Crystal structure of the cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5
Language English Country United States Media print-electronic
Document type Journal Article
Grant support
CZ.1.05/2.1.00/01.0024
Ministerstvo Školství, Mládeže a Tělovýchovy
CZ.1.05/2.1.00/01.0001
Ministerstvo Školství, Mládeže a Tělovýchovy
CZ.02.1.01/0.0/0.0/15_003/0000441
Ministerstvo Školství, Mládeže a Tělovýchovy
17-24321S
Grantová Agentura České Republiky
PubMed
31045561
PubMed Central
PMC6497103
DOI
10.1107/s2053230x19002796
PII: S2053230X19002796
Knihovny.cz E-resources
- Keywords
- Psychrobacter cryohalolentis, X-ray diffraction, haloalkane dehalogenase, psychrophiles, structural analysis, α/β-hydrolase,
- MeSH
- Bacterial Proteins chemistry genetics metabolism MeSH
- Escherichia coli genetics metabolism MeSH
- Gene Expression MeSH
- Genetic Vectors chemistry metabolism MeSH
- Hydrocarbons, Halogenated chemistry metabolism MeSH
- Hydrolases chemistry genetics metabolism MeSH
- Protein Interaction Domains and Motifs MeSH
- Cloning, Molecular MeSH
- Protein Conformation, alpha-Helical MeSH
- Protein Conformation, beta-Strand MeSH
- Crystallography, X-Ray MeSH
- Cold Temperature MeSH
- Psychrobacter chemistry enzymology MeSH
- Recombinant Fusion Proteins chemistry genetics metabolism MeSH
- Amino Acid Sequence MeSH
- Molecular Docking Simulation MeSH
- Structural Homology, Protein MeSH
- Substrate Specificity MeSH
- Thermodynamics MeSH
- Protein Binding MeSH
- Binding Sites MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- 1-bromohexane MeSH Browser
- Bacterial Proteins MeSH
- haloalkane dehalogenase MeSH Browser
- Hydrocarbons, Halogenated MeSH
- Hydrolases MeSH
- Recombinant Fusion Proteins MeSH
Haloalkane dehalogenases (HLDs) convert halogenated aliphatic pollutants to less toxic compounds by a hydrolytic mechanism. Owing to their broad substrate specificity and high enantioselectivity, haloalkane dehalogenases can function as biosensors to detect toxic compounds in the environment or can be used for the production of optically pure compounds. Here, the structural analysis of the haloalkane dehalogenase DpcA isolated from the psychrophilic bacterium Psychrobacter cryohalolentis K5 is presented at the atomic resolution of 1.05 Å. This enzyme exhibits a low temperature optimum, making it attractive for environmental applications such as biosensing at the subsurface environment, where the temperature typically does not exceed 25°C. The structure revealed that DpcA possesses the shortest access tunnel and one of the most widely open main tunnels among structural homologs of the HLD-I subfamily. Comparative analysis revealed major differences in the region of the α4 helix of the cap domain, which is one of the key determinants of the anatomy of the tunnels. The crystal structure of DpcA will contribute to better understanding of the structure-function relationships of cold-adapted enzymes.
See more in PubMed
Adams, M. W. W., Perler, F. B. & Kelly, R. M. (1995). Biotechnology, 13, 662–668. PubMed
Adrio, J. & Demain, A. (2014). Biomolecules, 4, 117–139. PubMed PMC
Belkin, S. (1992). Biodegradation, 3, 299–313.
Berman, H., Henrick, K. & Nakamura, H. (2003). Nature Struct. Mol. Biol. 10, 980. PubMed
Bidmanova, S., Chaloupkova, R., Damborsky, J. & Prokop, Z. (2010). Anal. Bioanal. Chem. 398, 1891–1898. PubMed
Bidmanova, S., Kotlanova, M., Rataj, T., Damborsky, J., Trtilek, M. & Prokop, Z. (2016). Biosens. Bioelectron. 84, 97–105. PubMed
Brünger, A. T. (1992). Nature (London), 355, 472–475. PubMed
Carlucci, L., Zhou, E., Malashkevich, V. N., Almo, S. C. & Mundorff, E. C. (2016). Protein Sci. 25, 877–886. PubMed PMC
Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). Acta Cryst. D66, 12–21. PubMed PMC
Chovancová, E., Kosinski, J., Bujnicki, J. M. & Damborský, J. (2007). Proteins, 67, 305–316. PubMed
Chovancova, E., Pavelka, A., Benes, P., Strnad, O., Brezovsky, J., Kozlikova, B., Gora, A., Sustr, V., Klvana, M., Medek, P., Biedermannova, L., Sochor, J. & Damborsky, J. (2012). PLoS Comput. Biol. 8, e1002708. PubMed PMC
Drienovska, I., Chovancova, E., Koudelakova, T., Damborsky, J. & Chaloupkova, R. (2012). Appl. Environ. Microbiol. 78, 4995–4998. PubMed PMC
Dundas, J., Ouyang, Z., Tseng, J., Binkowski, A., Turpaz, Y. & Liang, J. (2006). Nucleic Acids Res. 34, W116–W118. PubMed PMC
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486–501. PubMed PMC
Feller, G. & Gerday, C. (2003). Nature Rev. Microbiol. 1, 200–208. PubMed
Fung, H. K. H., Gadd, M. S., Drury, T. A., Cheung, S., Guss, J. M., Coleman, N. V. & Matthews, J. M. (2015). Mol. Microbiol. 97, 439–453. PubMed
Georlette, D., Damien, B., Blaise, V., Depiereux, E., Uversky, V. N., Gerday, C. & Feller, G. (2003). J. Biol. Chem. 278, 37015–37023. PubMed
Gomes, J. & Steiner, W. (2004). Food Technol. Biotechnol. 42, 223–235.
