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Title: Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis

Abstract

During catalysis by liver alcohol dehydrogenase (ADH), a water bound to the catalytic zinc is replaced by the oxygen of the substrates. The mechanism might involve a pentacoordinated zinc or a double-displacement reaction with participation by a nearby glutamate residue, as suggested by studies of human ADH3, yeast ADH1, and some other tetrameric ADHs. Zinc coordination and participation of water in the enzyme mechanism were investigated by X-ray crystallography. The apoenzyme and its complex with adenosine 5'-diphosphoribose have an open protein conformation with the catalytic zinc in one position, tetracoordinated by Cys-46, His-67, Cys-174, and a water molecule. The bidentate chelators 2,2'-bipyridine and 1,10-phenanthroline displace the water and form a pentacoordinated zinc. The enzyme–NADH complex has a closed conformation similar to that of ternary complexes with coenzyme and substrate analogues; the coordination of the catalytic zinc is similar to that found in the apoenzyme, except that a minor, alternative position for the catalytic zinc is ~1.3 Å from the major position and closer to Glu-68, which could form the alternative coordination to the catalytic zinc. Complexes with NADH and N-1-methylhexylformamide or N-benzylformamide (or with NAD+ and fluoro alcohols) have the classical tetracoordinated zinc, and no water is bound to themore » zinc or the nicotinamide rings. The major forms of the enzyme in the mechanism have a tetracoordinated zinc, where the carboxylate group of Glu-68 could participate in the exchange of water and substrates on the zinc. Hydride transfer in the Michaelis complexes does not involve a nearby water.« less

Authors:
ORCiD logo [1];  [1];  [1];  [1];  [1];  [1]
  1. Department of Biochemistry, The University of Iowa, Iowa City, Iowa 52242, United States
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
UNIVERSITYNIH
OSTI Identifier:
1375359
Resource Type:
Journal Article
Resource Relation:
Journal Name: Biochemistry; Journal Volume: 56; Journal Issue: 28
Country of Publication:
United States
Language:
ENGLISH
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Plapp, Bryce V., Savarimuthu, Baskar Raj, Ferraro, Daniel J., Rubach, Jon K., Brown, Eric N., and Ramaswamy, S. Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis. United States: N. p., 2017. Web. doi:10.1021/acs.biochem.7b00446.
Plapp, Bryce V., Savarimuthu, Baskar Raj, Ferraro, Daniel J., Rubach, Jon K., Brown, Eric N., & Ramaswamy, S. Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis. United States. doi:10.1021/acs.biochem.7b00446.
Plapp, Bryce V., Savarimuthu, Baskar Raj, Ferraro, Daniel J., Rubach, Jon K., Brown, Eric N., and Ramaswamy, S. Fri . "Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis". United States. doi:10.1021/acs.biochem.7b00446.
@article{osti_1375359,
title = {Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis},
author = {Plapp, Bryce V. and Savarimuthu, Baskar Raj and Ferraro, Daniel J. and Rubach, Jon K. and Brown, Eric N. and Ramaswamy, S.},
abstractNote = {During catalysis by liver alcohol dehydrogenase (ADH), a water bound to the catalytic zinc is replaced by the oxygen of the substrates. The mechanism might involve a pentacoordinated zinc or a double-displacement reaction with participation by a nearby glutamate residue, as suggested by studies of human ADH3, yeast ADH1, and some other tetrameric ADHs. Zinc coordination and participation of water in the enzyme mechanism were investigated by X-ray crystallography. The apoenzyme and its complex with adenosine 5'-diphosphoribose have an open protein conformation with the catalytic zinc in one position, tetracoordinated by Cys-46, His-67, Cys-174, and a water molecule. The bidentate chelators 2,2'-bipyridine and 1,10-phenanthroline displace the water and form a pentacoordinated zinc. The enzyme–NADH complex has a closed conformation similar to that of ternary complexes with coenzyme and substrate analogues; the coordination of the catalytic zinc is similar to that found in the apoenzyme, except that a minor, alternative position for the catalytic zinc is ~1.3 Å from the major position and closer to Glu-68, which could form the alternative coordination to the catalytic zinc. Complexes with NADH and N-1-methylhexylformamide or N-benzylformamide (or with NAD+ and fluoro alcohols) have the classical tetracoordinated zinc, and no water is bound to the zinc or the nicotinamide rings. The major forms of the enzyme in the mechanism have a tetracoordinated zinc, where the carboxylate group of Glu-68 could participate in the exchange of water and substrates on the zinc. Hydride transfer in the Michaelis complexes does not involve a nearby water.},
doi = {10.1021/acs.biochem.7b00446},
journal = {Biochemistry},
number = 28,
volume = 56,
place = {United States},
year = {Fri Jul 07 00:00:00 EDT 2017},
month = {Fri Jul 07 00:00:00 EDT 2017}
}