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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF A DEHALOGENASE
 
Authors :  J. W. Schmidberger, M. C. J. Wilce
Date :  24 Oct 06  (Deposition) - 25 Sep 07  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Haloacid Dehalogenase, Had Superfamily, Rossmann Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. W. Schmidberger, J. A. Wilce, J. S. H. Tsang, M. C. J. Wilce
Crystal Structures Of The Substrate Free-Enzyme, And Reaction Intermediate Of The Had Superfamily Member, Haloacid Dehalogenase Dehiva From Burkholderia Cepacia Mba4
J. Mol. Biol. V. 368 706 2007
PubMed-ID: 17368477  |  Reference-DOI: 10.1016/J.JMB.2007.02.015

(-) Compounds

Molecule 1 - (S)-2-HALOACID DEHALOGENASE IVA
    Chains: A, B
    EC Number: 3.8.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHKU201
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BURKHOLDERIA CEPACIA
    Organism Taxid: 292
    Strain: MBA4
    Synonym: DEHALOGENASE, 2-HALOALKANOIC ACID DEHALOGENASE IVA, L-2- HALOACID DEHALOGENASE IVA, HALOCARBOXYLIC ACID HALIDOHYDROLASE IVA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2SO410Ligand/IonSULFATE ION
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO410Ligand/IonSULFATE ION
Biological Unit 2 (1, 20)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO420Ligand/IonSULFATE ION

(-) Sites  (0, 0)

(no "Site" information available for 2NO4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NO4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:152 -Pro A:153
2Lys B:152 -Pro B:153

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NO4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2NO4)

(-) Exons   (0, 0)

(no "Exon" information available for 2NO4)

(-) 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:225
 aligned with HAD4_BURCE | Q51645 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     
           HAD4_BURCE     1 MVDSLRACVFDAYGTLLDVHSAVMRNADEVGASAEALSMLWRQRQLEYSWTRTLMHQYADFWQLTDEALTFALRTYHLEDRKGLKDRLMSAYKELSAYPDAAETLEKLKSAGYIVAILSNGNDEMLQAALKASKLDRVLDSCLSADDLKIYKPDPRIYQFACDRLGVNPNEVCFVSSNAWDLGGAGKFGFNTVRINRQGNPPEYEFAPLKHQVNSLSELWPLLAK 225
               SCOP domains d2no4a_ A: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains 2no4A01           2no4A02 A:19-93 Putative phosphatase; domain 2                             2no4A01 A:1-18,A:94-225  [code=3.40.50.1000, no name defined]                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhh..eeeeee..hhhhhhhhhhhh.hhhhh.eeee.hhh.....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh.eeeee...............eee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2no4 A   1 LVDSLRACVFDAYGTLLDVHSAVMRNADEVGASAEALSMLWRQRQLEYSWTRTLMHQYADFWQLTDEALTFALRTYHLEDRKGLKDRLMSAYKELSAYPDAAETLEKLKSAGYIVAILSNGNDEMLQAALKASKLDRVLDSCLSADDLKIYKPDPRIYQFACDRLGVNPNEVCFVSSNAWDLGGAGKFGFNTVRINRQGNPPEYEFAPLKHQVNSLSELWPLLAK 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     


Chain B from PDB  Type:PROTEIN  Length:226
 aligned with HAD4_BURCE | Q51645 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
           HAD4_BURCE     1 MVDSLRACVFDAYGTLLDVHSAVMRNADEVGASAEALSMLWRQRQLEYSWTRTLMHQYADFWQLTDEALTFALRTYHLEDRKGLKDRLMSAYKELSAYPDAAETLEKLKSAGYIVAILSNGNDEMLQAALKASKLDRVLDSCLSADDLKIYKPDPRIYQFACDRLGVNPNEVCFVSSNAWDLGGAGKFGFNTVRINRQGNPPEYEFAPLKHQVNSLSELWPLLAKN 226
               SCOP domains d2no4b_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains 2no4B01           2no4B02 B:19-93 Putative phosphatase; domain 2                             2no4B01 B:1-18,B:94-226  [code=3.40.50.1000, no name defined]                                                                         CATH domains
           Pfam domains (1) ----Hydrolase-2no4B01 B:5-189                                                                                                                                                                ------------------------------------- Pfam domains (1)
           Pfam domains (2) ----Hydrolase-2no4B02 B:5-189                                                                                                                                                                ------------------------------------- Pfam domains (2)
         Sec.struct. author ......eeee.........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhh..eeeeee..hhhhhhhhhhhh.hhhhh.eeee.........hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh.eeeee...............eee.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2no4 B   1 LVDSLRACVFDAYGTLLDVHSAVMRNADEVGASAEALSMLWRQRQLEYSWTRTLMHQYADFWQLTDEALTFALRTYHLEDRKGLKDRLMSAYKELSAYPDAAETLEKLKSAGYIVAILSNGNDEMLQAALKASKLDRVLDSCLSADDLKIYKPDPRIYQFACDRLGVNPNEVCFVSSNAWDLGGAGKFGFNTVRINRQGNPPEYEFAPLKHQVNSLSELWPLLAKN 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HAD4_BURCE | Q51645)
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
        HAD4_BURCE | Q51645: 2no5

(-) Related Entries Specified in the PDB File

2no5