Haloalkane dehalogenase (subfamily 1)

 

Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons. Has a broad substrate specificity, which includes terminally mono- and di- chlorinated and brominated alkanes (up to C4 only). The highest activity was found with 1,2-dichloroethane, 1,3-dichloropropane, and 1,2-dibromoethane.

 

Reference Protein and Structure

Sequence
P22643 UniProt (3.8.1.5) IPR023489 (Sequence Homologues) (PDB Homologues)
Biological species
Xanthobacter autotrophicus (Bacteria) Uniprot
PDB
1b6g - HALOALKANE DEHALOGENASE AT PH 5.0 CONTAINING CHLORIDE (1.15 Å) PDBe PDBsum 1b6g
Catalytic CATH Domains
3.40.50.1820 CATHdb (see all for 1b6g)
Click To Show Structure

Enzyme Reaction (EC:3.8.1.5)

1-haloalkane
CHEBI:18060ChEBI
+
water
CHEBI:15377ChEBI
→
hydron
CHEBI:15378ChEBI
+
halide anion
CHEBI:16042ChEBI
+
primary alcohol
CHEBI:15734ChEBI
Alternative enzyme names: 1-chlorohexane halidohydrolase, 1-haloalkane dehalogenase,

Enzyme Mechanism

Introduction

Asp124 (activated through an Asp-His-HOH-Asp charge relay system) initiates a nucleophilic attack on the halide substrate, forming a covalent alkyl-enzyme intermediate with the halide ion being eliminated in an Sn2 reaction.

The water in the Asp-His-HOH-Asp charge relay system is activated by the histidine, and initiates the cleavage of the alkyl-enzyme intermediate. It is thought that the halide remains in the active site until the reaction is complete.

Catalytic Residues Roles

UniProt PDB* (1b6g)
Asp124 Asp124A Acts as the catalytic nucleophile. covalent catalysis
Asp260 Asp260A Activates the catalytic nucleophile through its interaction with the second residue of the triad (histidine). activator, electrostatic stabiliser
His289 His289A Activates the nucleophilic aspartate and acts as a general acid/base to activate the catalytic water molecule. proton shuttle (general acid/base)
Trp125, Trp175 Trp125A, Trp175A Act to stabilise the halide ion. electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. Pavlová M et al. (2007), J Struct Biol, 157, 384-392. The identification of catalytic pentad in the haloalkane dehalogenase DhmA from Mycobacterium avium N85: Reaction mechanism and molecular evolution. DOI:10.1016/j.jsb.2006.09.004. PMID:17084094.
  2. Zhang Y et al. (2012), Int J Quantum Chem, 112, 889-899. Effect of electrostatic interaction on the mechanism of dehalogenation catalyzed by haloalkane dehalogenase. DOI:10.1002/qua.22509.
  3. Silberstein M et al. (2007), Biochemistry, 46, 9239-9249. Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA fromXanthobacter autotrophicusGJ10†. DOI:10.1021/bi700336y. PMID:17645312.
  4. Lau EY et al. (2000), Proc Natl Acad Sci U S A, 97, 9937-9942. The importance of reactant positioning in enzyme catalysis: A hybrid quantum mechanics/molecular mechanics study of a haloalkane dehalogenase. DOI:10.1073/pnas.97.18.9937.
  5. Ridder IS et al. (1999), Acta Crystallogr D Biol Crystallogr, 55, 1273-1290. Haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 refined at 1.15 Å resolution. DOI:10.1107/s090744499900534x. PMID:10393294.
  6. Pikkemaat MG et al. (1999), Biochemistry, 38, 12052-12061. Crystallographic and Kinetic Evidence of a Collision Complex Formed during Halide Import in Haloalkane Dehalogenase†. DOI:10.1021/bi990849w.

Step 1.

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Catalytic Residues Roles

Residue Roles
Asp124A covalent catalysis
His289A proton shuttle (general acid/base)
Asp260A activator
Trp125A electrostatic stabiliser
Trp175A electrostatic stabiliser
Asp260A electrostatic stabiliser

Chemical Components

Step 1.

Contributors

Alex Gutteridge, Craig Porter, Gemma L. Holliday