DB code: D00248

RLCP classification 1.20.30800.980 : Hydrolysis
CATH domain 3.40.50.1000 : Rossmann fold Catalytic domain
1.10.164.10 : L-2-haloacid Dehalogenase; domain 2 Catalytic domain
E.C. 3.8.1.2
CSA 1qh9 1qq5
M-CSA 1qh9 1qq5
MACiE M0036

CATH domain Related DB codes (homologues)
3.40.50.1000 : Rossmann fold M00102

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
Q53464 (S)-2-haloacid dehalogenase
EC 3.8.1.2
2-haloalkanoic acid dehalogenase
L-2-haloacid dehalogenase
Halocarboxylic acid halidohydrolase
L-DEX
PF00702 (Hydrolase)
[Graphical View]
Q60099 (S)-2-haloacid dehalogenase
EC 3.8.1.2
2-haloalkanoic acid dehalogenase
L-2-haloacid dehalogenase
Halocarboxylic acid halidohydrolase
PF00702 (Hydrolase)
[Graphical View]

KEGG enzyme name
(S)-2-haloacid dehalogenase
2-haloacid dehalogenase[ambiguous]
2-haloacid halidohydrolase [ambiguous][ambiguous]
2-haloalkanoic acid dehalogenase
2-haloalkanoid acid halidohydrolase
2-halocarboxylic acid dehalogenase II
DL-2-haloacid dehalogenase[ambiguous]
L-2-haloacid dehalogenase
L-DEX

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q53464 HAD_PSEUY (S)-2-haloacid + H(2)O = (R)-2-hydroxyacid + halide. Homodimer.
Q60099 HAD_XANAU (S)-2-haloacid + H(2)O = (R)-2-hydroxyacid + halide. Homodimer.

KEGG Pathways
Map code Pathways E.C.
MAP00361 gamma-Hexachlorocyclohexane degradation
MAP00631 1,2-Dichloroethane degradation

Compound table
Substrates Products Intermediates
KEGG-id C02103 C00001 C02489 C00462
E.C.
Compound (S)-2-Haloacid H2O (R)-2-Hydroxyacid Halide
Type carboxyl group,halide H2O carbohydrate,carboxyl group halide
ChEBI 15377
 15377
PubChem 22247451
 962
 22247451
 962
1aq6A01 Analogue:FMT_2 Unbound Unbound Unbound
1aq6B01 Analogue:FMT_1 Unbound Unbound Unbound
1judA01 Unbound Unbound Unbound Unbound
1qh9A01 Unbound Bound:LAC Unbound Unbound
1qq5A01 Analogue:FMT Unbound Unbound Unbound
1qq5B01 Analogue:FMT Unbound Unbound Unbound
1qq6A01 Unbound Unbound Unbound Unbound Intermediate-bound:ASB
1qq6B01 Unbound Unbound Unbound Unbound Intermediate-bound:ASB
1qq7A01 Unbound Unbound Unbound Intermediate-bound:ASB
1qq7B01 Unbound Unbound Unbound Intermediate-bound:ASB
1zrmA01 Unbound Bound:HOH_500 Unbound Unbound Intermediate-bound:BUA
1zrnA01 Unbound Bound:HOH_500 Unbound Unbound Intermediate-bound:ACY
1aq6A02 Analogue:FMT Unbound Unbound Unbound
1aq6B02 Unbound Unbound Unbound Unbound
1judA02 Unbound Unbound Unbound Unbound
1qh9A02 Unbound Unbound Unbound Unbound
1qq5A02 Unbound Unbound Unbound Unbound
1qq5B02 Unbound Unbound Unbound Unbound
1qq6A02 Unbound Unbound Bound:_CL Unbound
1qq6B02 Unbound Unbound Bound:_CL Unbound
1qq7A02 Unbound Unbound Bound:_CL Unbound
1qq7B02 Unbound Unbound Bound:_CL Unbound
1zrmA02 Unbound Unbound Unbound Unbound
1zrnA02 Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;Q53464, Q60099 & literature [10], [13] & [16]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1aq6A01 ASP 8;THR 12;LYS 147;TYR 153;SER 171;ASN 173;ASP 176
1aq6B01 ASP 8;THR 12;LYS 147;TYR 153;SER 171;ASN 173;ASP 176
1judA01 ASP 10;THR 14;LYS 151;TYR 157;SER 175;ASN 177;ASP 180
1qh9A01 ASP 10;THR 14;LYS 151;TYR 157;SER 175;ASN 177;ASP 180
1qq5A01 ASP 8;THR 12;LYS 147;TYR 153;SER 171;ASN 173;ASP 176
1qq5B01 ASP 8;THR 12;LYS 147;TYR 153;SER 171;ASN 173;ASP 176
1qq6A01 ;THR 12;LYS 147;TYR 153;SER 171;ASN 173;ASP 176 ASB 8(aspartic acid-4-carboxymethyl ester)
1qq6B01 ;THR 12;LYS 147;TYR 153;SER 171;ASN 173;ASP 176 ASB 8(aspartic acid-4-carboxymethyl ester)
1qq7A01 ;THR 12;LYS 147;TYR 153;SER 171;ASN 173;ASP 176 ASB 8(aspartic acid-4-carboxymethyl ester)
1qq7B01 ;THR 12;LYS 147;TYR 153;SER 171;ASN 173;ASP 176 ASB 8(aspartic acid-4-carboxymethyl ester)
1zrmA01 ASP 10;THR 14;LYS 151;TYR 157;;ASN 177;ASP 180 mutant S175A
1zrnA01 ASP 10;THR 14;LYS 151;TYR 157;;ASN 177;ASP 180 mutant S175A
1aq6A02 ARG 39
1aq6B02 ARG 39
1judA02 ARG 41
1qh9A02 ARG 41
1qq5A02 ARG 39
1qq5B02 ARG 39
1qq6A02 ARG 39
1qq6B02 ARG 39
1qq7A02 ARG 39
1qq7B02 ARG 39
1zrmA02 ARG 41
1zrnA02 ARG 41

