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PDBsum entry 2dhe
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.3.8.1.5
- haloalkane dehalogenase.
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Reaction:
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1-haloalkane + H2O = a halide anion + a primary alcohol + H+
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1-haloalkane
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+
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H2O
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=
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halide anion
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+
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primary alcohol
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+
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H(+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Nature
363:693-698
(1993)
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PubMed id:
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Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase.
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K.H.Verschueren,
F.Seljée,
H.J.Rozeboom,
K.H.Kalk,
B.W.Dijkstra.
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ABSTRACT
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Crystal structures of haloalkane dehalogenase were determined in the presence of
the substrate 1,2-dichloroethane. At pH 5 and 4 degrees C, substrate is bound in
the active site without being converted; warming to room temperature causes the
substrate's carbon-chlorine bond to be broken, producing a chloride ion with
concomitant alkylation of the active-site residue Asp124. At pH 6 and room
temperature the alkylated enzyme is hydrolysed by a water molecule activated by
the His289-Asp260 pair in the active site. These results show that catalysis by
the dehalogenase proceeds by a two-step mechanism involving an ester
intermediate covalently bound at Asp124.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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R.Shi,
L.McDonald,
Q.Cui,
A.Matte,
M.Cygler,
and
I.Ekiel
(2011).
Structural and mechanistic insight into covalent substrate binding by Escherichia coli dihydroxyacetone kinase.
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Proc Natl Acad Sci U S A,
108,
1302-1307.
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PDB codes:
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T.Kurihara
(2011).
A mechanistic analysis of enzymatic degradation of organohalogen compounds.
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Biosci Biotechnol Biochem,
75,
189-198.
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D.J.Brugh,
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The conformational landscape of the volatile anesthetic sevoflurane.
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Phys Chem Chem Phys,
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The complexes of halothane with benzene: the temperature dependent direction of the complexation shift of the aliphatic C-H stretching.
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Phys Chem Chem Phys,
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Widespread head-to-head hydrocarbon biosynthesis in bacteria and role of OleA.
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D.O'Hagan,
and
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Enzymes that catalyse SN2 reaction mechanisms.
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| |
Nat Prod Rep,
27,
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G.Wang,
R.Li,
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(2010).
A novel hydrolytic dehalogenase for the chlorinated aromatic compound chlorothalonil.
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| |
J Bacteriol,
192,
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L.Simón,
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Synthesis of a chiral artificial receptor with catalytic activity in Michael additions and its chiral resolution by a new methodology.
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Org Biomol Chem,
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P.Domínguez de María,
R.W.van Gemert,
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and
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(2010).
Biosynthesis of ethers: unusual or common natural events?
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Nat Prod Rep,
27,
370-392.
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R.A.Steiner,
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A.J.Oakley,
and
S.Fetzner
(2010).
Structural basis for cofactor-independent dioxygenation of N-heteroaromatic compounds at the alpha/beta-hydrolase fold.
|
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Proc Natl Acad Sci U S A,
107,
657-662.
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PDB codes:
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B.A.Robertson,
G.K.Schroeder,
Z.Jin,
K.A.Johnson,
and
C.P.Whitman
(2009).
Pre-steady-state kinetic analysis of cis-3-chloroacrylic acid dehalogenase: analysis and implications.
|
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Biochemistry,
48,
11737-11744.
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D.Makuc,
M.Lenarcic,
G.W.Bates,
P.A.Gale,
and
J.Plavec
(2009).
Anion-induced conformational changes in 2,7-disubstituted indole-based receptors.
|
| |
Org Biomol Chem,
7,
3505-3511.
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K.Jitsumori,
R.Omi,
T.Kurihara,
A.Kurata,
H.Mihara,
I.Miyahara,
K.Hirotsu,
and
N.Esaki
(2009).
X-Ray crystallographic and mutational studies of fluoroacetate dehalogenase from Burkholderia sp. strain FA1.
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J Bacteriol,
191,
2630-2637.
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M.Pavlova,
M.Klvana,
Z.Prokop,
R.Chaloupkova,
P.Banas,
M.Otyepka,
R.C.Wade,
M.Tsuda,
Y.Nagata,
and
J.Damborsky
(2009).
Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate.
