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Research Articles

Multi-template homology-based structural model of L-2-haloacid dehalogenase (DehL) from Rhizobium sp. RC1

, , ORCID Icon, &
Pages 3285-3296 | Received 08 Jul 2016, Accepted 20 Oct 2016, Published online: 21 Nov 2016

References

  • Adamu, A., Wahab, R. A., & Huyop, F. (2016). l-2-Haloacid dehalogenase (DehL) from Rhizobium sp. RC1. SpringerPlus, 1–17. doi:10.1186/s40064-016-2328-9
  • Anfinsen, C. B. (1993). Studies on the principle that govern the folding of protein chains. In T. Frangsmyr & S. Forsén (Eds.), Nobel lectures in chemistry 1971–1980 (pp. 55–72). Singapore: World Scientific.
  • Bohác, M., Nagata, Y., Prokop, Z., Prokop, M., Monincová, M., Tsuda, M., … Damborský, J. (2002). Halide-stabilizing residues of haloalkane dehalogenases studied by quantum mechanic calculations and site-directed mutagenesis. Biochemistry, 41, 14272–14280.10.1021/bi026427v
  • Brändén, C.-I. (1980). Relation between structure and function of α/β–protejns. Quarterly Reviews of Biophysics, 13, 317–338.10.1017/S0033583500001712
  • Cairns, S. S., Cornish, A., & Cooper, R. A. (1996). Cloning, sequencing and expression in Escherichia coli of two Rhizobium sp. genes encoding haloalkanoate dehalogenases of opposite stereospecificity. European Journal of Biochemistry, 235, 744–749.10.1111/ejb.1996.235.issue-3
  • Cantor, K. P., Lynch, C. F., Hildesheim, M., Dosemeci, M., Lubin, J., Alavanja, M., & Craun, G. (1998). Drinking water source and chlorination byproducts I. Risk of Bladder Cancer. Epidemiology, 9, 21–28.
  • Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2, 1511–1519.10.1002/pro.v2:9
  • de Jong, R. M., & Dijkstra, B. W. (2003). Structure and mechanism of bacterial dehalogenases: Different ways to cleave a carbon–halogen bond. Current Opinion in Structural Biology, 13, 722–730. doi:10.1016/j.sbi.2003.10.009
  • Fan, H., & Mark, A. E. (2004). Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Science, 13, 211–220.10.1110/ps.03381404
  • Gasteiger, E., Hoogland, C., Gattiker, A., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. New York: Springer.
  • Gribble, G. W. (2003). The diversity of naturally produced organohalogens. Chemosphere, 52, 289–297. doi:10.1016/s0045-6535(03)00207-8
  • Hill, K. E., Marchesi, J. R., & Weightman, A. J. (1999). Investigation of two evolutionarily unrelated halocarboxylic acid dehalogenase gene families. Journal of Bacteriology, 181, 2535–2547.
  • Hisano, T., Hata, Y., Fujii, T., Liu, J. Q., Kurihara, T., Esaki, N., & Soda, K. (1996a). Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp YL – An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold. Journal of Biological Chemistry, 271, 20322–20330.10.1074/jbc.271.34.20322
  • Hisano, T., Hata, Y., Fujii, T., Liu, J. Q., Kurihara, T., Esaki, N., & Soda, K. (1996b). Crystallization and preliminary X-ray crystallographic studies of L-2-haloacid dehalogenase from Pseudomonas sp. YL. Proteins: Structure, Function, and Genetics, 24, 520–522.10.1002/(ISSN)1097-0134
  • Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, 65, 712–725.10.1002/prot.v65:3
  • Humphrey, W., Dalke, A., & Schulten, S. (1996). VMD: Vidual molecular dynamics. Journal of Molecular Graphics and Modelling, 14, 33–38.10.1016/0263-7855(96)00018-5
  • Hur, S., Kahn, K., & Bruice, T. C. (2003). Comparison of formation of reactive conformers for the SN2 displacements by CH3CO in water and by Asp124-CO in a haloalkane dehalogenase. Proceedings of the National Academy of Sciences, 100, 2215–2219.10.1073/pnas.242721799
  • Huyop, F., Jing, N. H., & Cooper, R. A. (2008). Overexpression, purification and analysis of dehalogenase D of Rhizobium sp. Canadian Journal of Pure and Applied Sciences, 2, 389–392.
  • Huyop, F., Rashid, N. A., Wahab, R. A., & Cooper, R. A. (2008). Purification and properties of Rhizobial DehL expressed in Escherichia coli. African Journal of Biotechnology, 7, 1944–1949.
