                                                                                                                                                                                                                                                    254  259                                         


Chain B from PDB  Type:PROTEIN  Length:289
 aligned with DEHA_RHOPA | Q6NAM1 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:297
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       
           DEHA_RHOPA     4 LADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAPKLAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHVHFALAGHDRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALKIYHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHYRIAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGASGIAQSAATPLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFSA 300
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------Abhydrolase_6-3r3xB01 B:34-293                                                                                                                                                                                                                                      ------- Pfam domains (1)
           Pfam domains (2) ------------------------------Abhydrolase_6-3r3xB02 B:34-293                                                                                                                                                                                                                                      ------- Pfam domains (2)
         Sec.struct. author ........eeeee......eeeeee....eeeee.....hhhhhh.hhhhhhh..eeeee................hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee...hhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..--------hhhhhhh....eeeeee....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r3x B   4 LADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAPKLAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHVHFALAGHNRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALKIYHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHYRIAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGAS--------PLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFSA 300
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       | -      |263       273       283       293       
                                                                                                                                                                                                                                                                                 251      260
   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 3R3X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R3X)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DEHA_RHOPA | Q6NAM1)
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.

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  3.8.1.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        DEHA_RHOPA | Q6NAM1: 3r3u 3r3v 3r3w 3r3y 3r3z 3r40 3r41 5k3a 5k3b 5k3c 5k3d 5k3e 5k3f 5swn 5t4t

(-) Related Entries Specified in the PDB File

3r3u THE WT/APO CRYSTAL STRUCTURE.
3r3v THE ASP110ASN MUTANT IN COMPLEX WITH FLUOROACETATE.
3r3w THE ASP110ASN MUTANT IN COMPLEX WITH CHLOROACETATE.
3r3y THE HIS280ASN MUTANT IN COVALENT COMPLEX WITH FLUOROACETATE
3r3z THE WT IN COMPLEX WITH GLYCOLATE
3r40 THE ASP110ASN MUTANT/APO CRYSTAL STRUCTURE
3r41 THE HIS280ASN/APO CRYSTAL STRUCTURE