Interactions of non-natural halogenated substrates with D-specific dehalogenase (DehD) mutants using in silico studies

References

• Kurihara T, Esaki N. Bacterial hydrolytic dehalogenases and related enzymes: occurrences, reaction mechanisms, and applications. Chem Record. 2008;8:67–74.
   PubMed Web of Science ®Google Scholar
• Barth PT, Bolton L, Thomson JC. Cloning and partial sequencing of an operon encoding two Pseudomonas putida haloalkanoate dehalogenases of opposite stereospecificity. J Bacteriol. 1992;174:2612–2619.
   PubMed Web of Science ®Google Scholar
• Leigh JA, Skinner AJ, Cooper RA. Partial purification, stereospecificity and stoichiometry of three dehalogenases from a Rhizobium species. FEMS Microbiol Lett. 1998;49:353–356.
   Google Scholar
• Nardi-Dei V, Kurihara T, Park C, Esaki N, Soda K. Bacterial DL-2-haloacid dehalogenase from Pseudomonas sp. strain 113: gene cloning and structural comparison with D- and L-2-haloacid dehalogenases. J Bacteriol. 1997;179:4232–4238.
   PubMed Web of Science ®Google Scholar
• Smith JM, Harrison K, Colby J. Purification and characterization of D-2-haloacid dehalogenase from Pseudomonas putida strain AJ1/23. J Gen Microbiol. 1990;136:881–886.
   PubMedGoogle Scholar
• Soda K, Kurihara T, Liu J-Q, Nardi-Dei V, Park C, Miyagi M, Tsunasawa S, Esaki N. Bacterial 2-haloacid dehalogenases: structures and catalytic properties. Pure Appl Chem. 1996;68:2097–2103.
   Web of Science ®Google Scholar
• Weightman AJ, Weightman AL, Slater JH. Stereospecificity of 2-monochloropropionate dehalogenation by the two dehalogenases of Pseudomonas putida PP3: evidence for two different dehalogenation mechanisms. J Gen Microbiol. 1982;128:1755–1762.
   PubMedGoogle Scholar
• Li YF, Hata Y, Fujii T, Hisano T, Nishihara M, Kurihara T, Esaki N. Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism. J Biol Chem. 1998;273:15035–15044.
   PubMed Web of Science ®Google Scholar
• Janssen DB, Oppentocht JE, Poelarends GJ. Microbial dehalogenation. Curr Opin Biotechnol. 2001;12:254–258.
   PubMed Web of Science ®Google Scholar
• Ridder IS, Rozeboom HJ, Kalk KH, Dijkstra BW. Crystal structures of intermediates in the dehalogenation of haloalkanoates by L-2-haloacid dehalogenase. J Biol Chem. 1999;274:30672–30678.
   PubMed Web of Science ®Google Scholar
• Hill KE, Marchesi JR, Weightman AJ. Investigation of two evolutionarily unrelated halocarboxylic acid dehalogenase gene families. J Bacteriol. 1999;181(8):2535–2547.
   PubMed Web of Science ®Google Scholar
• Cairns SS, Cornish A, Cooper RA. Cloning, sequencing and expression in Escherichia coli of two Rhizobium sp. genes encoding haloalkanoate dehalogenases of opposite stereospecificity. Eur J Biochem. 1996;235:744–749.
   PubMedGoogle Scholar
• Higgins TP, Hope SJ, Effendi AJ, Dawson S, Dancer BN. Biochemical and molecular characterisation of the 2,3-dichloro-1-propanol dehalogenase and stereospecific haloalkanoic dehalogenases from a versatile Agrobacterium sp. Biodegradation. 2005;16:485–492.
   PubMed Web of Science ®Google Scholar
• Huyop F, Jing NH, Cooper RA. Overexpression, purification and analysis of dehalogenase of Rhizobium sp. Can J Pure Appl Sci. 2008;2(2):389–392.
   Google Scholar
• Huyop F, Nemati M. Properties of dehalogenase from Rhizobium sp. RC1. Afr J Microbiol Res. 2010;4:2836–2847.
   Google Scholar
• Huyop FZ, Cooper RA. A potential use of dehalogenase D (DehD) from Rhizobium sp. for industrial process. J Teknol. 2003;38:69–75.
   Google Scholar
• Sudi I, Wong E, Joyce-Tan K, Shamsir M, Jamaluddin H, Huyop F. Structure prediction, molecular dynamics simulation and docking studies of D-specific dehalogenase from Rhizobium sp. RC1. Intl J Mol Sci. 2012;13:15724–15754.
   PubMed Web of Science ®Google Scholar
• Schmidberger JW, Wilce JA, Weightman AJ, Whisstock JC, Wilce MCJ. The crystal structure of dehI reveals a new α-haloacid dehalogenase fold and active-site mechanism. J Mol Biol. 2008;378:284–294.