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.6, p.494
[2]
Fig.1
[3]
Fig.2, p.1321
[6]
p.20328-20329
[8]
p.33020-33021
[9]
p.21
[10]
Fig.8, p.15041-15043
[13]
Fig.5, p.30676-30677
[16]
SCHEME 1

References
[1]
Resource
Comments
Medline ID
PubMed ID 8216900
Journal Biol Chem Hoppe Seyler
Year 1993
Volume 374
Pages 489-96
Authors Schneider B, Muller R, Frank R, Lingens F
Title Site-directed mutagenesis of the 2-haloalkanoic acid dehalogenase I gene from Pseudomonas sp. strain CBS3 and its effect on catalytic activity.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 7822238
Journal J Biochem (Tokyo)
Year 1994
Volume 116
Pages 248-9
Authors Liu JQ, Kurihara T, Esaki N, Soda K
Title Reconsideration of the essential role of a histidine residue of L-2-halo acid dehalogenase.
Related PDB
Related UniProtKB
[3]
Resource
Comments MUTAGENESIS.
Medline ID 96105006
PubMed ID 7490277
Journal J Biochem (Tokyo)
Year 1995
Volume 117
Pages 1317-22
Authors Kurihara T, Liu JQ, Nardi-Dei V, Koshikawa H, Esaki N, Soda K
Title Comprehensive site-directed mutagenesis of L-2-halo acid dehalogenase to probe catalytic amino acid residues.
Related PDB
Related UniProtKB Q53464
[4]
Resource
Comments
Medline ID
PubMed ID 8580854
Journal Protein Sci
Year 1995
Volume 4
Pages 2619-20
Authors Ridder IS, Rozeboom HJ, Kingma J, Janssen DB, Dijkstra BW
Title Crystallization and preliminary X-ray analysis of L-2-haloacid dehalogenase from Xanthobacter autotrophicus GJ10.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 8607850
Journal Biochem Biophys Res Commun
Year 1996
Volume 220
Pages 828-33
Authors Diez A, Prieto MI, Alvarez MJ, Bautista JM, Garrido J, Puyet A
Title Improved catalytic performance of a 2-haloacid dehalogenase from Azotobacter sp. by ion-exchange immobilisation.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
Medline ID 96355356
PubMed ID 8702766
Journal J Biol Chem
Year 1996
Volume 271
Pages 20322-30
Authors Hisano T, Hata Y, Fujii T, Liu JQ, Kurihara T, Esaki N, Soda K
Title 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.
Related PDB 1jud
Related UniProtKB Q53464
[7]
Resource
Comments
Medline ID
PubMed ID 8860001
Journal Proteins
Year 1996
Volume 24
Pages 520-2
Authors Hisano T, Hata Y, Fujii T, Liu JQ, Kurihara T, Esaki N, Soda K
Title Crystallization and preliminary x-ray crystallographic studies of L-2-haloacid dehalogenase from Pseudomonas sp. YL.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) AND REVISION TO 84
Medline ID 98070500
PubMed ID 9407083
Journal J Biol Chem
Year 1997
Volume 272
Pages 33015-22
Authors Ridder IS, Rozeboom HJ, Kalk KH, Janssen DB, Dijkstra BW
Title Three-dimensional structure of L-2-haloacid dehalogenase from Xanthobacter autotrophicus GJ10 complexed with the substrate-analogue formate.
Related PDB 1aq6
Related UniProtKB Q60099
[9]
Resource
Comments
Medline ID
PubMed ID 9644239
Journal J Biochem (Tokyo)
Year 1998
Volume 124
Pages 20-2
Authors Li YF, Hata Y, Fujii T, Kurihara T, Esaki N
Title X-ray structure of a reaction intermediate of L-2-haloacid dehalogenase with L-2-chloropropionamide.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID 98279020
PubMed ID 9614112
Journal J Biol Chem
Year 1998
Volume 273
Pages 15035-44
Authors Li YF, Hata Y, Fujii T, Hisano T, Nishihara M, Kurihara T, Esaki N
Title Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism.
Related PDB 1zrm 1zrn
Related UniProtKB Q53464
[11]
Resource
Comments
Medline ID
PubMed ID 10191250
Journal Biochem J
Year 1999
Volume 339
Pages 223-6
Authors Ridder IS, Dijkstra BW
Title Identification of the Mg2+-binding site in the P-type ATPase and phosphatase members of the HAD (haloacid dehalogenase) superfamily by structural similarity to the response regulator protein CheY.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 10449315
Journal Curr Opin Biotechnol
Year 1999
Volume 10
