Weak activity of haloalkane dehalogenase LinB with 1,2,3-trichloropropane revealed by X-Ray crystallography and microcalorimetry
Jazyk angličtina Země Spojené státy americké Médium print-electronic
Typ dokumentu časopisecké články, práce podpořená grantem
PubMed
17259360
PubMed Central
PMC1828796
DOI
10.1128/aem.02416-06
PII: AEM.02416-06
Knihovny.cz E-zdroje
- MeSH
- hydrolasy metabolismus MeSH
- kalorimetrie MeSH
- kinetika MeSH
- krystalografie rentgenová MeSH
- molekulární modely MeSH
- propan analogy a deriváty metabolismus MeSH
- Sphingomonadaceae enzymologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- 1,2,3-trichloropropane MeSH Prohlížeč
- haloalkane dehalogenase MeSH Prohlížeč
- hydrolasy MeSH
- propan MeSH
1,2,3-Trichloropropane (TCP) is a highly toxic and recalcitrant compound. Haloalkane dehalogenases are bacterial enzymes that catalyze the cleavage of a carbon-halogen bond in a wide range of organic halogenated compounds. Haloalkane dehalogenase LinB from Sphingobium japonicum UT26 has, for a long time, been considered inactive with TCP, since the reaction cannot be easily detected by conventional analytical methods. Here we demonstrate detection of the weak activity (k(cat) = 0.005 s(-1)) of LinB with TCP using X-ray crystallography and microcalorimetry. This observation makes LinB a useful starting material for the development of a new biocatalyst toward TCP by protein engineering. Microcalorimetry is proposed to be a universal method for the detection of weak enzymatic activities. Detection of these activities is becoming increasingly important for engineering novel biocatalysts using the scaffolds of proteins with promiscuous activities.
Zobrazit více v PubMed
Agency for Toxic Substances and Disease Registry. 1992. Toxicological profile for 1,2,3-trichloropropane. U.S. Department of Health and Human Services, Public Health Service, Washington, DC. PubMed
Aharoni, A., L. Gaidukov, O. Khersonsky, S. M. Gould, C. Roodveldt, and D. S. Tawfik. 2004. The “evolvability” of promiscuous protein functions. Nat. Genet. 37:73-76. PubMed
Banas, P., M. Otyepka, P. Jerabek, M. Petrek, and J. Damborsky. 2006. Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling. J. Comput.-Aided Mol. Des. 20:375-383. PubMed
Bosma, T., J. Damborsky, G. Stucki, and D. B. Janssen. 2002. Biodegradation of 1,2,3-trichloropropane through directed evolution and heterologous expression of a haloalkane dehalogenase gene. Appl. Environ. Microbiol. 68:3582-3587. PubMed PMC
Cai, L., A. Cao, and L. Lai. 2001. An isothermal titration calorimetric method to determine the kinetics parameters of enzyme catalytic reaction by employing the product inhibition as probe. Anal. Biochem. 299:19-23. PubMed
Chaloupkova, R., J. Sykorova, Z. Prokop, A. Jesenska, M. Monincova, M. Pavlova, Y. Nagata, and J. Damborsky. 2003. Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel. J. Biol. Chem. 278:52622-52628. PubMed
Collaborative Computational Project, Number 4. 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. Sect. D Biol. Crystallogr. 50:760-763. PubMed
D′Amico, S., J. S. Sohier, and G. Feller. 2006. Kinetics and energetics of ligand binding determined by microcalorimetry: insights into active site mobility in a psychrophilic alpha-amylase. J. Mol. Biol. 358(5):1296-1304. PubMed
Debord, J., B. Verneuil, J.-C. Bollinger, L. Merle, and T. Dantoine. 2006. Flow microcalorimetry study of butyrylcholinesterase kinetics and inhibition. Anal. Biochem. 354:299-304. PubMed
Gray, K. A., T. H. Richardson, K. Kretz, J. M. Short, F. Bartnek, R. Knowles, L. Kan, P. E. Swanson, and D. E. Robertson. 2001. Rapid evolution of reversible denaturation and elevated melting temperature in a microbial haloalkane dehalogenase. Adv. Synth. Catal. 343:607-617.
Jeoh, T., J. O. Baker, A. K. Mursheda, M. E. Himmel, and W. S. Adney. 2005. Beta-D-glucosidase reaction kinetics from isothermal titration microcalorimetry. Anal. Biochem. 347:244-253. PubMed
Kmunicek, J., K. Hynkova, T. Jedlicka, Y. Nagata, A. Negri, F. Gago, R. C. Wade, and J. Damborsky. 2005. Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26. Biochemistry 44:3390-3401. PubMed
Lamzin, V. S., and K. S. Wilson. 1997. Automated refinement for protein crystallography. Methods Enzymol. 277:269-305. PubMed
Marek, J., J. Vevodova, I. Kuta-Smatanova, Y. Nagata, L. A. Svensson, J. Newman, M. Takagi, and J. Damborsky. 2000. Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26. Biochemistry 39:14082-14086. PubMed
McRee, D. E. 1999. XtalView/Xfit—a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125:156-165. PubMed
Nagata, Y., K. Miyauchi, J. Damborsky, K. Manova, A. Ansorgova, and M. Takagi. 1997. Purification and characterization of haloalkane dehalogenase of a new substrate class from a γ-hexachlorocyclohexane-degrading bacterium, Sphingomonas paucimobilis UT26. Appl. Environ. Microbiol. 63:3707-3710. PubMed PMC
Oakley, A. J., Z. Prokop, M. Bohac, J. Kmunicek, T. Jedlicka, M. Monincova, I. Kuta-Smatanova, Y. Nagata, J. Damborsky, and M. C. J. Wilce. 2002. Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product and water mediated inhibition. Biochemistry 41:4847-4855. PubMed
Otwinowski, Z., and W. Minor. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:307-326. PubMed
Saboury, A. A., and A. A. Moosavi-Movahedi. 1997. A simple novel method for determination of an inhibition constant by isothermal titration microcalorimetry. The effect of fluoride ion on urease. J. Enzyme Inhib. 12:273-279. PubMed
Stodeman, A., and F. P. Schwarz. 2002. Importance of product inhibition in the kinetics of the acylase hydrolysis reaction by differential stopped flow microcalorimetry. Anal. Biochem. 308:285-293. PubMed
Streltsov, V. A., Z. Prokop, J. Damborsky, Y. Nagata, A. J. Oakley, and M. C. J. Wilce. 2003. Haloalkane dehalogenase LinB from Sphingomonas paucimbilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates. Biochemistry 42:10104-10112. PubMed
Todd, M. J., and J. Gomez. 2001. Enzyme kinetics determined using calorimetry: a general assay for enzyme activity? Anal. Biochem. 296:179-187. PubMed
ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era
Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics