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(-) Description

Title :  STRUCTURE OF L-2-HALOACID DEHALOGENASE FROM XANTHOBACTER AUTOTROPHICUS WITH CHLOROPROPIONIC ACID COVALENTLY BOUND
 
Authors :  I. S. Ridder, H. J. Rozeboom, K. H. Kalk, B. W. Dijkstra
Date :  11 Jun 99  (Deposition) - 25 Oct 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  L-2-Haloacid Dehalogenase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. S. Ridder, H. J. Rozeboom, K. H. Kalk, B. W. Dijkstra
Crystal Structures Of Intermediates In The Dehalogenation Of Haloalkanoates By L-2-Haloacid Dehalogenase.
J. Biol. Chem. V. 274 30672 1999
PubMed-ID: 10521454  |  Reference-DOI: 10.1074/JBC.274.43.30672
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (L-2-HALOACID DEHALOGENASE)
    ChainsA, B
    EC Number3.8.1.2
    Organism ScientificXANTHOBACTER AUTOTROPHICUS
    Organism Taxid280
    Other Details2-CHLOROPROPIONIC ACID MOIETY COVALENTLY BOUND TO ASP 8 IN ACTIVE SITES OF BOTH CHAINS
    StrainGJ10

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ASB2Mod. Amino AcidASPARTIC ACID-4-CARBOXYMETHYL ESTER
2CL2Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASB A:8 , TYR A:10 , ARG A:39 , ASN A:115BINDING SITE FOR RESIDUE CL A 1401
2AC2SOFTWAREASB B:8 , ARG B:39 , ASN B:115BINDING SITE FOR RESIDUE CL B 1402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QQ7)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:106 -Pro A:107
2Lys A:147 -Pro A:148
3Lys B:147 -Pro B:148

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QQ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QQ7)

(-) Exons   (0, 0)

(no "Exon" information available for 1QQ7)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:245
 aligned with HAD_XANAU | Q60099 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
            HAD_XANAU     1 MIKAVVFDAYGTLFDVQSVADATERAYPGRGEYITQVWRQKQLEYSWLRALMGRYADFWGVTREALAYTLGTLGLEPDESFLADMAQAYNRLTPYPDAAQCLAELAPLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQEALARELVSGTIAPLTMFKALRMREETYAEAPDFVVPALGDLPRLVRGMA 245
               SCOP domains d1qq7a_ A: L-2-Haloacid dehalogenase, HAD                                                                                                                                                                                                             SCOP domains
               CATH domains 1qq7A01        1qq7A02 A:16-90 Putative phosphatase; domain 2                             1qq7A01 A:1-15,A:91-241  [code=3.40.50.1000, no name defined]                                                                                          ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhh..eeeeee..hhhhhhhhhhhh.hhhhh.eeee.hhhh....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh.eeeee...hhhhhhhhh.....hhhhhhhhhhh..........eee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qq7 A   1 MIKAVVFdAYGTLFDVQSVADATERAYPGRGEYITQVWRQKQLEYSWLRALMGRYADFWSVTREALAYTLGTLGLEPDESFLADMAQAYNRLTPYPDAAQCLAELAPLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQEALARELVSGTIAPLTMFKALRMREETYAEAPDFVVPALGDLPRLVRGMA 245
                                   |10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
                                   8-ASB                                                                                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with HAD_XANAU | Q60099 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
            HAD_XANAU     1 MIKAVVFDAYGTLFDVQSVADATERAYPGRGEYITQVWRQKQLEYSWLRALMGRYADFWGVTREALAYTLGTLGLEPDESFLADMAQAYNRLTPYPDAAQCLAELAPLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQEALARELVSGTIAPLTMFKALRMREETYAEAPDFVVPALGDLPRLVRGMA 245
               SCOP domains d1qq7b_ B: L-2-Haloacid dehalogenase, HAD                                                                                                                                                                                                             SCOP domains
               CATH domains 1qq7B01        1qq7B02 B:16-90 Putative phosphatase; domain 2                             1qq7B01 B:1-15,B:91-241  [code=3.40.50.1000, no name defined]                                                                                          ---- CATH domains
           Pfam domains (1) -Hydrolase-1qq7B01 B:2-184                                                                                                                                                              ------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -Hydrolase-1qq7B02 B:2-184                                                                                                                                                              ------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhh....eeeeee..hhhhhhhhhhhh.hhhhh.eeee.hhhh....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh.eeeee...hhhhhhhhh.....hhhhhhhhhhh..........eee.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qq7 B   1 MIKAVVFdAYGTLFDVQSVADATERAYPGRGEYITQVWRQKQLEYSWLRALMGRYADFWSVTREALAYTLGTLGLEPDESFLADMAQAYNRLTPYPDAAQCLAELAPLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQEALARELVSGTIAPLTMFKALRMREETYAEAPDFVVPALGDLPRLVRGMA 245
                                   |10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
                                   8-ASB                                                                                                                                                                                                                                         

   Legend:   → Mismatch (orange background)
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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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HAD_XANAU | Q60099)
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_XANAU | Q600991aq6 1qq5 1qq6

(-) Related Entries Specified in the PDB File

1aq6 FIRST NATIVE STRUCTURE OF THE L-2-HALOACID DEHALOGENASE ENZYME
1qq5
1qq6