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(-) Description

Title :  L-2-HALOACID DEHALOGENASE
 
Authors :  T. Hisano, Y. Hata, T. Fujii, J. -Q. Liu, T. Kurihara, N. Esaki, K. Soda
Date :  03 Jun 96  (Deposition) - 07 Dec 96  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dehalogenase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hisano, Y. Hata, T. Fujii, J. Q. Liu, T. Kurihara, N. Esaki, K. Soda
Crystal Structure Of L-2-Haloacid Dehalogenase From Pseudomonas Sp. Yl. An Alpha/Beta Hydrolase Structure That Is Different From The Alpha/Beta Hydrolase Fold.
J. Biol. Chem. V. 271 20322 1996
PubMed-ID: 8702766  |  Reference-DOI: 10.1074/JBC.271.34.20322
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-2-HALOACID DEHALOGENASE
    Chains: A
    EC Number: 3.8.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: L-DEX YL
    Expression System Plasmid: PKK223-3
    Expression System Taxid: 562
    Gene: L-DEX YL
    Organism Scientific: PSEUDOMONAS SP.
    Organism Taxid: 66693
    Strain: YL

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1JUD)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1CATUNKNOWNASP A:10 , THR A:14 , ARG A:41 , SER A:118 , LYS A:151 , TYR A:157 , SER A:175 , ASN A:177 , ASP A:180MUTAGENESIS EXPERIMENTS HAVE SHOWN THAT THESE NINE RESIDUES ARE CRITICALLY IMPORTANT IN CATALYSIS. ESPECIALLY, O18 INCORPORATION, CHEMICAL MODIFICATION AND TANDEM MS-MS SPECTROSCOPY EXPERIMENTS HAVE SHOWN THAT ASP-10 IS A NUCLEOPHILE WHICH ATTACKS THE ALPHA-CARBON OF THE SUBSTRATE.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JUD)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:151 -Pro A:152

 Sequence-Structure Mapping

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(-) PROSITE Motifs  (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:220
 aligned with HAD_PSEUY | Q53464 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:220
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
            HAD_PSEUY     3 YIKGIAFDLYGTLFDVHSVVGRCDEAFPGRGREISALWRQKQLEYTWLRSLMNRYVNFQQATEDALRFTCRHLGLDLDARTRSTLCDAYLRLAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVSSNAWDATGARYFGFPTCWINRTGNVFEEMGQTPDWEVTSLRAVVELF 222
               SCOP domains d1juda_ A: L-2-Haloacid dehalogenase, HAD                                                                                                                                                                                    SCOP domains
               CATH domains 1judA01        1judA02 A:18-92 Putative phosphatase; domain 2                             1judA01 A:3-17,A:93-222  [code=3.40.50.1000, no name defined]                                                                      CATH domains
               Pfam domains -Hydrolase-1judA01 A:4-188                                                                                                                                                                ---------------------------------- Pfam domains
         Sec.struct. author ...eeee.........hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh......hhhhhhhhhh...eeeeee...hhhhhhhhhh...hhh..eeee.hhh......hhhhhhhhhhh...hhheeeee..hhhhhhhhhh..eeeee...............eee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jud A   3 YIKGIAFDLYGTLFDVHSVVGRCDEAFPGRGREISALWRQKQLEYTWLRSLMNRYVNFQQATEDALRFTCRHLGLDLDARTRSTLCDAYLRLAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVSSNAWDATGARYFGFPTCWINRTGNVFEEMGQTPDWEVTSLRAVVELF 222
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (HAD_PSEUY | Q53464)
molecular function
    GO:0018784    (S)-2-haloacid dehalogenase activity    Catalysis of the reaction: (S)-2-haloacid + H2O = (R)-2-hydroxyacid + 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.
    GO:0019120    hydrolase activity, acting on acid halide bonds, in C-halide compounds    Catalysis of the hydrolysis of any acid halide bond in substances containing halogen atoms in organic linkage.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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    Lys A:151 - Pro A:152   [ RasMol ]  
 
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        HAD_PSEUY | Q53464: 1qh9 1zrm 1zrn

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