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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. Here, 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];  [2];  [3];  [4];  [5]
  1. Univ. of Iowa, Iowa City, IA (United States)
  2. Univ. of Iowa, Iowa City, IA (United States); Southern Illinois Univ. School of Medicine, Springfield, IL (United States)
  3. Univ. of Iowa, Iowa City, IA (United States); Kemin Industries, Des Moines, IA (United States)
  4. Univ. of Iowa, Iowa City, IA (United States); Vanderbilt University of Visual Sciences, Nashville, TN (United States)
  5. Univ. of Iowa, Iowa City, IA (United States); Institute for Stem Cell Biology and Regenerative Medicine (inSTEM), Bangalore (India)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division; National Institutes of Health (NIH)
OSTI Identifier:
1375359
Grant/Contract Number:  
AC02-06CH11357; AA00279
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Biochemistry
Additional Journal Information:
Journal Volume: 56; Journal Issue: 28; Journal ID: ISSN 0006-2960
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
ENGLISH
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; zinc; alcohols; peptides and proteins; chemical structure; nicotinamide

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. https://doi.org/10.1021/acs.biochem.7b00446
Plapp, Bryce V., Savarimuthu, Baskar Raj, Ferraro, Daniel J., Rubach, Jon K., Brown, Eric N., and Ramaswamy, S. 2017. "Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis". United States. https://doi.org/10.1021/acs.biochem.7b00446. https://www.osti.gov/servlets/purl/1375359.
@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. Here, 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},
url = {https://www.osti.gov/biblio/1375359}, journal = {Biochemistry},
issn = {0006-2960},
number = 28,
volume = 56,
place = {United States},
year = {Thu Jun 22 00:00:00 EDT 2017},
month = {Thu Jun 22 00:00:00 EDT 2017}
}

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Cited by: 26 works
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Works referenced in this record:

Hydride Transfer in Liver Alcohol Dehydrogenase:  Quantum Dynamics, Kinetic Isotope Effects, and Role of Enzyme Motion
journal, November 2001


Structure of human χχ alcohol dehydrogenase: a glutathione-dependent formaldehyde dehydrogenase
journal, January 1997


Combining Electronic Structure Methods with the Calculation of Hydrogen Vibrational Wavefunctions:  Application to Hydride Transfer in Liver Alcohol Dehydrogenase
journal, September 2000


Structural study of a single-point mutant of Sulfolobus solfataricus alcohol dehydrogenase with enhanced activity
journal, March 2003


The finer things in X-ray diffraction data collection
journal, October 1999


Effect of pH on the Process of Ternary-Complex Interconversion in the liver-Alcohol-Dehydrogenase Reaction
journal, June 1978


Crystal structures of the active site in specifically metal-depleted and cobalt-substituted horse liver alcohol dehydrogenase derivatives.
journal, September 1983


Human Glutathione-Dependent Formaldehyde Dehydrogenase. Structures of Apo, Binary, and Inhibitory Ternary Complexes
journal, September 2002


Flexibility of Liver Alcohol Dehydrogenase in Stereoselective Binding of 3-Butylthiolane 1-Oxides ,
journal, January 1997


Comparison of computer modelling and X-ray results of the binding of a pyrazole derivative to liver alcohol dehydrogenase
journal, October 1987


Structure of a triclinic ternary complex of horse liver alcohol dehydrogenase at 2.9 Å resolution
journal, March 1981


The Structure of an Alcohol Dehydrogenase from the Hyperthermophilic Archaeon Aeropyrum pernix
journal, August 2003


Yeast Alcohol Dehydrogenase Structure and Catalysis
journal, September 2014


Crystallization of Horse Liver Alcohol Dehydrogenase Complexes from Alcohol Solutions.
journal, January 1967


The Conformation of Adenosine Diphosphoribose and 8-Bromoadenosine Diphosphoribose when Bound to Liver Alcohol Dehydrogenase
journal, January 1975


Inhibition of Human Alcohol Dehydrogenases by Formamides
journal, May 1998


Proton equilibriums and kinetics in the liver alcohol dehydrogenase reaction mechanism
journal, September 1974


On the Enzymatic Activation of NADH
journal, March 2001


Active site electronic structure and dynamics during metalloenzyme catalysis
journal, January 2003


Nuclear magnetic resonance studies of substrate interaction with cobalt substituted alcohol dehydrogenase from liver
journal, May 1975


Pyrazole binding in crystalline binary and ternary complexes with liver alcohol dehydrogenase
journal, September 1982


XDS
journal, January 2010


X-Ray Crystallographic and Kinetic Studies of Human Sorbitol Dehydrogenase
journal, September 2003


Coordination environment of the active-site metal ion of liver alcohol dehydrogenase.
journal, October 1981


