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References

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    CrossRef
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    Pubmed PMC CrossRef
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    CrossRef
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    Pubmed CrossRef
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    Pubmed CrossRef
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    Pubmed CrossRef
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    Pubmed
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    Pubmed CrossRef
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    Pubmed CrossRef
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    Pubmed CrossRef
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    CrossRef
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    Pubmed PMC CrossRef
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    Pubmed PMC CrossRef
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    Pubmed CrossRef
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    Pubmed CrossRef
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    Pubmed CrossRef
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    Pubmed CrossRef
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Article

Research article

J. Microbiol. Biotechnol. 2016; 26(12): 2087-2097

Published online December 28, 2016 https://doi.org/10.4014/jmb.1608.08049

Copyright © The Korean Society for Microbiology and Biotechnology.

Cloning, Expression, and Characterization of a Cold-Adapted Shikimate Kinase from the Psychrophilic Bacterium Colwellia psychrerythraea 34H

Wahyu Sri Kunto Nugroho 1, Dong-Woo Kim 1, Jong-Cheol Han 2, Young Baek Hur 2, Soo-Wan Nam 3 and Hak Jun Kim 1*

1Department of Chemistry, Pukyong National University, Busan 48547, Republic of Korea, 2Southeast Sea Fisheries Research Institute, National Fisheries Research and Development Institute, Tongyeong 53085, Republic of Korea, 3Department of Biotechnology and Bioengineering, Dong-Eui University, Busan 47340, Republic of Korea

Received: August 24, 2016; Accepted: September 5, 2016

Abstract

Most cold-adapted enzymes possess higher Km and kcat values than those of their mesophilic
counterparts to maximize the reaction rate. This characteristic is often ascribed to a high
structural flexibility and improved dynamics in the active site. However, this may be less
convincing to cold-adapted metabolic enzymes, which work at substrate concentrations near
Km. In this respect, cold adaptation of a shikimate kinase (SK) in the shikimate pathway from
psychrophilic Colwellia psychrerythraea (CpSK) was characterized by comparing it with a
mesophilic Escherichia coli homolog (EcSK). The optimum temperatures for CpSK and EcSK
activity were approximately 30°C and 40°C, respectively. The melting points were 33°C and
45°C for CpSK and EcSK, respectively. The ΔGH2O (denaturation in the absence of denaturing
agent) values were 3.94 and 5.74 kcal/mol for CpSK and EcSK, respectively. These results
indicated that CpSK was a cold-adapted enzyme. However, contrary to typical kinetic data,
CpSK had a lower Km for its substrate shikimate than most mesophilic SKs, and the kcat was not
increased. This observation suggested that CpSK may have evolved to exhibit increased
substrate affinity at low intracellular concentrations of shikimate in the cold environment.
Sequence analysis and homology modeling also showed that some important salt bridges were
lost in CpSK, and higher Arg residues around critical Arg 140 seemed to increase flexibility for
catalysis. Taken together, these data demonstrate that CpSK exhibits characteristics of cold
adaptation with unusual kinetic parameters, which may provide important insights into the
cold adaptation of metabolic enzymes.

Keywords: cold adaptation, shikimate kinase, psychrophile, The Michaelis-Menten constant, turnover number