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Nat Chem Biol,
5,
727-733.
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M.Sunbul,
and
J.Yin
(2009).
Site specific protein labeling by enzymatic posttranslational modification.
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Org Biomol Chem,
7,
3361-3371.
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T.Kamachi,
T.Nakayama,
O.Shitamichi,
K.Jitsumori,
T.Kurihara,
N.Esaki,
and
K.Yoshizawa
(2009).
The catalytic mechanism of fluoroacetate dehalogenase: a computational exploration of biological dehalogenation.
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Chemistry,
15,
7394-7403.
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C.Caltagirone,
P.A.Gale,
J.R.Hiscock,
S.J.Brooks,
M.B.Hursthouse,
and
M.E.Light
(2008).
1,3-Diindolylureas: high affinity dihydrogen phosphate receptors.
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Chem Commun (Camb),
(),
3007-3009.
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E.Yaffe,
D.Fishelovitch,
H.J.Wolfson,
D.Halperin,
and
R.Nussinov
(2008).
MolAxis: efficient and accurate identification of channels in macromolecules.
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Proteins,
73,
72-86.
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M.Otyepka,
P.Banás,
A.Magistrato,
P.Carloni,
and
J.Damborský
(2008).
Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods.
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Proteins,
70,
707-717.
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P.A.Gale
(2008).
Synthetic indole, carbazole, biindole and indolocarbazole-based receptors: applications in anion complexation and sensing.
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Chem Commun (Camb),
(),
4525-4540.
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U.I.Kim,
J.M.Suk,
V.R.Naidu,
and
K.S.Jeong
(2008).
Folding and anion-binding properties of fluorescent oligoindole foldamers.
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Chemistry,
14,
11406-11414.
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E.J.Bertaccini,
J.R.Trudell,
and
N.P.Franks
(2007).
The common chemical motifs within anesthetic binding sites.
|
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Anesth Analg,
104,
318-324.
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M.Ito,
Z.Prokop,
M.Klvana,
Y.Otsubo,
M.Tsuda,
J.Damborský,
and
Y.Nagata
(2007).
Degradation of beta-hexachlorocyclohexane by haloalkane dehalogenase LinB from gamma-hexachlorocyclohexane-utilizing bacterium Sphingobium sp. MI1205.
|
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Arch Microbiol,
188,
313-325.
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R.Omi,
K.Jitsumori,
T.Yamauchi,
S.Ichiyama,
T.Kurihara,
N.Esaki,
N.Kamiya,
K.Hirotsu,
and
I.Miyahara
(2007).
Expression, purification and preliminary X-ray characterization of DL-2-haloacid dehalogenase from Methylobacterium sp. CPA1.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
586-589.
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X.Liu,
B.L.Hanson,
P.Langan,
and
R.E.Viola
(2007).
The effect of deuteration on protein structure: a high-resolution comparison of hydrogenous and perdeuterated haloalkane dehalogenase.
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Acta Crystallogr D Biol Crystallogr,
63,
1000-1008.
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PDB codes:
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Y.Sato,
R.Natsume,
M.Tsuda,
J.Damborsky,
Y.Nagata,
and
T.Senda
(2007).
Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, DbjA, from Bradyrhizobium japonicum USDA110.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
294-296.
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M.Nikolausz,
I.Nijenhuis,
K.Ziller,
H.H.Richnow,
and
M.Kästner
(2006).
Stable carbon isotope fractionation during degradation of dichloromethane by methylotrophic bacteria.
|
| |
Environ Microbiol,
8,
156-164.
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M.Petrek,
M.Otyepka,
P.Banás,
P.Kosinová,
J.Koca,
and
J.Damborský
(2006).
CAVER: a new tool to explore routes from protein clefts, pockets and cavities.
|
| |
BMC Bioinformatics,
7,
316.
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P.Banás,
M.Otyepka,
P.Jerábek,
M.Petrek,
and
J.Damborský
(2006).
Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling.
|
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J Comput Aided Mol Des,
20,
375-383.
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Z.Hasan,
R.Renirie,
R.Kerkman,
H.J.Ruijssenaars,
A.F.Hartog,
and
R.Wever
(2006).
