Probing the enzyme catalytic mechanism by nuclear magnetic resonance - A case study of a serine protease

Sergiy I. Tyukhtenko, Yao Te Huang, Ta Hsin Lin, Chinpan Chen, Chi Fon Chang, Shin Jye Lee, Alexandra V. Litvinchuk, Jei Fu Shaw, Yen Chywan Liaw, Tai Huang Huang

Research output: Contribution to journalArticle

Abstract

Serine proteases are among the most studied enzymes for their role as model enzymes for studying the enzyme catalytic mechanism and medical interest in their inhibition. We have applied NMR methods to determine the structure, dynamics, and catalytic mechanism of a serine protease, E. coli thioesterase/protease I (TEP-I): In this article we review the results of our efforts. We showed that TEP-I is an α/β/α type SNGH-hydrolase with Ser10, Asp154 and His157 as the catalytic triad residues. In free TEP-I, His157 was found to form a strong hydrogen bond to Asp154, but not to Ser10-O γH. Modetfree analysis of 15N-T1, 15N-T2 and 1H-15N NOE data revealed that TEP-I is a rigid protein with a flexible catalytic binding pocket. Slow motion involving segments around the catalytic site was detected. The formation of Michaelis complex (MC) between TEP-I and a transition state analogue, diethyl p-nitrophenyl phosphate (DENP), and its subsequent conversion to the tetrahedral complex (TC) follow a two-step process, a fast formation of MC followed by a slow conversion to TC. In both steps residues perturbed were confined mainly to four conserved segments comprising the active site. Comparable magnitudes of chemical shift perturbations were detected in both steps. From the large chemical shift perturbation upon conversion from MC to TC we proposed that the amide protons of Ser10 and Gly44 serve as the oxyanion-hole proton donors to stabilize the tetrahedral adduct. The pattern of residues perturbed in both steps suggests a sequential, stepwise structural change upon binding of DENP.

Original languageEnglish
Pages (from-to)1133-1140
Number of pages8
JournalJournal of the Chinese Chemical Society
Volume51
Issue number5 B
DOIs
Publication statusPublished - 2004 Jan 1

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Serine Proteases
Peptide Hydrolases
Nuclear magnetic resonance
Paraoxon
Enzymes
Chemical shift
Protons
Hydrolases
Amides
Escherichia coli
Hydrogen bonds
Proteins

Keywords

  • Enzyme catalysis
  • NMR
  • Protein structure
  • Serine protease
  • Thioesterase

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Probing the enzyme catalytic mechanism by nuclear magnetic resonance - A case study of a serine protease. / Tyukhtenko, Sergiy I.; Huang, Yao Te; Lin, Ta Hsin; Chen, Chinpan; Chang, Chi Fon; Lee, Shin Jye; Litvinchuk, Alexandra V.; Shaw, Jei Fu; Liaw, Yen Chywan; Huang, Tai Huang.

In: Journal of the Chinese Chemical Society, Vol. 51, No. 5 B, 01.01.2004, p. 1133-1140.

Research output: Contribution to journalArticle

Tyukhtenko, SI, Huang, YT, Lin, TH, Chen, C, Chang, CF, Lee, SJ, Litvinchuk, AV, Shaw, JF, Liaw, YC & Huang, TH 2004, 'Probing the enzyme catalytic mechanism by nuclear magnetic resonance - A case study of a serine protease', Journal of the Chinese Chemical Society, vol. 51, no. 5 B, pp. 1133-1140. https://doi.org/10.1002/jccs.200400168
Tyukhtenko, Sergiy I. ; Huang, Yao Te ; Lin, Ta Hsin ; Chen, Chinpan ; Chang, Chi Fon ; Lee, Shin Jye ; Litvinchuk, Alexandra V. ; Shaw, Jei Fu ; Liaw, Yen Chywan ; Huang, Tai Huang. / Probing the enzyme catalytic mechanism by nuclear magnetic resonance - A case study of a serine protease. In: Journal of the Chinese Chemical Society. 2004 ; Vol. 51, No. 5 B. pp. 1133-1140.
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AU - Huang, Yao Te

AU - Lin, Ta Hsin

AU - Chen, Chinpan

AU - Chang, Chi Fon

AU - Lee, Shin Jye

AU - Litvinchuk, Alexandra V.

AU - Shaw, Jei Fu

AU - Liaw, Yen Chywan

AU - Huang, Tai Huang

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AB - Serine proteases are among the most studied enzymes for their role as model enzymes for studying the enzyme catalytic mechanism and medical interest in their inhibition. We have applied NMR methods to determine the structure, dynamics, and catalytic mechanism of a serine protease, E. coli thioesterase/protease I (TEP-I): In this article we review the results of our efforts. We showed that TEP-I is an α/β/α type SNGH-hydrolase with Ser10, Asp154 and His157 as the catalytic triad residues. In free TEP-I, His157 was found to form a strong hydrogen bond to Asp154, but not to Ser10-O γH. Modetfree analysis of 15N-T1, 15N-T2 and 1H-15N NOE data revealed that TEP-I is a rigid protein with a flexible catalytic binding pocket. Slow motion involving segments around the catalytic site was detected. The formation of Michaelis complex (MC) between TEP-I and a transition state analogue, diethyl p-nitrophenyl phosphate (DENP), and its subsequent conversion to the tetrahedral complex (TC) follow a two-step process, a fast formation of MC followed by a slow conversion to TC. In both steps residues perturbed were confined mainly to four conserved segments comprising the active site. Comparable magnitudes of chemical shift perturbations were detected in both steps. From the large chemical shift perturbation upon conversion from MC to TC we proposed that the amide protons of Ser10 and Gly44 serve as the oxyanion-hole proton donors to stabilize the tetrahedral adduct. The pattern of residues perturbed in both steps suggests a sequential, stepwise structural change upon binding of DENP.

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KW - Thioesterase

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