References

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    Pubmed CrossRef
  2. Bentahir M. 2000. Structural, kinetic, and calorimetric characterization of the cold-active phosphoglycerate kinase from the antarctic Pseudomonas sp. TACII18. J. Biol. Chem. 275: 11147-11153.
    Pubmed CrossRef
  3. Cerasoli E, Kelly SM, Coggins JR, Boam DJ, Clarke DT, Price NC. 2002. The refolding of type II shikimate kinase from Erwinia chrysanthemi a ft er d enat urat ion in u rea. Eur. J. Biochem. 269: 2124-2132.
    Pubmed CrossRef
  4. Cheng W-C, Chang Y-N, Wang W-C. 2005. Structural basis for shikimate-binding specificity of Helicobacter pylori shikimate kinase. J. Bacteriol. 187: 8156-8163.
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    Pubmed CrossRef
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    Pubmed CrossRef
  28. Kim YO, Park IS, Nam BH, Kim DG, Jee YJ, Lee SJ, et al. 2014. A novel esterase from Paenibacillus sp. PBS-2 is a new member of the β-lactamase belonging to the family VIII lipases/esterases. J. Microbiol. Biotechnol. 24: 1260-1268.
    Pubmed CrossRef
  29. Krell T, Maclean J, Boam DJ, Cooper A, Resmini M, Brocklehurst K, et al. 2001. Biochemical and X-ray crystallographic studies on shikimate kinase: the important structural role of the P-loop lysine. Protein Sci. 10: 1137-1149.
    Pubmed KoreaMed CrossRef
  30. Kulakova L, Galkin A, Nakayama T, Nishino T, Esaki N. 2004. Cold-active esterase from Psychrobacter s p. A nt 300:gene cloning, characterization, and the effects of Gly → Pro substitution near the active site on its catalytic activity and stability. Biochim. Biophys. Acta 1696: 59-65.
    Pubmed CrossRef
  31. Kumar M, Thakur V, Raghava GPS. 2008. COPid: composition based protein identification. In Silico Biol. 8: 121-128.
    Pubmed
  32. Lakowicz JR. 2006. Principles of Fluorescence Spectroscopy. Springer US, Boston, MA.
    CrossRef
  33. Lee Y S, B ok H J, L ee J H, C hoi YL. 2014. A c old-adapt ed carbohydrate esterase from the oil-degrading marine bacterium Microbulbifer thermotolerans DAU221: gene cloning, purification, and characterization. J. Microbiol. Biotechnol. 24: 925-935.
    Pubmed CrossRef
  34. Leiros I, Moe E, Lanes O, Smalås AO, Willassen NP. 2003. The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features. Acta Crystallogr. D Biol. Crystallogr. 59: 1357-1365.
    Pubmed CrossRef
  35. Li S, Yang X, Zhang L, Yu W, Han F. 2015. Cloning, expression and characterization of a cold-adapted and surfactant-stable alginate lyase from marine bacterium Agarivorans sp. L11. J. Microbiol. Biotechnol. 25: 681-686.
    Pubmed CrossRef
  36. Maiangwa J, Ali MSM, Salleh AB, Rahman RNZRA, Shariff FM, Leow TC. 2015. Adaptational properties and applications of cold-active lipases from psychrophilic bacteria. Extremophiles 19: 235-247.
    Pubmed CrossRef
  37. Metpally RPR, Reddy BVB. 2009. Comparative proteome analysis of psychrophilic versus mesophilic bacterial species:insights into the molecular basis of cold adaptation of proteins. BMC Genomics 10: 11.
    Pubmed KoreaMed CrossRef
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    CrossRef
  39. Pace CN, Treviño S, Prabhakaran E, Scholtz JM. 2004. Protein structure, stability and solubility in water and other solvents. Philos. Trans. R. Soc. Lond. B Biol. Sci. 359: 12251234; discussion 1234-5.
  40. Paredes DI, Watters K, Pitman DJ, Bystroff C, Dordick JS. 2011. Comparative void-volume analysis of psychrophilic and mesophilic enzymes: structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility. BMC Struct. Biol. 11: 42.
    Pubmed KoreaMed CrossRef
  41. Robert X, Gouet P. 2014. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res. 42: W320-W324.
    Pubmed KoreaMed CrossRef
  42. Romanowski MJ, Burley SK. 2002. Crystal structure of the Escherichia coli shikimate kinase I (AroK) that confers sensitivity to mecillinam. Proteins 47: 558-562.
    Pubmed CrossRef
  43. Rosado LA, Vasconcelos IB, Palma MS, Frappier V, Najmanovich RJ, Santos DS, et al. 2013. The mode of action of recombinant Mycobacterium tuberculosis shikimate kinase:kinetics and thermodynamics analyses. PLoS One 8: e61918.
    Pubmed KoreaMed CrossRef
  44. Siddiqui KS, Cavicchioli R. 2006. Cold-adapted enzymes. Annu. Rev. Biochem. 75: 403-433.
    Pubmed CrossRef
  45. Siddiqui KS, Poljak A, Guilhaus M, De Francisci D, Curmi PMG, Feller G, et al. 2006. Role of lysine versus arginine in enzyme cold-adaptation: modifying lysine to homo-arginine stabilizes the cold-adapted α-amylase from Pseudoalteramonas haloplanktis. Proteins 64: 486-501.
    Pubmed CrossRef
  46. Simithy J, Gill G, Wang Y, Goodwin DC, Calderón AI. 2015. Development of an ESI-LC-MS-based assay for kinetic evaluation of Mycobacterium tuberculosis shikimate kinase activity and inhibition. Anal. Chem. 87: 2129-2136.
    Pubmed CrossRef
  47. Simithy J, Reeve N, Hobrath JV, Reynolds RC, Calderón AI. 2014. Identification of shikimate kinase inhibitors among anti-Mycobacterium tuberculosis compounds by LC-MS. Tuberculosis (Edinb.) 94: 152-158.
    Pubmed CrossRef
  48. Simpson BK, Haard NF. 2011. Purification and characterization of trypsin from the Greenland cod (Gadus ogac). 1. Kinetic and thermodynamic characteristics. Can. J. Biochem. Cell Biol. 62: 894-900.
    CrossRef
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