Crystal Structures of the Substrate Free-enzyme, and Reaction Intermediate of the HAD Superfamily Member, Haloacid Dehalogenase DehIVa from Burkholderia cepacia MBA4

Schmidberger, J.W.; Wilce, Jacqueline Anne; Tsang, Jwh; Wilce, Matthew Charles James

doi:10.1016/j.jmb.2007.02.015

Cited by 52 publications

(76 citation statements)

References 64 publications

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“…the positively charged pocket for the binding of the carboxylate residue was proposed at the active site and found close to the basic group that promotes nucleophilic attack (36), which proceeds via an S n 2 mechanism (27,30,31), as is observed for the hadD of P. putida AJ1/23 (4). lys and Arg residues were proposed to be at the active site (22).…”

Section: Proposed Catalytic Site Of Dehalogenase D (Dehd) That Underlmentioning

confidence: 85%

“…consequently, certain group i dehalogenases degrade both D-and l-haloacids (6,36), whereas others process only D-enantiomers or l-enantiomers. Group ii α-dehalogenases specifically degrade substrates containing a halogen bound to α-carbon that has an L-configuration resulting into inversion of configuration of the chiral carbon (30). Group iii dehalogenases, unlike other groups, degrade only D-enantiomers.…”

Section: Dehalogenase Specificitiesmentioning

confidence: 99%

“…the use of dehalogenases in industrial processes is well established (34), and potentially can be used for the biodegradation of environmentally toxic halogenated compounds such as man-made chemicals used as refrigerants, fire retardants, paints, solvents, herbicides and pesticides (8). certain dehalogenases initiate the breakdown of halogenated organic compounds by cleaving the carbon-halogen bond with the inversion the configuration of the chiral carbon (13,27,30,35).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

D-Specific Dehalogenases, a Review

Huyop

Sudi

2012

Biotechnology & Biotechnological Equipment

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Section: Proposed Catalytic Site Of Dehalogenase D (Dehd) That Underlmentioning

confidence: 85%

Section: Dehalogenase Specificitiesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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D-Specific Dehalogenases, a Review

Huyop

Sudi

2012

Biotechnology & Biotechnological Equipment

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“…The sequence alignment results showed that it belonged to the haloacid dehalogenase (HAD)-like superfamily, but it showed only 36 % identity with the sequence of ESHs from Rhodococcus opacus and Nocardia tartaricans (Liu et al 2007;Wang et al 2012). ESHs from R. opacus and N. tartaricans, and a selection of proteins (Schmidberger et al 2007;Ridder et al 1999;Novak et al 2013;Hisano et al 1996;Li et al 1998) with low but significant sequence identity (between 27 and 36 %), are shown in a ClustalW2 alignment result (Fig. 2).…”

Section: Sequence Comparison Of Esh and Reported Ehsmentioning

confidence: 99%

“…JS666 (YP_547390); 1JUD, 2-haloacid dehalogenase from Pseudomonas sp. YL (Q53464) three members (DehIVa, DhlB, and L -DEX) of the HAD-like superfamily with reported crystal structures (Pan et al 2011;Schmidberger et al 2007;Ridder et al 1999;Hisano et al 1996;Li et al 1998). They all have a mixed a/b core domain and a four-helix bundle domain.…”

Section: Characterization Of the Mutant Enzymesmentioning

confidence: 99%

Cloning, homology modeling, and reaction mechanism analysis of a novel cis-epoxysuccinate hydrolase from Klebsiella sp.

et al. 2014

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The gene encoding a novel cis-epoxysuccinate hydrolase, which hydrolyzes cis-epoxysuccinate to L (+)-tartaric acid, was cloned from Klebsiella sp. BK-58 and expressed in Escherichia coli. The ORF was 825 bp encoding a mature protein of 274 amino acids with a molecular mass of 30.1 kDa. Multiple sequence alignment showed that the enzyme belonged to the haloacid dehalogenase-like super family. Homology modeling and site-directed mutagenesis were performed to investigate the structural characteristics of the enzyme. Its overall structure consisted of a core domain formed by six-stranded parallel β-sheets flanked by seven α-helices and a subdomain that had a four helix bundle structure. Residues D48, T52, R85, N165, K195, Y201, A219, H221, and D224 were catalytically important forming the active pocket between the two domains. An (18)O-labeling study suggested that the catalytic reaction of the enzyme proceeded through a two-step mechanism.

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Enhanced degradation of haloacid by heterologous expression in related Burkholderia species

Deng

Kong

et al. 2013

Biotech & Bioengineering

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Haloacids are environmental pollutant and can be transformed to non-toxic alkanoic acids by microbial dehalogenase. Bacterium Burkholderia species MBA4 was enriched from soil for its ability to bioremediate haloacids such as mono-chloroacetate (MCA), mono-bromoacetate (MBA), 2-mono-chloropropionate, and 2-mono-bromopropionate. MBA4 produces an inducible dehalogenase Deh4a that catalyzes the dehalogenation process. The growth of MBA4 on haloacid also relies on the presence of a haloacid-uptake system. Similar dehalogenase genes can be found in the genome of many related species. However, wildtype Burkholderia caribensis MWAP64, Burkholderia phymatum STM815, and Burkholderia xenovorans LB400 were not able to grow on MCA. When a plasmid containing the regulatory and structural gene of Deh4a was transformed to these species, they were able to grow on haloacid. The specific enzyme activities in these recombinants ranges from 2- to 30-fold that of MBA4 in similar condition. Reverse transcription-quantitative real-time PCR showed that the relative transcript levels in these recombinant strains ranges from 9 to over 1,600 times that of MBA4 in similar condition. A recombinant has produced nearly five times of dehalogenase that MBA4 could ever achieve. While the expressions of Deh4a were more relaxed in these phylogenetically related species, an MCA-uptake activity was found to be inducible. These metabolically engineered strains are better degraders than the haloacid-enriched MBA4.

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Crystal Structures of the Substrate Free-enzyme, and Reaction Intermediate of the HAD Superfamily Member, Haloacid Dehalogenase DehIVa from Burkholderia cepacia MBA4

Cited by 52 publications

References 64 publications

D-Specific Dehalogenases, a Review

D-Specific Dehalogenases, a Review

Cloning, homology modeling, and reaction mechanism analysis of a novel cis-epoxysuccinate hydrolase from Klebsiella sp.

Enhanced degradation of haloacid by heterologous expression in related Burkholderia species

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