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Literature summary extracted from

  • Sudi, I.Y.; Wong, E.L.; Joyce-Tan, K.H.; Shamsir, M.S.; Jamaluddin, H.; Huyop, F.
    Structure prediction, molecular dynamics simulation and docking studies of D-specific dehalogenase from Rhizobium sp. RC1 (2012), Int. J. Mol. Sci., 13, 15724-15754.
    View publication on PubMedView publication on EuropePMC

Application

EC Number Application Comment Organism
3.8.1.9 additional information D-specific dehalogenase DehD from Rhizobium sp. strain RC1 can be exploited as a potential target enzyme for industrial, pharmaceutical and other biotechnological applications Rhizobium sp.

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.8.1.9 additional information
-
 additional information kinetic studies Rhizobium sp.

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.8.1.9 (R)-2-haloacid + H2O Rhizobium sp.
-
 (S)-2-hydroxyacid + halide
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.8.1.9 Rhizobium sp. Q8KLS9
-
-

Reaction

EC Number Reaction Comment Organism Reaction ID
3.8.1.9 (R)-2-haloacid + H2O = (S)-2-hydroxyacid + halide proposed reaction mechanism, conserved residue Arg134 plays a key role in the dehalogenation process. Residues Arg107, Arg134 and Tyr135 interact with the substrates and are the catalytic residues of DehD that are involved in the dehalogenation of D-2-chloropropionate and D-2-bromopropionate, while Glu20 activates the water molecule that attacks the carbon halogen bond on the alpha-carbon, thereby releasing chloride ion Rhizobium sp.
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.8.1.9 (R)-2-haloacid + H2O
-
 Rhizobium sp. (S)-2-hydroxyacid + halide
-
 ?
3.8.1.9 2,2-dichloropropionate + H2O
-
 Rhizobium sp. ?
-
 ?
3.8.1.9 3-chloropropionate + H2O
-
 Rhizobium sp. 3-hydroxypropionate + chloride
-
 ?
3.8.1.9 D-2-bromopropionate + H2O
-
 Rhizobium sp. L-2-hydroxypropionate + bromide
-
 ?
3.8.1.9 D-2-chloropropionate + H2O
-
 Rhizobium sp. L-2-hydroxypropionate + chloride
-
 ?
3.8.1.9 DL-2,3-dichloropropionate + H2O
-
 Rhizobium sp. ?
-
 ?
3.8.1.9 monobromoacetate + H2O
-
 Rhizobium sp. hydroxyacetate + bromide
-
 ?
3.8.1.9 monochloroacetate + H2O
-
 Rhizobium sp. hydroxyacetate + chloride
-
 ?
3.8.1.9 additional information molecular docking of D-2-chloropropionate, D-2-bromopropionate, monochloroacetate, monobromoacetate, 2,2-dichloropropionate, DL-2,3-dichloropropionate, and 3-chloropropionate into the DehD active site, residues Arg107, Arg134 and Tyr135 interact with D-2-chloropropionate, and Glu20 activates the water molecule for hydrolytic dehalogenation Rhizobium sp. ?
-
 ?

Subunits

EC Number Subunits Comment Organism
3.8.1.9 More three-dimensional enzyme structure modeling and analysis. The secondary structure is predominantly alpha-helical. The N-terminus consists of 24 residues, primarily in the loop region, whereas the C-terminus had only one residue in the loop region. The D-2-specific dehalogenase (DehD) is predominantly made of alpha-helices and coil-coils with highly curved bends and is without strands, secondary structural elements, overview Rhizobium sp.

Synonyms

EC Number Synonyms Comment Organism
3.8.1.9 D-specific dehalogenase
-
 Rhizobium sp.
3.8.1.9 DehD
-
 Rhizobium sp.

General Information

EC Number General Information Comment Organism
3.8.1.9 additional information three-dimensional enzyme structure modeling and analysis, molecular dynamics simulations, comparison with Pseudomonas putida enzyme structures from strain AJ1 and PP3, overview. Residues Arg107, Arg134 and Tyr135 interact with D-2-chloropropionate, and Glu20 activated the water molecule for hydrolytic dehalogenation Rhizobium sp.