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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FLUOROACETATE DEHALOGENASE RPA1163 - ASP110ASN/GLYCOLATE - COCRYSTALLIZED
 
Authors :  P. Mehrabi, T. H. Kim, S. R. Prosser, E. F. Pai
Date :  19 May 16  (Deposition) - 01 Feb 17  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Homodimer, Hydrolase, Dehalogenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. H. Kim, P. Mehrabi, Z. Ren, A. Sljoka, C. Ing, A. Bezginov, L. Ye, R. Pomes, R. S. Prosser, E. F. Pai
The Role Of Dimer Asymmetry And Protomer Dynamics In Enzyme Catalysis.
Science V. 355 2017
PubMed-ID: 28104837  |  Reference-DOI: 10.1126/SCIENCE.AAG2355

(-) Compounds

Molecule 1 - FLUOROACETATE DEHALOGENASE
    Chains: A, B
    EC Number: 3.8.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RPA1163
    Mutation: YES
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS (STRAIN ATCC BAA-98 / CGA009)
    Organism Taxid: 258594
    Strain: ATCC BAA-98 / CGA009

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOA1Ligand/IonGLYCOLIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:110 , ARG A:111 , ARG A:114 , ILE A:135 , HIS A:155 , TRP A:156 , TYR A:219 , HIS A:280 , HOH A:548binding site for residue GOA A 401
2AC2SOFTWAREARG A:114 , LEU A:136 , HOH A:548binding site for residue CL A 402
3AC3SOFTWAREASN B:110 , ARG B:111 , ARG B:114 , HOH B:547 , HOH B:654binding site for residue CL B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K3E)

(-) 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 5K3E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K3E)

(-) Exons   (0, 0)

(no "Exon" information available for 5K3E)

(-) 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:295
                                                                                                                                                                                                                                                                                                                                       
               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........hhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k3e A   4 LADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAPKLAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHVHFALAGHNRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALKIYHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHYRIAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGASGIAQSTPLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFSA 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  ||   265       275       285       295     
                                                                                                                                                                                                                                                                                      256|                                         
                                                                                                                                                                                                                                                                                       259                                         


Chain B from PDB  Type:PROTEIN  Length:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee......eeeeeee...eeeee.....hhhhhh.hhhhhh...eeeee................hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee...hhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee.......hhhhhhh....eeeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k3e B   4 LADLFPGFGSEWINTSSGRIFARVGGDGPPLLLLHGFPQTHVMWHRVAPKLAERFKVIVADLPGYGWSDMPESDEQHTPYTKRAMAKQLIEAMEQLGHVHFALAGHNRGARVSYRLALDSPGRLSKLAVLDILPTYEYWQRMNRAYALKIYHWSFLAQPAPLPENLLGGDPDFYVKAKLASWTRAGDLSAFDPRAVEHYRIAFADPMRRHVMCEDYRAGAYADFEHDKIDVEAGNKIPVPMLALWGASGIAQTPLDVWRKWASDVQGAPIESGHFLPEEAPDQTAEALVRFFSA 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 ||    266       276       286       296    
                                                                                                                                                                                                                                                                                     255|                                         
                                                                                                                                                                                                                                                                                      259
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 5K3E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K3E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K3E)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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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 3r3z 3r40 3r41 5k3a 5k3b 5k3c 5k3d 5k3f 5swn 5t4t

(-) Related Entries Specified in the PDB File

5k3a 5k3b 5k3c 5k3d 5k3f