General Base–General Acid Catalysis in Human Histone Deacetylase 8

Gantt, Sister M. Lucy; Decroos, Christophe; Lee, Matthew S.; Gullett, Laura E.; Bowman, Christine M.; Christianson, David W.; Fierke, Carol A.

doi:10.1021/acs.biochem.5b01327

Title: General Base–General Acid Catalysis in Human Histone Deacetylase 8

Journal Article · Mon Jan 25 00:00:00 EST 2016 · Biochemistry

DOI:https://doi.org/10.1021/acs.biochem.5b01327· OSTI ID:1238290

Gantt, Sister M. Lucy ^[1]; Decroos, Christophe ^[2]; Lee, Matthew S. ^[3]; Gullett, Laura E. ^[4]; Bowman, Christine M. ^[5]; Christianson, David W. ^[4]; Fierke, Carol A. ^[6]

Univ. of Michigan, Ann Arbor, MI (United States); Franciscan Univ. of Steubenville, OH (United States)
Univ. of Pennsylvania, Philadelphia, PA (United States); Aix Marseille Univ., Centrale Marseille (France)
Univ. of Pennsylvania, Philadelphia, PA (United States)
Univ. of Pennsylvania, Philadelphia, PA (United States); Harvard Univ., Cambridge, MA (United States)
Univ. of Pennsylvania, Philadelphia, PA (United States); Univ. of California, San Francisco, CA (United States)
Univ. of Michigan, Ann Arbor, MI (United States)

Histone deacetylases (HDACs) regulate cellular processes such as differentiation and apoptosis and are targeted by anticancer therapeutics in development and in the clinic. HDAC8 is a metal-dependent class I HDAC and is proposed to use a general acid–base catalytic pair in the mechanism of amide bond hydrolysis. Here, we report site-directed mutagenesis and enzymological measurements to elucidate the catalytic mechanism of HDAC8. Specifically, we focus on the catalytic function of Y306 and the histidine-aspartate dyads H142-D176 and H143-D183. Additionally, we report X-ray crystal structures of four representative HDAC8 mutants: D176N, D176N/Y306F, D176A/Y306F, and H142A/Y306F. These structures provide a useful framework for understanding enzymological measurements. We report the pH dependence of k_cat/K_M for wild-type Co(II)-HDAC8 is bell-shaped with two pK_a values of 7.4 and 10.0. The upper pK_a reflects the ionization of the metal-bound water molecule and shifts to 9.1 in Zn(II)-HDAC8. The H142A mutant has activity 230-fold lower than that of wild-type HDAC8, but the pK_a1 value is not altered. Y306F HDAC8 is 150-fold less active than the wild-type enzyme; crystal structures show that Y306 hydrogen bonds with the zinc-bound substrate carbonyl, poised for transition state stabilization. The H143A and H142A/H143A mutants exhibit activity that is >80000-fold lower than that of wild-type HDAC8; the buried D176N and D176A mutants have significant catalytic effects, with more subtle effects caused by D183N and D183A. These enzymological and structural studies strongly suggest that H143 functions as a single general base–general acid catalyst, while H142 remains positively charged and serves as an electrostatic catalyst for transition state stabilization.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: National Institutes of Health (NIH)

Grant/Contract Number:: GM40602; GM49758

OSTI ID:: 1238290

Journal Information:: Biochemistry, Vol. 55, Issue 5; ISSN 0006-2960

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Cited by: 50 works

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References (58)