Laboratory-evolved vanadium chloroperoxidase exhibits 100-fold higher halogenating activity at alkaline pH: catalytic effects from first and second coordination sphere mutations.
|
| |
J Biol Chem,
281,
9738-9744.
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A.Jesenská,
M.Pavlová,
M.Strouhal,
R.Chaloupková,
I.Tesínská,
M.Monincová,
Z.Prokop,
M.Bartos,
I.Pavlík,
I.Rychlík,
P.Möbius,
Y.Nagata,
and
J.Damborsky
(2005).
Cloning, biochemical properties, and distribution of mycobacterial haloalkane dehalogenases.
|
| |
Appl Environ Microbiol,
71,
6736-6745.
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C.Morisseau,
and
B.D.Hammock
(2005).
Epoxide hydrolases: mechanisms, inhibitor designs, and biological roles.
|
| |
Annu Rev Pharmacol Toxicol,
45,
311-333.
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D.B.Janssen,
I.J.Dinkla,
G.J.Poelarends,
and
P.Terpstra
(2005).
Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities.
|
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Environ Microbiol,
7,
1868-1882.
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E.Blée,
S.Summerer,
M.Flenet,
H.Rogniaux,
A.Van Dorsselaer,
and
F.Schuber
(2005).
Soybean epoxide hydrolase: identification of the catalytic residues and probing of the reaction mechanism with secondary kinetic isotope effects.
|
| |
J Biol Chem,
280,
6479-6487.
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U.Frerichs-Deeken,
and
S.Fetzner
(2005).
Dioxygenases without requirement for cofactors: identification of amino acid residues involved in substrate binding and catalysis, and testing for rate-limiting steps in the reaction of 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase.
|
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Curr Microbiol,
51,
344-352.
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Y.Sato,
M.Monincová,
R.Chaloupková,
Z.Prokop,
Y.Ohtsubo,
K.Minamisawa,
M.Tsuda,
J.Damborsky,
and
Y.Nagata
(2005).
Two rhizobial strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium japonicum USDA110, encode haloalkane dehalogenases with novel structures and substrate specificities.
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Appl Environ Microbiol,
71,
4372-4379.
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D.B.Janssen
(2004).
Evolving haloalkane dehalogenases.
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Curr Opin Chem Biol,
8,
150-159.
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L.Rui,
L.Cao,
W.Chen,
K.F.Reardon,
and
T.K.Wood
(2004).
Active site engineering of the epoxide hydrolase from Agrobacterium radiobacter AD1 to enhance aerobic mineralization of cis-1,2-dichloroethylene in cells expressing an evolved toluene ortho-monooxygenase.
|
| |
J Biol Chem,
279,
46810-46817.
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M.Garcia-Viloca,
J.Gao,
M.Karplus,
and
D.G.Truhlar
(2004).
How enzymes work: analysis by modern rate theory and computer simulations.
|
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Science,
303,
186-195.
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R.M.de Jong,
W.Brugman,
G.J.Poelarends,
C.P.Whitman,
and
B.W.Dijkstra
(2004).
The X-ray structure of trans-3-chloroacrylic acid dehalogenase reveals a novel hydration mechanism in the tautomerase superfamily.
|
| |
J Biol Chem,
279,
11546-11552.
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PDB code:
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R.Chaloupková,
J.Sýkorová,
Z.Prokop,
A.Jesenská,
M.Monincová,
M.Pavlová,
M.Tsuda,
Y.Nagata,
and
J.Damborský
(2003).
Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel.
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J Biol Chem,
278,
52622-52628.
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R.M.de Jong,
and
B.W.Dijkstra
(2003).
Structure and mechanism of bacterial dehalogenases: different ways to cleave a carbon-halogen bond.
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| |
Curr Opin Struct Biol,
13,
722-730.
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R.M.de Jong,
J.J.Tiesinga,
H.J.Rozeboom,
K.H.Kalk,
L.Tang,
D.B.Janssen,
and
B.W.Dijkstra
(2003).
Structure and mechanism of a bacterial haloalcohol dehalogenase: a new variation of the short-chain dehydrogenase/reductase fold without an NAD(P)H binding site.
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EMBO J,
22,
4933-4944.
