DB code: S00356

RLCP classification 1.20.30810.950 : Hydrolysis
CATH domain 3.40.50.1820 : Rossmann fold Catalytic domain
E.C. 3.8.1.5
CSA 1b6g
M-CSA 1b6g
MACiE

CATH domain Related DB codes (homologues)
3.40.50.1820 : Rossmann fold S00544 S00344 S00517 S00525 S00526 S00720 S00723 S00724 S00725 S00919 S00057 S00374 S00345 S00347 S00348 S00346 S00350 S00352 S00353 S00355 S00358 D00189 D00210 D00539 T00253

Uniprot Enzyme Name
UniprotKB Protein name Synonyms MEROPS Pfam
P22643 Haloalkane dehalogenase
EC 3.8.1.5
S33.990 (Serine)
PF00561 (Abhydrolase_1)
[Graphical View]

KEGG enzyme name
haloalkane dehalogenase
1-chlorohexane halidohydrolase
1-haloalkane dehalogenase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P22643 DHLA_XANAU 1-haloalkane + H(2)O = a primary alcohol + halide. 1,2-dichloroethane + H(2)O = 2-chloroethanol + hydrogen chloride. Monomer.

KEGG Pathways
Map code Pathways E.C.
MAP00361 gamma-Hexachlorocyclohexane degradation
MAP00626 Naphthalene and anthracene degradation
MAP00631 1,2-Dichloroethane degradation
MAP00641 3-Chloroacrylic acid degradation

Compound table
Substrates Products Intermediates
KEGG-id C01872 C00001 C01813 C01706 C00226 C00462
E.C.
Compound 1-Haloalkane H2O Haloalcohol Haloalkene Primary alcohol Halide
Type halide H2O carbohydrate,halide halide carbohydrate halide
ChEBI 15377
PubChem 22247451
962
1b6gA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:_CL_1998 Unbound
1be0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1beeA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1bezA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1cijA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:_BR_401 Unbound
1edbA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:_CL Unbound
1eddA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:_CL Unbound
1edeA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1hdeA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1hdeB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
2dhcA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:DCE Unbound Unbound Unbound Unbound Unbound
2dhdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:_CL_552 Bound:MCE
2dheA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:_CL Unbound
2edaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:IOD Unbound
2edcA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:IOD Unbound
2hadA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1b6gA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 124;ASP 260;HIS 289;TRP 125;TRP 175 GLU 56;TRP 125
1be0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 124;ASP 260;HIS 289;TRP 125;TRP 175 GLU 56;TRP 125 mutant I2V
1beeA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 124;ASP 260;HIS 289;TRP 125; GLU 56;TRP 125 mutant I2V, W175Y
1bezA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 124;ASP 260;HIS 289;TRP 125; GLU 56;TRP 125 mutant I2V, W175Y
1cijA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 124;ASP 260;HIS 289;TRP 125;TRP 175 GLU 56;TRP 125 mutant I2V
1edbA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 124;ASP 260;HIS 289;TRP 125;TRP 175 GLU 56;TRP 125
1eddA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 124;ASP 260;HIS 289;TRP 125;TRP 175 GLU 56;TRP 125
1edeA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 124;ASP 260;HIS 289;TRP 125;TRP 175 GLU 56;TRP 125
1hdeA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 124;ASP 260;HIS 289;TRP 125;TRP 175 GLU 56;TRP 125 mutant F172W
1hdeB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 124;ASP 260;HIS 289;TRP 125;TRP 175 GLU 56;TRP 125 mutant F172W
2dhcA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 124;ASP 260;HIS 289;TRP 125;TRP 175 GLU 56;TRP 125
2dhdA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 124;ASP 260;HIS 289;TRP 125;TRP 175 GLU 56;TRP 125
2dheA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 124;ASP 260;HIS 289;TRP 125;TRP 175 GLU 56;TRP 125
2edaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 124;ASP 260;HIS 289;TRP 125;TRP 175 GLU 56;TRP 125
2edcA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 124;ASP 260;HIS 289;TRP 125;TRP 175 GLU 56;TRP 125
2hadA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 124;ASP 260;HIS 289;TRP 125;TRP 175 GLU 56;TRP 125

