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Title: Structural and dynamical description of the enzymatic reaction of a phosphohexomutase

Abstract

Enzymes are known to adopt various conformations at different points along their catalytic cycles. Here, we present a comprehensive analysis of 15 isomorphous, high resolution crystal structures of the enzyme phosphoglucomutase from the bacterium Xanthomonas citri. The protein was captured in distinct states critical to function, including enzyme-substrate, enzyme-product, and enzyme-intermediate complexes. Key residues in ligand recognition and regions undergoing conformational change are identified and correlated with the various steps of the catalytic reaction. In addition, we use principal component analysis to examine various subsets of these structures with two goals: (1) identifying sites of conformational heterogeneity through a comparison of room temperature and cryogenic structures of the apo-enzyme and (2) a priori clustering of the enzyme-ligand complexes into functionally related groups, showing sensitivity of this method to structural features difficult to detect by traditional methods. This study captures, in a single system, the structural basis of diverse substrate recognition, the subtle impact of covalent modification, and the role of ligand-induced conformational change in this representative enzyme of the α-D-phosphohexomutase superfamily.

Authors:
ORCiD logo [1];  [1];  [2]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [1]
  1. Univ. of Missouri, Columbia, MO (United States)
  2. Dalhousie Univ., Halifax, NS (Canada)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); National Science Foundation (NSF)
OSTI Identifier:
1619116
Alternate Identifier(s):
OSTI ID: 1504500
Grant/Contract Number:  
AC02-05CH11231; T32 GM008396-26; MCB-0918389; P30 GM124169-01
Resource Type:
Accepted Manuscript
Journal Name:
Structural Dynamics
Additional Journal Information:
Journal Volume: 6; Journal Issue: 2; Journal ID: ISSN 2329-7778
Publisher:
American Crystallographic Association/AIP
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Stiers, Kyle M., Graham, Abigail C., Zhu, Jian-She, Jakeman, David L., Nix, Jay C., and Beamer, Lesa J. Structural and dynamical description of the enzymatic reaction of a phosphohexomutase. United States: N. p., 2019. Web. doi:10.1063/1.5092803.
Stiers, Kyle M., Graham, Abigail C., Zhu, Jian-She, Jakeman, David L., Nix, Jay C., & Beamer, Lesa J. Structural and dynamical description of the enzymatic reaction of a phosphohexomutase. United States. doi:10.1063/1.5092803.
Stiers, Kyle M., Graham, Abigail C., Zhu, Jian-She, Jakeman, David L., Nix, Jay C., and Beamer, Lesa J. Mon . "Structural and dynamical description of the enzymatic reaction of a phosphohexomutase". United States. doi:10.1063/1.5092803. https://www.osti.gov/servlets/purl/1619116.
@article{osti_1619116,
title = {Structural and dynamical description of the enzymatic reaction of a phosphohexomutase},
author = {Stiers, Kyle M. and Graham, Abigail C. and Zhu, Jian-She and Jakeman, David L. and Nix, Jay C. and Beamer, Lesa J.},
abstractNote = {Enzymes are known to adopt various conformations at different points along their catalytic cycles. Here, we present a comprehensive analysis of 15 isomorphous, high resolution crystal structures of the enzyme phosphoglucomutase from the bacterium Xanthomonas citri. The protein was captured in distinct states critical to function, including enzyme-substrate, enzyme-product, and enzyme-intermediate complexes. Key residues in ligand recognition and regions undergoing conformational change are identified and correlated with the various steps of the catalytic reaction. In addition, we use principal component analysis to examine various subsets of these structures with two goals: (1) identifying sites of conformational heterogeneity through a comparison of room temperature and cryogenic structures of the apo-enzyme and (2) a priori clustering of the enzyme-ligand complexes into functionally related groups, showing sensitivity of this method to structural features difficult to detect by traditional methods. This study captures, in a single system, the structural basis of diverse substrate recognition, the subtle impact of covalent modification, and the role of ligand-induced conformational change in this representative enzyme of the α-D-phosphohexomutase superfamily.},
doi = {10.1063/1.5092803},
journal = {Structural Dynamics},
number = 2,
volume = 6,
place = {United States},
year = {2019},
month = {4}
}

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