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PDB codes:
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Y.Nagata,
Z.Prokop,
S.Marvanová,
J.Sýkorová,
M.Monincová,
M.Tsuda,
and
J.Damborský
(2003).
Reconstruction of mycobacterial dehalogenase Rv2579 by cumulative mutagenesis of haloalkane dehalogenase LinB.
|
| |
Appl Environ Microbiol,
69,
2349-2355.
|
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Z.Prokop,
M.Monincová,
R.Chaloupková,
M.Klvana,
Y.Nagata,
D.B.Janssen,
and
J.Damborský
(2003).
Catalytic mechanism of the maloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26.
|
| |
J Biol Chem,
278,
45094-45100.
|
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A.J.Oakley,
Z.Prokop,
M.Bohác,
J.Kmunícek,
T.Jedlicka,
M.Monincová,
I.Kutá-Smatanová,
Y.Nagata,
J.Damborský,
and
M.C.Wilce
(2002).
Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition.
|
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Biochemistry,
41,
4847-4855.
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PDB codes:
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A.Jesenská,
M.Bartos,
V.Czerneková,
I.Rychlík,
I.Pavlík,
and
J.Damborský
(2002).
Cloning and expression of the haloalkane dehalogenase gene dhmA from Mycobacterium avium N85 and preliminary characterization of DhmA.
|
| |
Appl Environ Microbiol,
68,
3724-3730.
|
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T.Bosma,
J.Damborský,
G.Stucki,
and
D.B.Janssen
(2002).
Biodegradation of 1,2,3-trichloropropane through directed evolution and heterologous expression of a haloalkane dehalogenase gene.
|
| |
Appl Environ Microbiol,
68,
3582-3587.
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D.A.Whittington,
A.C.Rosenzweig,
C.A.Frederick,
and
S.J.Lippard
(2001).
Xenon and halogenated alkanes track putative substrate binding cavities in the soluble methane monooxygenase hydroxylase.
|
| |
Biochemistry,
40,
3476-3482.
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PDB codes:
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D.B.Janssen,
J.E.Oppentocht,
and
G.J.Poelarends
(2001).
Microbial dehalogenation.
|
| |
Curr Opin Biotechnol,
12,
254-258.
|
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|
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G.J.Poelarends,
R.Saunier,
and
D.B.Janssen
(2001).
trans-3-Chloroacrylic acid dehalogenase from Pseudomonas pavonaceae 170 shares structural and mechanistic similarities with 4-oxalocrotonate tautomerase.
|
| |
J Bacteriol,
183,
4269-4277.
|
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J.Damborský,
E.Rorije,
A.Jesenská,
Y.Nagata,
G.Klopman,
and
W.J.Peijnenburg
(2001).
Structure-specificity relationships for haloalkane dehalogenases.
|
| |
Environ Toxicol Chem,
20,
2681-2689.
|
|
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J.E.van Hylckama Vlieg,
L.Tang,
J.H.Lutje Spelberg,
T.Smilda,
G.J.Poelarends,
T.Bosma,
A.E.van Merode,
M.W.Fraaije,
and
D.B.Janssen
(2001).
Halohydrin dehalogenases are structurally and mechanistically related to short-chain dehydrogenases/reductases.
|
| |
J Bacteriol,
183,
5058-5066.
|
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J.Hartleib,
and
H.Rüterjans
(2001).
Insights into the reaction mechanism of the diisopropyl fluorophosphatase from Loligo vulgaris by means of kinetic studies, chemical modification and site-directed mutagenesis.
|
| |
Biochim Biophys Acta,
1546,
312-324.
|
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M.S.Brody,
K.Vijay,
and
C.W.Price
(2001).
Catalytic function of an alpha/beta hydrolase is required for energy stress activation of the sigma(B) transcription factor in Bacillus subtilis.
|
| |
J Bacteriol,
183,
6422-6428.
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B.Golinelli-Pimpaneau,
O.Goncalves,
T.Dintinger,
D.Blanchard,
M.Knossow,
and
C.Tellier
(2000).
Structural evidence for a programmed general base in the active site of a catalytic antibody.
|
| |
Proc Natl Acad Sci U S A,
97,
9892-9895.
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PDB code:
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D.Hunkeler,
and
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The most recent references are shown first.
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Where a reference describes a PDB structure, the PDB
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