Histone deacetylases and cancer Glozak, M. A.; Seto, E. Oncogene, Vol. 26, Issue 37 https://doi.org/10.1038/sj.onc.1210610	journal	August 2007
Histone deacetylase inhibitors: molecular mechanisms of action Xu, W. S.; Parmigiani, R. B.; Marks, P. A. Oncogene, Vol. 26, Issue 37 https://doi.org/10.1038/sj.onc.1210620	journal	August 2007
HDAC inhibitor-based therapies: Can we interpret the code? New, Maria; Olzscha, Heidi; La Thangue, Nicholas B. Molecular Oncology, Vol. 6, Issue 6 https://doi.org/10.1016/j.molonc.2012.09.003	journal	October 2012
Metabolic reprogramming by class I and II histone deacetylases Mihaylova, Maria M.; Shaw, Reuben J. Trends in Endocrinology & Metabolism, Vol. 24, Issue 1 https://doi.org/10.1016/j.tem.2012.09.003	journal	January 2013
Acetylation and Methylation of Histones and Their Possible role in the Regulation of rna Synthesis Allfrey, V. G.; Faulkner, R.; Mirsky, A. E. Proceedings of the National Academy of Sciences, Vol. 51, Issue 5 https://doi.org/10.1073/pnas.51.5.786	journal	May 1964
Lysine acetylation and the bromodomain: a new partnership for signaling Yang, Xiang-Jiao BioEssays, Vol. 26, Issue 10 https://doi.org/10.1002/bies.20104	journal	January 2004
Acetylation and deacetylation of non-histone proteins Glozak, Michele A.; Sengupta, Nilanjan; Zhang, Xiaohong Gene, Vol. 363 https://doi.org/10.1016/j.gene.2005.09.010	journal	December 2005
The Biochemistry of Sirtuins Sauve, Anthony A.; Wolberger, Cynthia; Schramm, Vern L. Annual Review of Biochemistry, Vol. 75, Issue 1 https://doi.org/10.1146/annurev.biochem.74.082803.133500	journal	June 2006
Molecular Evolution of the Histone Deacetylase Family: Functional Implications of Phylogenetic Analysis Gregoretti, IvanV; Lee, Yun-Mi; Goodson, Holly V. Journal of Molecular Biology, Vol. 338, Issue 1 https://doi.org/10.1016/j.jmb.2004.02.006	journal	April 2004
Catalytic Activity and Inhibition of Human Histone Deacetylase 8 Is Dependent on the Identity of the Active Site Metal Ion ^† Gantt, Stephanie L.; Gattis, Samuel G.; Fierke, Carol A. Biochemistry, Vol. 45, Issue 19 https://doi.org/10.1021/bi060212u	journal	May 2006
Vorinostat: a new oral histone deacetylase inhibitor approved for cutaneous T-cell lymphoma Duvic, Madeleine; Vu, Jenny Expert Opinion on Investigational Drugs, Vol. 16, Issue 7 https://doi.org/10.1517/13543784.16.7.1111	journal	June 2007
Dimethyl sulfoxide to vorinostat: development of this histone deacetylase inhibitor as an anticancer drug Marks, Paul A.; Breslow, Ronald Nature Biotechnology, Vol. 25, Issue 1 https://doi.org/10.1038/nbt1272	journal	January 2007
FDA Approval Summary: Vorinostat for Treatment of Advanced Primary Cutaneous T-Cell Lymphoma Mann, B. S.; Johnson, J. R.; Cohen, M. H. The Oncologist, Vol. 12, Issue 10 https://doi.org/10.1634/theoncologist.12-10-1247	journal	October 2007
FDA Approval: Belinostat for the Treatment of Patients with Relapsed or Refractory Peripheral T-cell Lymphoma Lee, Hyon-Zu; Kwitkowski, Virginia E.; Del Valle, Pedro L. Clinical Cancer Research, Vol. 21, Issue 12 https://doi.org/10.1158/1078-0432.CCR-14-3119	journal	March 2015
Panobinostat for the Treatment of Multiple Myeloma Laubach, Jacob P.; Moreau, Philippe; San-Miguel, Jesús F. Clinical Cancer Research, Vol. 21, Issue 21 https://doi.org/10.1158/1078-0432.CCR-15-0530	journal	September 2015
Therapeutic application of histone deacetylase inhibitors for central nervous system disorders Kazantsev, Aleksey G.; Thompson, Leslie M. Nature Reviews Drug Discovery, Vol. 7, Issue 10 https://doi.org/10.1038/nrd2681	journal	October 2008
