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Literature summary for 3.8.1.10 extracted from

  • Siwek, A.; Omi, R.; Hirotsu, K.; Jitsumori, K.; Esaki, N.; Kurihara, T.; Paneth, P.
    Binding modes of DL-2-haloacid dehalogenase revealed by crystallography, modeling and isotope effects studies (2013), Arch. Biochem. Biophys., 540, 26-32.
    View publication on PubMed
Search for more literature for 3.8.1.10

Cloned(Commentary)

Cloned (Comment) Organism
recombinant expresssion of enzyme DL-DEX Mb in Escherichia coli Methylobacterium sp.

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant native and selenomethionine-labeled wild-type enzyme and recombinant D194N enzyme mutant complexed with inhibitor 2-bromo-2-methylpropionate, 15 mg/mL protein in 10 mM Hepes-NaOH, pH 7.5, is mixed with 3 M sodium formate, 5% glycerol v/v, as the reservoir solution, X-ray diffraction structure determination and analysis at 1.7-2.7 A resolution Methylobacterium sp.

Protein Variants

Protein Variants Comment Organism
D194N site-directed mutagenesis Methylobacterium sp.

Inhibitors

Inhibitors Comment Organism Structure
2-bromo-2-methylpropionate an inhibitor of the D194N mutant enzyme and slow substrate of the wild-type enzyme Methylobacterium sp.

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
additional information Methylobacterium sp. DL-2-haloacid dehalogenase, DL-DEX, converts both enantiomers of the substrate ?
-
 ?

Organism

Organism UniProt Comment Textmining
Methylobacterium sp. A6BM74
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-

Purification (Commentary)

Purification (Comment) Organism
recombinant enzyme DL-DEX Mb from Escherichia coli Methylobacterium sp.

Reaction

Reaction Comment Organism Reaction ID
(R)-2-haloacid + H2O = (S)-2-hydroxyacid + halide group I enzymes, including DL-2-haloacid dehalogenase and D-2-haloacid dehalogenase, catalyze the reaction without forming an ester intermediate. Instead, a solvent water molecule directly attacks the alpha-carbon atom of the substrate to release the halide ion. DL-2-haloacid dehalogenase acts on both enantiomers of the substrate Methylobacterium sp.
a
(S)-2-haloacid + H2O = (R)-2-hydroxyacid + halide group I enzymes, including DL-2-haloacid dehalogenase and D-2-haloacid dehalogenase, catalyze the reaction without forming an ester intermediate. Instead, a solvent water molecule directly attacks the alpha-carbon atom of the substrate to release the halide ion. DL-2-haloacid dehalogenase acts on both enantiomers of the substrate Methylobacterium sp.
a

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
(R)-2-chloropropionate + H2O
-
 Methylobacterium sp. (S)-2-hydroxypropionate + chloride
-
 ?
(S)-2-chloropropionate + H2O
-
 Methylobacterium sp. (R)-2-hydroxypropionate + chloride
-
 ?
2-bromo-2-methylpropionate + H2O slow substrate for the wild-type enzyme, but inhibitory for enzyme mutant D194N Methylobacterium sp. 2-hydroxy-2-methylpropionate + bromide
-
 ?
additional information DL-2-haloacid dehalogenase, DL-DEX, converts both enantiomers of the substrate Methylobacterium sp. ?
-
 ?

Synonyms

Synonyms Comment Organism
DL-2-haloacid dehalogenase
-
 Methylobacterium sp.
DL-DEX
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 Methylobacterium sp.
DL-DEX Mb
-
 Methylobacterium sp.

General Information

General Information Comment Organism
evolution the reaction proceeds in two steps, in the first step, a catalytic aspartate residue nucleophilically attacks the alpha-carbon atom of the substrate to release the halide ion, resulting in the formation of an ester intermediate in which the aspartate residue is covalently bound to the alpha-carbon atom of the substrate. In the second step, the ester intermediate is hydrolyzed by a solvent water molecule. This mechanism is not restricted to this group of enzymes, e.g., fluoroacetate dehalogenase catalyzes the reaction in the same manner, although this enzyme is not evolutionarily related to the group II enzymes. Group I enzymes, including DL-2-haloacid dehalogenase and D-2-haloacid dehalogenase, catalyze the reaction without forming an ester intermediate. Instead, a solvent water molecule directly attacks the alpha-carbon atom of the substrate to release the halide ion. DL-2-haloacid dehalogenase is an extraordinary enzyme that acts on both enantiomers of the substrate Methylobacterium sp.
additional information modeling of binding pocket and the active site and QM/QM calculations, docking study using (R)- and (S)-2-chloropropionates, overview. The binding site cavity is shielded from the solvent region, and is composed of eight hydrophobic residues (Trp37, Ala39, Phe40, Gly41, Ala192, Phe273, Ile274, and Ile277), and five hydrophilic residues (Asn117, Tyr120, Ser193, Asp194, and Tyr270) Methylobacterium sp.