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.1300
[2]
Fig.1 2
[4]
Fig.4 4
[10]
p.995-996

References
[1]
Resource
Comments X-ray crystallography (2.4 Angstroms)
Medline ID 91224078
PubMed ID 2026135
Journal EMBO J
Year 1991
Volume 10
Pages 1297-1302
Authors Franken S.M., Rozeboom H.J., Kalk K.H., Dijkstra B.W
Title Crystal structure of haloalkane dehalogenase: an enzyme to detoxify halogenated alkanes.
Related PDB 2had
Related UniProtKB
[2]
Resource
Comments X-ray crystallography, catalysis
Medline ID
PubMed ID 8369276
Journal Biochemistry
Year 1993
Volume 32
Pages 9031-7
Authors Verschueren KH, Kingma J, Rozeboom HJ, Kalk KH, Janssen DB, Dijkstra BW
Title Crystallographic and fluorescence studies of the interaction of haloalkane dehalogenase with halide ions. Studies with halide compounds reveal a halide binding site in the active site.
Related PDB 1edb 1edd 2eda 2edc
Related UniProtKB
[3]
Resource
Comments X-ray crystallography (1.9 Angstroms)
Medline ID
PubMed ID 8355275
Journal J Mol Biol
Year 1993
Volume 232
Pages 856-72
Authors Verschueren KH, Franken SM, Rozeboom HJ, Kalk KH, Dijkstra BW
Title Refined X-ray structures of haloalkane dehalogenase at pH 6.2 and pH 8.2 and implications for the reaction mechanism.
Related PDB 1ede
Related UniProtKB
[4]
Resource
Comments X-ray crystallography (2.4 Angstroms)
Medline ID 93295480
PubMed ID 8515812
Journal Nature
Year 1993
Volume 363
Pages 693-8
Authors Verschueren K.H.G., Seljee F., Rozeboom H.J., Kalk K.H., Dijkstra B.W
Title Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase.
Related PDB 2dhc 2dhd 2dhe
Related UniProtKB
[5]
Resource
Comments catalysis, X-ray crystallography
Medline ID
PubMed ID 8855957
Journal Biochemistry
Year 1996
Volume 35
Pages 13186-95
Authors Schanstra JP, Ridder IS, Heimeriks GJ, Rink R, Poelarends GJ, Kalk KH, Dijkstra BW, Janssen DB
Title Kinetic characterization and X-ray structure of a mutant of haloalkane dehalogenase with higher catalytic activity and modified substrate range.
Related PDB 1hde
Related UniProtKB
[6]
Resource
Comments X-ray crystallography (1.96 Angstroms)
Medline ID 99007117
PubMed ID 9790663
Journal Biochemistry
Year 1998
Volume 37
Pages 15013-23
Authors Krooshof G.H., Ridder I.S., Tepper A.W.J.W., Vos G.J., Rozeboom H.J., Kalk K.H., Dijkstra B.W., Janssen D.B
Title Kinetic analysis and X-ray structure of haloalkane dehalogenase with a modified halide-binding site.
Related PDB 1bee 1bez
Related UniProtKB
[7]
Resource
Comments X-ray crystallography (1.15 Angstroms)
Medline ID
PubMed ID 10393294
Journal Acta Crystallogr D Biol Crystallogr
Year 1999
Volume 55
Pages 1273-90
Authors Ridder IS, Rozeboom HJ, Dijkstra BW
Title Haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 refined at 1.15 A resolution
Related PDB 1b6g
Related UniProtKB
[8]
Resource
Comments X-ray crystallography (2.3 Angstroms)
Medline ID 99438358
PubMed ID 10508409
Journal Biochemistry
Year 1999
Volume 38
Pages 12052-61
Authors Pikkemaat M.G., Ridder I.S., Rozeboom H.J., Kalk K.H., Dijkstra B.W., Janssen D.B
Title Crystallographic and kinetic evidence of a collision complex formed during halide import in haloalkane dehalogenase.
Related PDB 1cij
Related UniProtKB
[9]
Resource
Comments X-ray crystallography (1.5 Angstroms)
Medline ID
PubMed ID 10587433
Journal Biochemistry
Year 1999
Volume 38
Pages 16105-14
Authors Newman J, Peat TS, Richard R, Kan L, Swanson PE, Affholter JA, Holmes IH, Schindler JF, Unkefer CJ, Terwilliger TC