   PubMed Web of Science ®Google Scholar
• Senior E, Bull AT, Slater JH. Enzyme evolution in a microbial community growing on the herbicide Dalapon. Nature. 1976;263:476–479.
   PubMed Web of Science ®Google Scholar
• Weightman AJ, Slater JH, Bull AT. The partial purification of two dehalogenases from Pseudomonas putida PP3. FEMS Microbiol Lett. 1979;6:231–234.
   Web of Science ®Google Scholar
• Nikolic B, Mac Nulty E, Mir B, Wiche G. Basic amino acid residue cluster within nuclear targeting sequence motif is essential for cytoplasmic plectin-vimentin network junctions. J Cell Biol. 1996;134:1455–1467.
   PubMed Web of Science ®Google Scholar
• Nardi-Dei V, Kurihara T, Park C, Miyagi M, Tsunasawa S, Soda K, Esaki N. DL-2-haloacid dehalogenase from Pseudomonas sp. 113 is a new class of dehalogenase catalyzing hydrolytic dehalogenation not involving enzyme-substrate ester intermediate. J Biol Chem. 1999;274:20977–20981.
   PubMed Web of Science ®Google Scholar
• Kurihara T, Esaki N, Soda K. Bacterial 2-haloacid dehalogenases: structures and reaction mechanism. J Mol Cat B: Enzymatic. 2000;10:57–65.
   Web of Science ®Google Scholar
• Huyop F, Sudi IY. D-specific dehalogenases, a review. Biotechnol Biotechnol Equipment. 2012;26:2817–2822.
   Web of Science ®Google Scholar
• Thallapally PK, Nangia A. A Cambridge structural database analysis of the C–H…Cl interaction: C–H…Cl− and C–H…Cl–M often behave as hydrogen bonds but C–H…Cl–C is generally a Van der Waals interaction. CrystEngComm. 2001;3:114–119.
   Google Scholar
• Omi R, Kurokawa S, Mihara H, Hayashi H, Goto M, Miyahara I, Kurihara T, Hirotsu K, Esaki N. Reaction mechanism and molecular basis for selenium/sulfur discrimination of selenocysteine lyase. J Biol Chem. 2010;285:12133–12139.
   PubMed Web of Science ®Google Scholar
• DeLano WL. The PyMOL molecular graphics system; 2002. Available from: http://www.pymol.org
   Google Scholar
• Bolton EE, Wang Y, Thiessen PA, Bryant SH. Chapter 12–PubChem: integrated platform of small molecules and biological activities. In: Wheeler RA, Spellmeyer DC, editors. Annual reports in computational chemistry. Vol. 4. New York: Elsevier; 2008. p. 217–241.
   Google Scholar
• Sanner MF. Python: a programming language for software integration and development. J Mol Graphics Model. 1999;17:57–61.
   PubMed Web of Science ®Google Scholar
• Rosenfeld RJ, Goodsell DS, Musah RA, Morris GM, Goodin DB, Olson AJ. Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling. J Comput Aided Mol Des. 2003;17:525–536.
   PubMed Web of Science ®Google Scholar
• Jeffrey GA. An introduction to hydrogen bonding. Vol. 12. New York: Oxford University Press; 1997.
   Google Scholar
• Hirsch P, Alexander M. Mcrobial decomposition of halogenated propionic and acetic acids. Can J Microbiol. 1960;6:241–249.
   PubMedGoogle Scholar
• McGrath JE, Harfoot CG. Reductive dehalogenation of halocarboxylic acids by the phototrophic genera Rhodospirillum and Rhodopseudomonas. Appl Environ Microbiol. 1997;63:3333–3335.
   PubMed Web of Science ®Google Scholar
• Mesri S, Wahab R, Huyop F. Degradation of 3-chloropropionic acid (3CP) by Pseudomonas sp. B6P isolated from a rice paddy field. Ann Microbiol. 2009;59:447–451.
   Web of Science ®Google Scholar
• Hamid TA, Haziyamin T, Hamid A, Zulkifly AH, Hamdan S, Ariffin SHZ, Huyop F. Purification and properties of a new dehalogenase enzyme from Pseudomonas sp. B6P grow in 3-chloropropionate (3CP). Afr J Biotechnol. 2011;10:610–614.
   Web of Science ®Google Scholar
• Ng HJ. Isolation of local bacterial capable of degrading halogenated compounds and analysis of putative haloacid permease gene [MSc thesis]. Johor Bahru: Universiti Teknologi Malaysia; 2007.
   Google Scholar
• Sudi IY, Hamid AAA, Shamsir MS, Jamaluddin H, Wahab R Ab, Huyop F. Insights into the stereospecificity of the D-specific dehalogenase from Rhizobium sp. RC1 toward D- and L-2-chloropropionate. Biotechnol Biotechnol Equipment. Forthcoming 2014;28(4) doi:10.1080/13102818.2014.937907.
   Google Scholar