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Title: Conserved residue His-257 of Vibrio cholerae flavin transferase ApbE plays a critical role in substrate binding and catalysis

Abstract

The flavin transferase ApbE plays essential roles in bacterial physiology, covalently incorporating FMN cofactors into numerous respiratory enzymes that use the integrated cofactors as electron carriers. In this work we performed a detailed kinetic and structural characterization of Vibrio cholerae WT ApbE and mutants of the conserved residue His-257, to understand its role in substrate binding and in the catalytic mechanism of this family. Bi-substrate kinetic experiments revealed that ApbE follows a random Bi Bi sequential kinetic mechanism, in which a ternary complex is formed, indicating that both substrates must be bound to the enzyme for the reaction to proceed. Steady-state kinetic analyses show that the turnover rates of His-257 mutants are significantly smaller than those of WT ApbE, and have increased Km values for both substrates, indicating that the His-257 residue plays important roles in catalysis and in enzyme-substrate complex formation. Analyses of the pH dependence of ApbE activity indicate that the pKa of the catalytic residue (pKES1) increases by 2 pH units in the His-257 mutants, suggesting that this residue plays a role in substrate deprotonation. The crystal structures of WT ApbE and an H257G mutant were determined at 1.61 and 1.92 Å resolutions, revealing that His-257 ismore » located in the catalytic site and that the substitution does not produce major conformational changes. In this paper, we propose a reaction mechanism in which His-257 acts as a general base that deprotonates the acceptor residue, which subsequently performs a nucleophilic attack on FAD for flavin transfer.« less

Authors:
 [1];  [2];  [3];  [1]; ORCiD logo [1];  [1];  [1];  [1];  [1];  [1];  [2]; ORCiD logo [4];  [1]
+ Show Author Affiliations
  1. Illinois Inst. of Technology, Chicago, IL (United States). Dept. of Biological Science
  2. Univ. of Chicago, Chicago, IL (United States). Center for Structural Genomics of Infectious Diseases (CSGID), Consortium for Advanced Science and Engineering; Argonne National Lab. (ANL), Lemont, IL (United States). Biosciences Division, Structural Biology Center
  3. Illinois Inst. of Technology, Chicago, IL (United States). Dept. of Biological Science; Argonne National Lab. (ANL), Lemont, IL (United States). Biophysics Collaborative Access Team, Advanced Proton Source
  4. Illinois Inst. of Technology, Chicago, IL (United States). Dept. of Chemistry
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
National Institutes of Health (NIH), National Institute of Allergy and Infectious Diseases (NIAID); Illinois Inst. of Technology, Chicago, IL (United States); USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1570236
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Biological Chemistry
Additional Journal Information:
Journal Volume: 294; Journal Issue: 37; Journal ID: ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular Biology
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; ApbE; NQR; RNF; flavin transferase; random sequential kinetic mechanism; pKa; general base catalysis; Histidine

Citation Formats

Fang, Xuan, Osipiuk, Jerzy, Chakravarthy, Srinivas, Yuan, Ming, Menzer, William M., Nissen, Devin, Liang, Pingdong, Raba, Daniel A., Tuz, Karina, Howard, Andrew J., Joachimiak, Andrzej, Minh, David D. L., and Juarez, Oscar. Conserved residue His-257 of Vibrio cholerae flavin transferase ApbE plays a critical role in substrate binding and catalysis. United States: N. p., 2019. Web. doi:10.1074/jbc.RA119.008261.
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Fang, Xuan, Osipiuk, Jerzy, Chakravarthy, Srinivas, Yuan, Ming, Menzer, William M., Nissen, Devin, Liang, Pingdong, Raba, Daniel A., Tuz, Karina, Howard, Andrew J., Joachimiak, Andrzej, Minh, David D. L., & Juarez, Oscar. Conserved residue His-257 of Vibrio cholerae flavin transferase ApbE plays a critical role in substrate binding and catalysis. United States. https://doi.org/10.1074/jbc.RA119.008261
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Fang, Xuan, Osipiuk, Jerzy, Chakravarthy, Srinivas, Yuan, Ming, Menzer, William M., Nissen, Devin, Liang, Pingdong, Raba, Daniel A., Tuz, Karina, Howard, Andrew J., Joachimiak, Andrzej, Minh, David D. L., and Juarez, Oscar. Fri . "Conserved residue His-257 of Vibrio cholerae flavin transferase ApbE plays a critical role in substrate binding and catalysis". United States. https://doi.org/10.1074/jbc.RA119.008261. https://www.osti.gov/servlets/purl/1570236.
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@article{osti_1570236,
title = {Conserved residue His-257 of Vibrio cholerae flavin transferase ApbE plays a critical role in substrate binding and catalysis},
author = {Fang, Xuan and Osipiuk, Jerzy and Chakravarthy, Srinivas and Yuan, Ming and Menzer, William M. and Nissen, Devin and Liang, Pingdong and Raba, Daniel A. and Tuz, Karina and Howard, Andrew J. and Joachimiak, Andrzej and Minh, David D. L. and Juarez, Oscar},
abstractNote = {The flavin transferase ApbE plays essential roles in bacterial physiology, covalently incorporating FMN cofactors into numerous respiratory enzymes that use the integrated cofactors as electron carriers. In this work we performed a detailed kinetic and structural characterization of Vibrio cholerae WT ApbE and mutants of the conserved residue His-257, to understand its role in substrate binding and in the catalytic mechanism of this family. Bi-substrate kinetic experiments revealed that ApbE follows a random Bi Bi sequential kinetic mechanism, in which a ternary complex is formed, indicating that both substrates must be bound to the enzyme for the reaction to proceed. Steady-state kinetic analyses show that the turnover rates of His-257 mutants are significantly smaller than those of WT ApbE, and have increased Km values for both substrates, indicating that the His-257 residue plays important roles in catalysis and in enzyme-substrate complex formation. Analyses of the pH dependence of ApbE activity indicate that the pKa of the catalytic residue (pKES1) increases by 2 pH units in the His-257 mutants, suggesting that this residue plays a role in substrate deprotonation. The crystal structures of WT ApbE and an H257G mutant were determined at 1.61 and 1.92 Å resolutions, revealing that His-257 is located in the catalytic site and that the substitution does not produce major conformational changes. In this paper, we propose a reaction mechanism in which His-257 acts as a general base that deprotonates the acceptor residue, which subsequently performs a nucleophilic attack on FAD for flavin transfer.},
doi = {10.1074/jbc.RA119.008261},
journal = {Journal of Biological Chemistry},
number = 37,
volume = 294,
place = {United States},
year = {Fri Jul 26 00:00:00 EDT 2019},
month = {Fri Jul 26 00:00:00 EDT 2019}
}
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https://doi.org/10.1074/jbc.RA119.008261
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Figures / Tables:

Table I Table I: Kinetic Parameters of ApbE Wild-type and Mutants. Activities were measured in buffer containing 100 mM KCl, 1 mM EDTA, 5 mM MgCl2, 50 mM Tris, pH 9.0.
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    Works referencing / citing this record:

    Mutational analysis of the flavinylation and binding motifs in two protein targets of the flavin transferase ApbE
    journal, November 2019

    • Bertsova, Yulia V.; Serebryakova, Marina V.; Anashkin, Victor A.
    • FEMS Microbiology Letters, Vol. 366, Issue 22
    • DOI: 10.1093/femsle/fnz252
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      Table VI (p. 20)table
      Fig. 1 (p. 21)figure
      Fig. 2 (p. 22)figure
      Fig. 3 (p. 23)figure
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