  • Huyop, F., Yusn, T. Y., Ismail, M., Wahab, R. A., & Cooper, R. A. (2004). Overexpression and characterisation of non-stereospecific haloacid dehalogenase E (DehE) of Rhizobium sp. Asia Pacific Journal of Molecular Biology and Biotechnology, 12, 15–20.
  • Jensen, H. (1957). Decomposition of chloro-substituted aliphatic acids by soil bacteria. Canadian Journal of Microbiology, 3, 151–164.10.1139/m57-019
  • Kondo, H., Nakamura, T., & Tanaka, S. (2014). A significant role of Arg41 residue in the enzymatic reaction of haloacid dehalogenase l-DEX YL studied by QM/MM method. Journal of Molecular Catalysis B-Enzymatic, 110, 23–31.10.1016/j.molcatb.2014.09.006
  • Kurihara, T., Liu, J. Q., Nardidei, V., Koshikawa, H., Esaki, N., & Soda, K. (1995). Comprehensive site-directed mutagenesis of L-2-halo acid dehalogenase to probe catalytic amino-acid-residues. Journal of Biochemistry, 117, 1317–1322.
  • Larsson, P., Wallner, B., Lindahl, E., & Elofsson, A. (2008). Using multiple templates to improve quality of homology models in automated homology modeling. Protein Science, 17, 990–1002.10.1110/ps.073344908
  • Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26, 283–291.10.1107/S0021889892009944
  • Leigh, J., Skinner, A., & Cooper, R. (1986). Isolation and partial characterisation of dehalogenase-deficient mutants of a Rhizobium sp. FEMS Microbiology Letters, 36, 163–166.10.1111/fml.1986.36.issue-2-3
  • Leigh, J., Skinner, A., & Cooper, R. (1988). Partial purification, stereospecificity and stoichiometry of three dehalogenases from a Rhizobium species. FEMS Microbiology Letters, 49, 353–356.10.1111/fml.1988.49.issue-3
  • Li, Y. F., Hata, Y., Fujii, T., Hisano, T., Nishihara, M., Kurihara, T., & Esaki, N. (1998). Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism. Journal of Biological Chemistry, 273, 15035–15044.10.1074/jbc.273.24.15035
  • Li, W., Shen, J., Liu, G., Tang, Y., & Hoshino, T. (2011). Exploring coumarin egress channels in human cytochrome p450 2a6 by random acceleration and steered molecular dynamics simulations. Proteins-Structure Function and Genetics, 79, 271–281.10.1002/prot.22880
  • Liithy, R., Bowie, J., & Eisenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature, 356, 83–85.10.1038/356083a0
  • Liu, J.-Q., Kurihara, T., Hasan, A., Nardi-Dei, V., Koshikawa, H., Esaki, N., & Soda, K. (1994). Purification and characterization of thermostable and nonthermostable 2-haloacid dehalogenases with different stereospecificities from Pseudomonas sp. strain YL. Applied and Environmental Microbiology, 60, 2389–2393.
  • Liu, J. Q., Kurihara, T., Miyagi, M., Esaki, N., & Soda, K. (1995). Reaction-mechanism of L-2-haloacid dehalogenase of Pseudomonas Sp. YL – Identification of Asp(10) as the active-site nucleophile by O-18 incorporation experiments. Journal of Biological Chemistry, 270, 18309–18312.10.1074/jbc.270.31.18309
  • Marianayagam, N. J., Sunde, M., & Matthews, J. M. (2004). The power of two: Protein dimerization in biology. Trends in Biochemical Sciences, 29, 618–625.10.1016/j.tibs.2004.09.006
  • Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19, 1639–1662.10.1002/(ISSN)1096-987X
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30, 2785–2791.
  • Nakamura, T., Yamaguchi, A., Kondo, H., Watanabe, H., Kurihara, T., Esaki, N., … Tanaka, S. (2009). Roles of K151 and D180 in L-2-haloacid dehalogenase from Pseudomonas sp. YL: Analysis by molecular dynamics and ab initio fragment molecular orbital calculations. Journal of Computational Chemistry, 30, 2625–2634.10.1002/jcc.v30:16
  • Novak, H. R., Sayer, C., Isupov, M. N., Paszkiewicz, K., Gotz, D., Spragg, A. M., & Littlechild, J. A. (2013). Marine Rhodobacteraceae L -haloacid dehalogenase contains a novel His/Glu dyad that could activate the catalytic water. FEBS Journal, 280, 1664–1680.10.1111/febs.2013.280.issue-7