Magnetic Circular Dichroism and Electron Paramagnetic Resonance Studies of Cobalt-Substituted Horse Liver Alcohol Dehydrogenase
journal, January 1995


Alternative pathways and reactions of benzyl alcohol and benzaldehyde with horse liver alcohol dehydrogenase
journal, October 1993


Energetics and Dynamics of Enzymatic Reactions
journal, August 2001


Crystallography of liver alcohol dehydrogenase complexed with substrates
journal, June 1978


A Theoretical Analysis of the Proton and Hydride Transfer in Liver Alcohol Dehydrogenase (LADH)
journal, March 2002


MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009


Limiting rates of ligand association to alcohol dehydrogenase
journal, August 1978


Active site electronic structure and dynamics during metalloenzyme catalysis
journal, January 2003


Neutral metal-bound water is the base catalyst in liver alcohol dehydrogenase.
journal, May 1983


Three-dimensional structure of horse liver alcohol dehydrogenase at 2.4 Å resolution
journal, March 1976


Effect of NADH on the pK a of Zinc-Bound Water in Liver Alcohol Dehydrogenase
journal, January 1981


Conformational changes and catalysis by alcohol dehydrogenase
journal, January 2010


Crystal Structure of the Alcohol Dehydrogenase from the Hyperthermophilic Archaeon Sulfolobus solfataricus at 1.85Å Resolution
journal, April 2002


The Kinetics of Replacement Reactions of Complexes of the Transition Metals with 1,10-Phenanthroline and 2,2'-Bipyridine
journal, July 1965


Inhibition of Human Alcohol Dehydrogenases by Formamides
journal, May 1998


Structural Evidence for a Ligand Coordination Switch in Liver Alcohol Dehydrogenase
journal, April 2007


Liver Alcohol Dehydrogenas
journal, January 1986


The Conformation of Adenosine Diphosphoribose and 8-Bromoadenosine Diphosphoribose when Bound to Liver Alcohol Dehydrogenase
journal, January 1975


Crystallization of Horse Liver Alcohol Dehydrogenase Complexes from Alcohol Solutions.
journal, January 1967


Evaluation of the factors influencing reactivity and stereospecificity in NAD(P)H dependent dehydrogenase enzymes
journal, March 1993


Mechanistic implications from structures of yeast alcohol dehydrogenase complexed with coenzyme and an alcohol
journal, February 2016


Complex Formation of 1,10-Phenanthroline with Zinc Ions and the Zinc of Alcohol Dehydrogenase of Horse Liver
journal, October 1959


Pyrazole binding in crystalline binary and ternary complexes with liver alcohol dehydrogenase
journal, September 1982


Effects of Cavities at the Nicotinamide Binding Site of Liver Alcohol Dehydrogenase on Structure, Dynamics and Catalysis
journal, January 2014


Human Glutathione-Dependent Formaldehyde Dehydrogenase. Structures of Apo, Binary, and Inhibitory Ternary Complexes
journal, September 2002


Effect of pH on Coenzyme Binding to Liver Alcohol Dehydrogenase
journal, October 1979


Formamides Mimic Aldehydes and Inhibit Liver Alcohol Dehydrogenases and Ethanol Metabolism
journal, September 2003


Hydride Transfer in Liver Alcohol Dehydrogenase:  Quantum Dynamics, Kinetic Isotope Effects, and Role of Enzyme Motion
journal, November 2001


Structure of human χχ alcohol dehydrogenase: a glutathione-dependent formaldehyde dehydrogenase
journal, January 1997


Combining Electronic Structure Methods with the Calculation of Hydrogen Vibrational Wavefunctions:  Application to Hydride Transfer in Liver Alcohol Dehydrogenase
journal, September 2000


Effect of pH on Coenzyme Binding to Liver Alcohol Dehydrogenase
journal, October 1979


Structure of a triclinic ternary complex of horse liver alcohol dehydrogenase at 2.9 Å resolution
journal, March 1981


Structure of the primary acid rearrangement product of reduced nicotinamide adenine dinucleotide (NADH)
journal, November 1974


Studies on liver alcohol dehydrogenase complexes
journal, January 1964


Crystal structures of the active site in specifically metal-depleted and cobalt-substituted horse liver alcohol dehydrogenase derivatives.
journal, September 1983


Nuclear magnetic resonance studies of substrate interaction with cobalt substituted alcohol dehydrogenase from liver
journal, May 1975


Refined crystal structure of liver alcohol dehydrogenase–NADH complex at 1.8 Å resolution
journal, November 1994


Evaluation of the factors influencing reactivity and stereospecificity in NAD(P)H dependent dehydrogenase enzymes
journal, March 1993


