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(-) Description

Title :  STRUCTURE OF L-2-HALOACID DEHALOGENASE FROM XANTHOBACTER AUTOTROPHICUS
 
Authors :  I. S. Ridder, H. J. Rozeboom, K. H. Kalk, B. W. Dijkstra
Date :  07 Aug 97  (Deposition) - 28 Jan 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  L-2-Haloacid Dehalogenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. S. Ridder, H. J. Rozeboom, K. H. Kalk, D. B. Janssen, B. W. Dijkstra
Three-Dimensional Structure Of L-2-Haloacid Dehalogenase From Xanthobacter Autotrophicus Gj10 Complexed With The Substrate-Analogue Formate.
J. Biol. Chem. V. 272 33015 1997
PubMed-ID: 9407083  |  Reference-DOI: 10.1074/JBC.272.52.33015
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-2-HALOACID DEHALOGENASE
    Chains: A, B
    EC Number: 3.8.1.2
    Organism Scientific: XANTHOBACTER AUTOTROPHICUS
    Organism Taxid: 280
    Other Details: SUBSTRATE ANALOGUE FORMATE PRESENT IN BOTH ACTIVE SITES
    Strain: GJ10

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1FMT3Ligand/IonFORMIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:8 , ALA B:9 , TYR B:10 , SER B:114 , ASN B:115 , LYS B:147BINDING SITE FOR RESIDUE FMT B 254
2AC2SOFTWAREASP A:8 , ALA A:9 , TYR A:10 , SER A:114 , ASN A:115 , LYS A:147BINDING SITE FOR RESIDUE FMT A 254
3AC3SOFTWAREGLN A:36 , ARG A:39 , PHE A:213 , ARG A:217 , HOH A:315 , HOH A:332BINDING SITE FOR RESIDUE FMT A 255

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1AQ6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:106 -Pro A:107
2Lys A:147 -Pro A:148
3Ala B:106 -Pro B:107
4Lys B:147 -Pro B:148

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AQ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1AQ6)

(-) Exons   (0, 0)

(no "Exon" information available for 1AQ6)

(-) 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: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 d1aq6a_ A: L-2-Haloacid dehalogenase, HAD                                                                                                                                                                                                             SCOP domains
               CATH domains 1aq6A01        1aq6A02 A:16-90 Putative phosphatase; domain 2                             1aq6A01 A:1-15,A:91-241  [code=3.40.50.1000, no name defined]                                                                                          ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......hhhhhhhhhhhhh......hhhhhhhh...eeeeee...hhhhhhhhhh...hhh..eeeehhhh......hhhhhhhhhhh...hhheeeee..hhhhhhhhhh..eeeee....hhhhhhhhh.....hhhhhhhhh...........eee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1aq6 A   1 MIKAVVFDAYGTLFDVQSVADATERAYPGRGEYITQVWRQKQLEYSWLRALMGRYADFWGVTREALAYTLGTLGLEPDESFLADMAQAYNRLTPYPDAAQCLAELAPLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQEALARELVSGTIAPLTMFKALRMREETYAEAPDFVVPALGDLPRLVRGMA 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     


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 d1aq6b_ B: L-2-Haloacid dehalogenase, HAD                                                                                                                                                                                                             SCOP domains
               CATH domains 1aq6B01        1aq6B02 B:16-90 Putative phosphatase; domain 2                             1aq6B01 B:1-15,B:91-241  [code=3.40.50.1000, no name defined]                                                                                          ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......hhhhhhhhhhhhh......hhhhhhhh...eeeeee...hhhhhhhhhh...hhh..eeeehhhh......hhhhhhhhhhh...hhheeeee..hhhhhhhhhh..eeeee....hhhhhhhhh.....hhhhhhhhh...........eee..hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1aq6 B   1 MIKAVVFDAYGTLFDVQSVADATERAYPGRGEYITQVWRQKQLEYSWLRALMGRYADFWGVTREALAYTLGTLGLEPDESFLADMAQAYNRLTPYPDAAQCLAELAPLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQEALARELVSGTIAPLTMFKALRMREETYAEAPDFVVPALGDLPRLVRGMA 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
   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  (1, 2)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AQ6)

(-) 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 | Q60099: 1qq5 1qq6 1qq7

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1AQ6)