Govardhan, C. P. (1999). Curr. Opin. Biotechnol. 10, 331–335. PubMed
Hesseler, M., Bogdanović, X., Hidalgo, A., Berenguer, J., Palm, G. J., Hinrichs, W. & Bornscheuer, U. T. (2011). Appl. Microbiol. Biotechnol. 91, 1049–1060. PubMed
Hintze, B. J., Lewis, S. M., Richardson, J. S. & Richardson, D. C. (2016). Proteins, 84, 1177–1189. PubMed PMC
Holm, L. & Rosenström, P. (2010). Nucleic Acids Res. 38, W545–W549. PubMed PMC
Janssen, D. B. (2004). Curr. Opin. Chem. Biol. 8, 150–159. PubMed
Janssen, D. B., Pries, F., van der Ploeg, J., Kazemier, B., Terpstra, P. & Witholt, B. (1989). J. Bacteriol. 171, 6791–6799. PubMed PMC
Janssen, D. B., Scheper, A., Dijkhuizen, L. & Witholt, B. (1985). Appl. Environ. Microbiol. 49, 673–677. PubMed PMC
Joosten, R. P., Long, F., Murshudov, G. N. & Perrakis, A. (2014). IUCrJ, 1, 213–220. PubMed PMC
Koudelakova, T., Bidmanova, S., Dvorak, P., Pavelka, A., Chaloupkova, R., Prokop, Z. & Damborsky, J. (2013). Biotechnol. J. 8, 32–45. PubMed
Lenfant, N., Hotelier, T., Velluet, E., Bourne, Y., Marchot, P. & Chatonnet, A. (2013). Nucleic Acids Res. 41, D423–D429. PubMed PMC
Mueller, U., Förster, R., Hellmig, M., Huschmann, F. U., Kastner, A., Malecki, P., Pühringer, S., Röwer, M., Sparta, K., Steffien, M., Ühlein, M., Wilk, P. & Weiss, M. S. (2015). Eur. Phys. J. Plus, 130, 141.
Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011). Acta Cryst. D67, 355–367. PubMed PMC
Nagata, Y., Ohtsubo, Y. & Tsuda, M. (2015). Appl. Microbiol. Biotechnol. 99, 9865–9881. PubMed
Niehaus, F., Bertoldo, C., Kähler, M. & Antranikian, G. (1999). Appl. Microbiol. Biotechnol. 51, 711–729. PubMed
Ollis, D. L., Cheah, E., Cygler, M., Dijkstra, B., Frolow, F., Franken, S. M., Harel, M., Remington, S. J., Silman, I., Schrag, J., Sussman, J. L., Verschueren, K. H. G. & Goldman, A. (1992). Protein Eng. Des. Sel. 5, 197–211. PubMed
Pavelka, A., Sebestova, E., Kozlikova, B., Brezovsky, J., Sochor, J. & Damborsky, J. (2016). IEEE/ACM Trans. Comput. Biol. Bioinform. 13, 505–517. PubMed
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C. & Ferrin, T. E. (2004). J. Comput. Chem. 25, 1605–1612. PubMed
Ridder, I. S., Rozeboom, H. J. & Dijkstra, B. W. (1999). Acta Cryst. D55, 1273–1290. PubMed
Russell, N. J. (1998). Adv. Biochem. Eng. Biotechnol. 61, 1–21. PubMed
Schmid, A., Dordick, J. S., Hauer, B., Kiener, A., Wubbolts, M. & Witholt, B. (2001). Nature (London), 409, 258–268. PubMed
Tratsiak, K., Degtjarik, O., Drienovska, I., Chrast, L., Rezacova, P., Kuty, M., Chaloupkova, R., Damborsky, J. & Kuta Smatanova, I. (2013). Acta Cryst. F69, 683–688. PubMed PMC
Tronelli, D., Maugini, E., Bossa, F. & Pascarella, S. (2007). FEBS J. 274, 4595–4608. PubMed
Trott, O. & Olson, A. J. (2010). J. Comput. Chem. 31, 455–461. PubMed PMC
Vagin, A. & Teplyakov, A. (2010). Acta Cryst. D66, 22–25. PubMed
Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., McNicholas, S. J., Murshudov, G. N., Pannu, N. S., Potterton, E. A., Powell, H. R., Read, R. J., Vagin, A. & Wilson, K. S. (2011). Acta Cryst. D67, 235–242. PubMed PMC