Structure Prediction, Molecular Dynamics Simulation and Docking Studies of D-Specific Dehalogenase from Rhizobium sp. RC1

Abstract

Currently, there is no three-dimensional structure of D-specific dehalogenase (DehD) in the protein database. We modeled DehD using ab initio technique, performed molecular dynamics (MD) simulation and docking of D-2-chloropropionate (D-2CP), D-2-bromopropionate (D-2BP), monochloroacetate (MCA), monobromoacetate (MBA), 2,2-dichloropropionate (2,2-DCP), D,L-2,3-dichloropropionate (D,L-2,3-DCP), and 3-chloropropionate (3-CP) into the DehD active site. The sequences of DehD and D-2-haloacid dehalogenase (HadD) from Pseudomonas putida AJ1 have 15% sequence similarity. The model had 80% of the amino acid residues in the most favored region when compared to the crystal structure of DehI from Pseudomonas putida PP3. Docking analysis revealed that Arg107, Arg134 and Tyr135 interacted with D-2CP, and Glu20 activated the water molecule for hydrolytic dehalogenation. Single residue substitutions at 25–30 °C showed that polar residues of DehD were stable when substituted with nonpolar residues and showed a decrease in activity within the same temperature range. The molecular dynamics simulation of DehD and its variants showed that in R134A variant, Arg107 interacted with D-2CP, while in Y135A, Gln221 and Arg231 interacted with D-2CP. It is our emphatic belief that the new model will be useful for the rational design of DehDs with enhanced potentials.

Inverting hydrolases and their use in enantioconvergent biotransformations

“…Recently, structure prediction, molecular dynamics simulation and substrate docking were conducted for DheI from Rhizobium sp. RC1 to elucidate the catalytic residues [74]. Recently, literature on d -specific haloacid dehalogenases has been summarized [75].…”

Molecular identification and biodegradation of 3-chloropropionic acid (3CP) by filamentous fungi-Mucor and Trichoderma species isolated from UTM agricultural land

“…However, empirical investigations suggested otherwise (Huyop et al, 2004). In contrast, computational analysis showed that 3CP could not bind with DehD (Group I dehalogenase) active site (Sudi et al, 2012) and 3CP was not a substrate for DehD enzyme (Huyop et al, 2008). Both dehalogenases were previously isolated from Rhizobium sp.…”

Interactions of non-natural halogenated substrates with D-specific dehalogenase (DehD) mutants usingin silicostudies

“…[ 3 ] Barth et al [ 2 ] cloned D- and L-specific dehalogenases from P. putida strain AJ1/23, which shares only 15% amino-acid sequence similarity with DehD. [ 17 ] DehD is a group I α-haloacid dehalogenase and the only available representative crystal structure of a group I α-haloacid dehalogenase is that of DehI. [ 18 ] The enzyme was isolated by Senior et al [ 19 ] from P. putida strain PP3 and was partially purified by Weightman et al [ 20 ].…”

“…A sequence comparison of DehI with the DehDs from P. putida strain PP3 and P. putida strain AJ1/23 shows that the amino-acid residues that line the active site are conserved, with the exception of the Ala187 residue that has been replaced by Asn in the DehDs. [ 18 ] In our previous study on DehD,[ 17 ] a total of 20 amino-acid residues were predicted to form the active site, including Val45, Met70, Thr131, Val132, Ser133, Arg134, Tyr135, Leu136, Glu138, Asp139, Ala145, Ile147, Ile148, His149, Leu150, Cys253 and Leu257. Docking of D-2-chloropropionate into the DehD active site revealed that Arg107, Arg134 and Tyr135 form hydrogen bonds with D-2-chloropropionate.…”