Title Haloalkane dehalogenases: structure of a Rhodococcus enzyme.
Related PDB 1bn6 1bn7 1cqw
Related UniProtKB
[10]
Resource
Comments reaction mechanism and substrate specificity (comparative study)
Medline ID
PubMed ID 10585505
Journal Protein Eng
Year 1999
Volume 12
Pages 989-98
Authors Damborsky J, Koca J
Title Analysis of the reaction mechanism and substrate specificity of haloalkane dehalogenases by sequential and structural comparisons.
Related PDB
Related UniProtKB
[11]
Resource
Comments X-ray crystallography (1.58 Angstroms)
Medline ID
PubMed ID 11087355
Journal Biochemistry
Year 2000
Volume 39
Pages 14082-6
Authors Marek J, Vevodova J, Smatanova IK, Nagata Y, Svensson LA, Newman J, Takagi M, Damborsky J
Title Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26.
Related PDB 1cv2 1d07
Related UniProtKB
[12]
Resource
Comments catalysis (mutatition analysis)
Medline ID
PubMed ID 10850790
Journal J Chem Inf Comput Sci
Year 2000
Volume 40
Pages 839-46
Authors Robert D, Girones X, Carbo-Dorca R
Title Quantification of the influence of single-point mutations on haloalkane dehalogenase activity: a molecular quantum similarity study.
Related PDB
Related UniProtKB
[13]
Resource
Comments catalysis
Medline ID
PubMed ID 10963662
Journal Proc Natl Acad Sci U S A
Year 2000
Volume 97
Pages 9937-42
Authors Lau EY, Kahn K, Bash PA, Bruice TC
Title The importance of reactant positioning in enzyme catalysis: a hybrid quantum mechanics/molecular mechanics study of a haloalkane dehalogenase.
Related PDB
Related UniProtKB
[14]
Resource
Comments catalysis (Erratum in:Biochemistry 2001 Sep 18;40(37):11288)
Medline ID
PubMed ID 11467952
Journal Biochemistry
Year 2001
Volume 40
Pages 8905-17
Authors Kmunicek J, Luengo S, Gago F, Ortiz AR, Wade RC, Damborsky J
Title Comparative binding energy analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10.
Related PDB
Related UniProtKB
[15]
Resource
Comments multiple computer-automated structure evaluation
Medline ID
PubMed ID 11764149
Journal Environ Toxicol Chem
Year 2001
Volume 20
Pages 2681-9
Authors Damborsky J, Rorije E, Jesenska A, Nagata Y, Klopman G, Peijnenburg WJ
Title Structure-specificity relationships for haloalkane dehalogenases.
Related PDB
Related UniProtKB

Comments
According to the literature [1], [2] & [4], the catalytic mechanism of this enzyme is very similar to that of trypsin (D00197 in EzCatDB), except for the fact that the reaction is assisted by the stabilizer for the leaving halide atom, Trp125 and Trp175. The reaction proceeds as follows:
(1) Asp124 acts as a nucleophile, which makes a nucleophilic attack on the C1 carbon of the substrate, to form a covalently bound ester inetermediate. In the meantime, slightly positively charged NH atoms of Trp125 and Trp175 stabilizes the leaving halogen atom, facilitating the reaction. (SN2-like mechanism) The transition state is stabilized by the mainchain amide groups of Glu56 and Trp125.
(2) The tetrahedral intermediate is formed, which is stabilized by the mainchain amide groups of Glu56 and Trp125.
(3) His289 acts as a general base to activate a water. (Asp260 modulates the activity of His289.)
(4) The activated water makes a nucleophilic attack on the intermediate, to complete the raction.
###
The data for the type-2 subfamily is deposited in S00525 of EzCatDB.
This enzyme belongs to haloalkane dehydrogenase Type-1 subfamily.

Created Updated
2002-09-05 2009-03-16