Molray – a web interface between O and the POV-Ray ray tracer
journal, July 2001


The limiting rate of chelation of liver alcohol dehydrogenase
journal, July 1970


Improved methods for building protein models in electron density maps and the location of errors in these models
journal, March 1991


X-Ray Investigation of the Binding of 1,10-Phenanthroline and Imidazole to Horse-Liver Alcohol Dehydrogenase
journal, July 1977


Human Glutathione-Dependent Formaldehyde Dehydrogenase. Structural Changes Associated with Ternary Complex Formation
journal, December 2002


Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion
journal, January 1995


Mechanistic implications from structures of yeast alcohol dehydrogenase complexed with coenzyme and an alcohol
journal, February 2016


Conformational changes and catalysis by alcohol dehydrogenase
journal, January 2010


Studies on liver alcohol dehydrogenase complexes
journal, January 1964


A nuclear magnetic resonance study of cobalt II alcohol dehydrogenase: Substrate analog-metal interactions
journal, November 1980


Crystallography of liver alcohol dehydrogenase complexed with substrates
journal, June 1978


Mechanism of binding of horse liver alcohol dehydrogenase and nicotinamide adenine dinucleotide
journal, July 1988


Alternative pathways and reactions of benzyl alcohol and benzaldehyde with horse liver alcohol dehydrogenase
journal, October 1993


Energetics and Dynamics of Enzymatic Reactions
journal, August 2001


Participation of Histidine-51 in Catalysis by Horse Liver Alcohol Dehydrogenase ,
journal, March 2004


A nuclear magnetic resonance study of cobalt II alcohol dehydrogenase: Substrate analog-metal interactions
journal, November 1980


Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion
journal, January 1995


Effects of Cavities at the Nicotinamide Binding Site of Liver Alcohol Dehydrogenase on Structure, Dynamics and Catalysis
journal, January 2014


Coordination environment of the active-site metal ion of liver alcohol dehydrogenase.
journal, October 1981


Crystal structure refinement with SHELXL
journal, January 2015


Geometry of metal–ligand interactions in proteins
journal, March 2001


X-Ray Investigation of the Binding of 1,10-Phenanthroline and Imidazole to Horse-Liver Alcohol Dehydrogenase
journal, July 1977


Structural Evidence for a Ligand Coordination Switch in Liver Alcohol Dehydrogenase
journal, April 2007


Effect of NADH on the pK a of Zinc-Bound Water in Liver Alcohol Dehydrogenase
journal, January 1981


Mechanism of binding of horse liver alcohol dehydrogenase and nicotinamide adenine dinucleotide
journal, July 1988


Neutral metal-bound water is the base catalyst in liver alcohol dehydrogenase.
journal, May 1983


Liver Alcohol Dehydrogenas
journal, January 1986


Limiting rates of ligand association to alcohol dehydrogenase
journal, August 1978


Human Glutathione-Dependent Formaldehyde Dehydrogenase. Structural Changes Associated with Ternary Complex Formation
journal, December 2002


The Kinetics of Replacement Reactions of Complexes of the Transition Metals with 1,10-Phenanthroline and 2,2'-Bipyridine
journal, July 1965


Three-dimensional structure of horse liver alcohol dehydrogenase at 2.4 Å resolution
journal, March 1976


Tetrameric NAD-dependent alcohol dehydrogenase
journal, February 2003


Structure of Escherichia coli AdhP (ethanol-inducible dehydrogenase) with bound NAD
journal, June 2013

  • Thomas, Leonard M.; Harper, Angelica R.; Miner, Whitney A.
  • Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 69, Issue 7
  • https://doi.org/10.1107/S1744309113015170

Yeast Alcohol Dehydrogenase Structure and Catalysis
journal, September 2014


Binding of Formamides to Liver Alcohol Dehydrogenase ,
journal, March 1997


The Role of Zinc in Alcohol Dehydrogenase
journal, October 1959


Liver alcohol dehydrogenase-coenzyme reaction rates.
journal, May 1977


The role of zinc-bound water in liver alcohol dehydrogenase catalysis.
journal, March 1980


Binding of substrate in a ternary complex of horse liver alcohol dehydrogenase.
journal, December 1982


Carboxyl groups near the active site zinc contribute to catalysis in yeast alcohol dehydrogenase.
journal, April 1988


The Effects of pH and Temperature on Hydrogen Transfer in the Liver Alcohol Dehydrogenase Mechanism
journal, April 1972


113Cd NMR in binary and ternary complexes of cadmium-substituted horse liver alcohol dehydrogenase.
journal, June 1981


Works referencing / citing this record:

Peroxidase activity of new mixed‐valence cobalt complexes with ligands derived from pyridoxal
journal, April 2019