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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FLUOROACETATE DEHALOGENASE RPA1163 - WT/GLYCOLATE
 
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 :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
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, C, D
    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
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS
    Organism Taxid: 1076
    Strain: CGA009

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1GOA4Ligand/IonGLYCOLIC ACID
2NI3Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOA2Ligand/IonGLYCOLIC ACID
2NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOA2Ligand/IonGLYCOLIC ACID
2NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:110 , ARG A:111 , ARG A:114 , ILE A:135 , HIS A:155 , TRP A:156 , TYR A:219 , HOH A:342 , HOH A:1180BINDING SITE FOR RESIDUE GOA A 305
2AC2SOFTWAREGLY A:-1 , HIS A:0 , HOH A:1262 , HIS B:103 , GLY B:125BINDING SITE FOR RESIDUE NI A 306
3AC3SOFTWAREASP B:110 , ARG B:111 , ARG B:114 , ILE B:135 , HIS B:155 , TRP B:156 , TYR B:219 , HOH B:316 , HOH B:486BINDING SITE FOR RESIDUE GOA B 305
4AC4SOFTWAREGLY B:-1 , HIS B:0 , HOH B:1263 , HOH B:1264 , HIS C:80BINDING SITE FOR RESIDUE NI B 306
5AC5SOFTWAREASP C:110 , ARG C:111 , ARG C:114 , ILE C:135 , HIS C:155 , TRP C:156 , TYR C:219 , HOH C:484 , HOH C:1232BINDING SITE FOR RESIDUE GOA C 305
6AC6SOFTWAREHIS A:103 , GLY A:125 , GLY C:-1 , HIS C:0 , MET C:1 , HOH C:1261BINDING SITE FOR RESIDUE NI C 306
7AC7SOFTWAREASP D:110 , ARG D:111 , ARG D:114 , ILE D:135 , HIS D:155 , TRP D:156 , TYR D:219 , HOH D:880 , HOH D:1207BINDING SITE FOR RESIDUE GOA D 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R3Z)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric 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
5Phe C:40 -Pro C:41
6Ala C:163 -Pro C:164
7Phe D:40 -Pro D:41
8Ala D:163 -Pro D:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R3Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R3Z)

(-) Exons   (0, 0)

(no "Exon" information available for 3R3Z)

(-) 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:304
 aligned with DEHA_RHOPA | Q6NAM1 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:304
                              1                                                                                                                                                                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298    
           DEHA_RHOPA     - --MPDLADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAPKLAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHVHFALAGHDRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALKIYHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHYRIAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGASGIAQSAATPLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFSAAP 302
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee......eeeeeee...eeeee.....hhhhhh.hhhhhhh..eeeee................hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee...hhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r3z A  -1 GHMPDLADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAPKLAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHVHFALAGHDRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALKIYHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHYRIAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGASGIAQSAATPLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFSAAP 302
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298    


Chain B from PDB  Type:PROTEIN  Length:295
 aligned with DEHA_RHOPA | Q6NAM1 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:303
                              1                                                                                                                                                                                                                                                                                                            
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298   
           DEHA_RHOPA     - --MPDLADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAPKLAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHVHFALAGHDRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALKIYHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHYRIAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGASGIAQSAATPLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFSAA 301
               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.hhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee..--------hhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r3z B  -1 GHMPDLADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAPKLAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHVHFALAGHDRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALKIYHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHYRIAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGAS--------PLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFSAA 301
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248  |      - |     268       278       288       298   
                                                                                                                                                                                                                                                                                      251      260                                         


Chain C from PDB  Type:PROTEIN  Length:301
 aligned with DEHA_RHOPA | Q6NAM1 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:301
                              1                                                                                                                                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298 
           DEHA_RHOPA     - --MPDLADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAPKLAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHVHFALAGHDRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALKIYHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHYRIAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGASGIAQSAATPLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFS 299
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee......eeeeeee...eeeee.....hhhhhh.hhhhhhh..eeeee................hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee...hhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r3z C  -1 GHMPDLADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAPKLAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHVHFALAGHDRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALKIYHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHYRIAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGASGIAQSAATPLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFS 299
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298 


Chain D from PDB  Type:PROTEIN  Length:296
 aligned with DEHA_RHOPA | Q6NAM1 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:296
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294      
           DEHA_RHOPA     5 ADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAPKLAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHVHFALAGHDRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALKIYHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHYRIAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGASGIAQSAATPLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFSA 300
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------Abhydrolase_6-3r3zD01 D:34-293                                                                                                                                                                                                                                      ------- Pfam domains (1)
           Pfam domains (2) -----------------------------Abhydrolase_6-3r3zD02 D:34-293                                                                                                                                                                                                                                      ------- Pfam domains (2)
           Pfam domains (3) -----------------------------Abhydrolase_6-3r3zD03 D:34-293                                                                                                                                                                                                                                      ------- Pfam domains (3)
           Pfam domains (4) -----------------------------Abhydrolase_6-3r3zD04 D:34-293                                                                                                                                                                                                                                      ------- Pfam domains (4)
         Sec.struct. author .......eeeee......eeeeee....eeeee.....hhhhhh.hhhhhh...eeeee................hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee...hhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r3z D   5 ADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAPKLAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHVHFALAGHDRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALKIYHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHYRIAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGASGIAQSAATPLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFSA 300
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294
   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 3R3Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R3Z)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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 3r3x 3r3y 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.
3r3x THE ASP110ASN MUTANT IN COMPLEX WITH BROMOACETATE.
3r3y THE HIS280ASN MUTANT IN COVALENT COMPLEX WITH FLUOROACETATE.
3r40 THE ASP110ASN MUTANT/APO CRYSTAL STRUCTURE
3r41 THE HIS280ASN MUTANT/APO CRYSTAL STRUCTURE