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(-) Description

Title :  INTERMEDIATE STRUCTURE OF L-2-HALOACID DEHALOGENASE WITH MONOCHLOROACETATE
 
Authors :  Y. -F. Li, Y. Hata, T. Fujii, T. Hisano, M. Nishihara, T. Kurihara, N. Esa
Date :  03 Mar 98  (Deposition) - 23 Mar 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dehalogenase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. F. Li, Y. Hata, T. Fujii, T. Hisano, M. Nishihara, T. Kurihara, N. Esaki
Crystal Structures Of Reaction Intermediates Of L-2-Haloaci Dehalogenase And Implications For The Reaction Mechanism.
J. Biol. Chem. V. 273 15035 1998
PubMed-ID: 9614112  |  Reference-DOI: 10.1074/JBC.273.24.15035

(-) 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: PBA501
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PUC119
    Gene: L-DEX_YL
    Mutation: YES
    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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:10 , LEU A:11 , TYR A:12 , SER A:118 , ASN A:119BINDING SITE FOR RESIDUE ACY A 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZRN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZRN)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZRN)

(-) 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: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 d1zrna_ A: L-2-Haloacid dehalogenase, HAD                                                                                                                                                                                    SCOP domains
               CATH domains 1zrnA01        1zrnA02 A:18-92 Putative phosphatase; domain 2                             1zrnA01 A:3-17,A:93-222  [code=3.40.50.1000, no name defined]                                                                      CATH domains
               Pfam domains -Hydrolase-1zrnA01 A:4-188                                                                                                                                                                ---------------------------------- Pfam domains
         Sec.struct. author ...eeee........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh......hhhhhhhhhhh..eeeeee...hhhhhhhhhh...hhh..eeee.hhh......hhhhhhhhhhh...hhheeeee..hhhhhhhhhh..eeeee...............eee..hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zrn A   3 YIKGIAFDLYGTLFDVHSVVGRCDEAFPGRGREISALWRQKQLEYTWLRSLMNRYVNFQQATEDALRFTCRHLGLDLDARTRSTLCDAYLRLAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVASNAWDATGARYFGFPTCWINRTGNVFEEMGQTPDWEVTSLRAVVELF 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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 Related Entries

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

UniProtKB/Swiss-Prot
        HAD_PSEUY | Q53464: 1jud 1qh9 1zrm

(-) Related Entries Specified in the PDB File

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