Pages 365-9
Authors Swanson PE
Title Dehalogenases applied to industrial-scale biocatalysis.
Related PDB
Related UniProtKB
[13]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10521454
Journal J Biol Chem
Year 1999
Volume 274
Pages 30672-8
Authors Ridder IS, Rozeboom HJ, Kalk KH, Dijkstra BW
Title Crystal structures of intermediates in the dehalogenation of haloalkanoates by L-2-haloacid dehalogenase.
Related PDB 1qq5 1qq6 1qq7
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 10485878
Journal Proc Natl Acad Sci U S A
Year 1999
Volume 96
Pages 10637-42
Authors Argiriadi MA, Morisseau C, Hammock BD, Christianson DW
Title Detoxification of environmental mutagens and carcinogens: structure, mechanism, and evolution of liver epoxide hydrolase.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 10919767
Journal Appl Environ Microbiol
Year 2000
Volume 66
Pages 3180-6
Authors Tsang JS, Pang BC
Title Identification of the dimerization domain of dehalogenase IVa of Burkholderia cepacia MBA4.
Related PDB
Related UniProtKB
[16]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11006296
Journal J Biol Chem
Year 2000
Volume 275
Pages 40804-9
Authors Ichiyama S, Kurihara T, Li YF, Kogure Y, Tsunasawa S, Esaki N
Title Novel catalytic mechanism of nucleophilic substitution by asparagine residue involving cyanoalanine intermediate revealed by mass spectrometric monitoring of an enzyme reaction.
Related PDB 1qh9
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11601995
Journal Biochemistry
Year 2001
Volume 40
Pages 12704-11
Authors Selengut JD
Title MDP-1 is a new and distinct member of the haloacid dehalogenase family of aspartate-dependent phosphohydrolases.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11404103
Journal Curr Opin Biotechnol
Year 2001
Volume 12
Pages 254-8
Authors Janssen DB, Oppentocht JE, Poelarends GJ
Title Microbial dehalogenation.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 15461449
Journal Biochemistry
Year 2004
Volume 43
Pages 12770-9
Authors Peisach E, Selengut JD, Dunaway-Mariano D, Allen KN
Title X-ray crystal structure of the hypothetical phosphotyrosine phosphatase MDP-1 of the haloacid dehalogenase superfamily.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 14983068
Journal Protein Eng
Year 2003
Volume 16
Pages 889-95
Authors Stewart AJ, Schmid R, Blindauer CA, Paisey SJ, Farquharson C
Title Comparative modelling of human PHOSPHO1 reveals a new group of phosphatases within the haloacid dehalogenase superfamily.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 14687572
Journal J Mol Biol
Year 2004
Volume 335
Pages 761-73
Authors Calderone V, Forleo C, Benvenuti M, Cristina Thaller M, Maria Rossolini G, Mangani S
Title The first structure of a bacterial class B Acid phosphatase reveals further structural heterogeneity among phosphatases of the haloacid dehalogenase fold.
Related PDB
Related UniProtKB

Comments
According to the literature [8], [10] & [13], the catalytic reaction proceeds as follows:
(1) Asp8 (of 1aq6) acts as a nucleophile, which makes a nucleophilic attack on the carbon, which is covalently bonded to halide atom, whereas Arg39 stabilizes and accepts the leaving halide atom. (The reaction proceeds via SN2 mechanism.)
(2) The intermediate is stabilized by an oxyanion hole, composed of Thr12/Ser173/Asn173 in the case of R=CH3 or larger alkyl group for the substrate, or Lys147 in the case of R=H for the substrate (see [10]). (substrate; R-CX-COOH)
(3) Lys147 and Tyr153 probably modulate the activity of Asp176, by lowering its pKa.
(4) Asp176 acts as a base, to activate a water. (The activated water might be stabilized by Asn173 (see [10] & [16].)
(5) The activated water makes a nucleophilic attack on the carbonyl carbon of Asp8-ligand intermediate, to complete the hydrolytic reaction.

Created Updated
2005-02-21 2009-02-26