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF chimera?A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25, 1605–1612.10.1002/(ISSN)1096-987X
  • Ridder, I. S., Rozeboom, H. J., Kalk, K. H., Janssen, D. B., & Dijkstra, B. W. (1997). Three-dimensional structure of L-2-haloacid dehalogenase from Xanthobacter autotrophicus GJ10 complexed with the substrate-analogue formate. Journal of Biological Chemistry, 272, 33015–33022.10.1074/jbc.272.52.33015
  • Ridder, I. S., Rozeboom, H. J., Kingma, J., Janssen, D. B., & Dijkstra, B. W. (1995). Crystallization and preliminary X-ray analysis of L-2-haloacid dehalogenase from xanthobacter autotrophicus GJ10. Protein Science, 4, 2619–2620.10.1002/pro.v4:12
  • Robert, X., & Gouet, P. (2014). Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Research, 42(Web Server issue), W320–324. doi:10.1093/nar/gku316
  • Roy, A., Kucukural, A., & Zhang, Y. (2010). I-TASSER: A unified platform for automated protein structure and function prediction. Nature Protocols, 5, 725–738.10.1038/nprot.2010.5
  • Rye, C. A., Isupov, M. N., Lebedev, A. A., & Littlechild, J. A. (2007). An order-disorder twin crystal of L-2-haloacid dehalogenase from Sulfolobus tokodaii. Acta Crystallographica Section D Biological Crystallography, 63, 926–930.10.1107/S0907444907026315
  • Schmidberger, J. W., Wilce, J. A., Tsang, J. S., & Wilce, M. C. (2007). Crystal structures of the substrate free-enzyme, and reaction intermediate of the HAD superfamily member, haloacid dehalogenase DehIVa from Burkholderia cepacia MBA4. Journal of Molecular Biology, 368, 706–717.10.1016/j.jmb.2007.02.015
  • Schmidberger, J. W., Wilce, J. A., Weightman, A. J., Whisstock, J. C., & Wilce, M. C. J. (2008). The crystal structure of dehi reveals a new α-haloacid dehalogenase fold and active-site mechanism. Journal of Molecular Biology, 378, 284–294.10.1016/j.jmb.2008.02.035
  • Schoonman, M., Knegtel, R. M., & Grootenhuis, P. D. (1998). Practical evaluation of comparative modelling and threading methods. Computers & Chemistry, 22, 369–375.10.1016/S0097-8485(98)00006-0
  • Shen, J., Zhang, W., Fang, H., Perkins, R., Tong, W., & Hong, H. (2013). Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes. BMC Bioinformatics, 14(Suppl. 14), 1–11. doi:10.1186/1471-2105-14-S14-S6
  • Shurki, A., Štrajbl, M., Villa, J., & Warshel, A. (2002). How much do enzymes really gain by restraining their reacting fragments? Journal of the American Chemical Society, 124, 4097–4107.10.1021/ja012230z
  • Taylor, S. (1990). S-2-chloropropionic acid by biotransformations. In L.G. Copping, R.E. Martin, J.A. Pickett, C. Buckle & A.W. Bunch (Eds.),Opportunities in Biotransformations (pp. 170–176). New York: Elsevier Applied Science Publishers.
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26, 1701–1718.10.1002/(ISSN)1096-987X
  • Weisburger, E. K. (1977). Carcinogenicity studies on halogenated hydrocarbons. Environmental Health Perspectives, 21, 7–16.10.1289/ehp.77217
  • Weissermel, K., & Arpe, H.-J. (2008). Industrial organic chemistry. New Jersey: John Wiley & Sons.
  • Xiong, J. (2006). Proptein tertiary structure prediction. In J. Xiong (Ed.), Essential bioinformatics (pp. 214–230). Cambridge: Cambridge University Press.
  • Yang, C.-Y., Chiu, H.-F., Cheng, M.-F., & Tsai, S.-S. (1998). Chlorination of drinking water and cancer mortality in Taiwan. Environmental Research, 78(1), 1–6.10.1006/enrs.1997.3823
  • Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015). The I-TASSER suite: Protein structure and function prediction. Nature Methods, 12, 7–8.
  • Yang, J., & Zhang, Y. (2015). I-TASSER server: New development for protein structure and function predictions. Nucleic Acids Research, 43, W174–W181.
  • Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9 (1), 1–8.10.1186/1471-2105-9-40

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