Epigenetic targeting of histone deacetylase: Therapeutic potential in Parkinson's disease? Harrison, Ian F.; Dexter, David T. Pharmacology & Therapeutics, Vol. 140, Issue 1 https://doi.org/10.1016/j.pharmthera.2013.05.010	journal	October 2013
Crystal structure of a eukaryotic zinc-dependent histone deacetylase, human HDAC8, complexed with a hydroxamic acid inhibitor Vannini, A.; Volpari, C.; Filocamo, G. Proceedings of the National Academy of Sciences, Vol. 101, Issue 42 https://doi.org/10.1073/pnas.0404603101	journal	October 2004
Structural Snapshots of Human HDAC8 Provide Insights into the Class I Histone Deacetylases Somoza, John R.; Skene, Robert J.; Katz, Bradley A. Structure, Vol. 12, Issue 7 https://doi.org/10.1016/j.str.2004.04.012	journal	July 2004
Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8–substrate complex Vannini, Alessandro; Volpari, Cinzia; Gallinari, Paola EMBO reports, Vol. 8, Issue 9 https://doi.org/10.1038/sj.embor.7401047	journal	August 2007
Zinc hydrolases: the mechanisms of zinc-dependent deacetylases Hernick, Marcy; Fierke, Carol A. Archives of Biochemistry and Biophysics, Vol. 433, Issue 1 https://doi.org/10.1016/j.abb.2004.08.006	journal	January 2005
Structural Studies of Human Histone Deacetylase 8 and Its Site-Specific Variants Complexed with Substrate and Inhibitors ^† ^, ^‡ Dowling, Daniel P.; Gantt, Stephanie L.; Gattis, Samuel G. Biochemistry, Vol. 47, Issue 51 https://doi.org/10.1021/bi801610c	journal	December 2008
Activation and Inhibition of Histone Deacetylase 8 by Monovalent Cations Gantt, Stephanie L.; Joseph, Caleb G.; Fierke, Carol A. Journal of Biological Chemistry, Vol. 285, Issue 9 https://doi.org/10.1074/jbc.M109.033399	journal	December 2009
Structures of Metal-Substituted Human Histone Deacetylase 8 Provide Mechanistic Inferences on Biological Function, Dowling, Daniel P.; Gattis, Samuel G.; Fierke, Carol A. Biochemistry, Vol. 49, Issue 24 https://doi.org/10.1021/bi1005046	journal	June 2010
Structural Basis of the Antiproliferative Activity of Largazole, a Depsipeptide Inhibitor of the Histone Deacetylases Cole, Kathryn E.; Dowling, Daniel P.; Boone, Matthew A. Journal of the American Chemical Society, Vol. 133, Issue 32 https://doi.org/10.1021/ja205972n	journal	August 2011
Compromised Structure and Function of HDAC8 Mutants Identified in Cornelia de Lange Syndrome Spectrum Disorders Decroos, Christophe; Bowman, Christine M.; Moser, Joe-Ann S. ACS Chemical Biology, Vol. 9, Issue 9 https://doi.org/10.1021/cb5003762	journal	July 2014
Variable Active Site Loop Conformations Accommodate the Binding of Macrocyclic Largazole Analogues to HDAC8 Decroos, Christophe; Clausen, Dane J.; Haines, Brandon E. Biochemistry, Vol. 54, Issue 12 https://doi.org/10.1021/acs.biochem.5b00010	journal	March 2015
Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors Finnin, Michael S.; Donigian, Jill R.; Cohen, Alona Nature, Vol. 401, Issue 6749 https://doi.org/10.1038/43710	journal	September 1999
On the importance of orientation in general base catalysis by carboxylate Gandour, Richard David Bioorganic Chemistry, Vol. 10, Issue 2 https://doi.org/10.1016/0045-2068(81)90020-1	journal	June 1981
Stereoelectronic effects at carboxylate: a syn-oriented model for the histidine-aspartate couple in enzymes Zimmerman, Steven C.; Cramer, Katherine D. Journal of the American Chemical Society, Vol. 110, Issue 17 https://doi.org/10.1021/ja00225a056	journal	August 1988
Carboxylate-histidine-zinc interactions in protein structure and function Christianson, David W.; Alexander, Richard S. Journal of the American Chemical Society, Vol. 111, Issue 16 https://doi.org/10.1021/ja00198a065	journal	August 1989
Conformational differences between various myoglobin ligated states as monitored by proton NMR spectroscopy Bradbury, J. Howard; Carver, John A. Biochemistry, Vol. 23, Issue 21 https://doi.org/10.1021/bi00316a013	journal	October 1984
Assignment of proton NMR resonances of histidine and other aromatic residues in met-, cyano-, oxy-, and (carbon monoxy)myoglobins Carver, John A.; Bradbury, J. Howard Biochemistry, Vol. 23, Issue 21 https://doi.org/10.1021/bi00316a012	journal	October 1984
The pKa values of two histidine residues in human haemoglobin, the Bohr effect, and the dipole moments of α-helices Perutz, Max F.; Gronenborn, Angela M.; Clore, G. Marius Journal of Molecular Biology, Vol. 183, Issue 3 https://doi.org/10.1016/0022-2836(85)90016-6	journal	June 1985
Crystal Structure of a Bacterial Class 2 Histone Deacetylase Homologue Nielsen, Tine Kragh; Hildmann, Christian; Dickmanns, Achim Journal of Molecular Biology, Vol. 354, Issue 1 https://doi.org/10.1016/j.jmb.2005.09.065	journal	November 2005
Probing the elusive catalytic activity of vertebrate class IIa histone deacetylases Jones, Philip; Altamura, Sergio; De Francesco, Raffaele Bioorganic & Medicinal Chemistry Letters, Vol. 18, Issue 6 https://doi.org/10.1016/j.bmcl.2008.02.025	journal	March 2008
Human HDAC7 Harbors a Class IIa Histone Deacetylase-specific Zinc Binding Motif and Cryptic Deacetylase Activity Schuetz, Anja; Min, Jinrong; Allali-Hassani, Abdellah Journal of Biological Chemistry, Vol. 283, Issue 17 https://doi.org/10.1074/jbc.M707362200	journal	April 2008
Structural basis of the action of thermolysin and related zinc peptidases Matthews, Brian W. Accounts of Chemical Research, Vol. 21, Issue 9 https://doi.org/10.1021/ar00153a003	journal	September 1988
Carboxypeptidase A Christianson, David W.; Lipscomb, William N. Accounts of Chemical Research, Vol. 22, Issue 2 https://doi.org/10.1021/ar00158a003	journal	February 1989
Noncomplexing Tertiary Amines as “Better” Buffers Covering the Range of pH 3−11. Temperature Dependence of Their Acid Dissociation Constants Kandegedara, Ashoka; Rorabacher, David B. Analytical Chemistry, Vol. 71, Issue 15 https://doi.org/10.1021/ac9902594	journal	August 1999
Kinetics and Comparative Reactivity of Human Class I and Class IIb Histone Deacetylases Schultz, Brian E.; Misialek, Shawn; Wu, Jiansheng Biochemistry, Vol. 43, Issue 34 https://doi.org/10.1021/bi0494471	journal	August 2004
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Pyrrole Hydrogen Ionization of Imidazole Derivatives in Metal Ion Complexes and Carbonic Anhydrase Martin, R. B. Proceedings of the National Academy of Sciences, Vol. 71, Issue 11 https://doi.org/10.1073/pnas.71.11.4346	journal	November 1974
Structure and activity of enzymes that remove histone modifications Holbert, Marc A.; Marmorstein, Ronen Current Opinion in Structural Biology, Vol. 15, Issue 6 https://doi.org/10.1016/j.sbi.2005.10.006	journal	December 2005
Structure, mechanism, and inhibition of histone deacetylases and related metalloenzymes Lombardi, Patrick M.; Cole, Kathryn E.; Dowling, Daniel P. Current Opinion in Structural Biology, Vol. 21, Issue 6 https://doi.org/10.1016/j.sbi.2011.08.004	journal	December 2011
Members of the histone deacetylase superfamily differ in substrate specificity towards small synthetic substrates Riester, Daniel; Wegener, Dennis; Hildmann, Christian Biochemical and Biophysical Research Communications, Vol. 324, Issue 3 https://doi.org/10.1016/j.bbrc.2004.09.155	journal	November 2004
Substrate and inhibitor specificity of class 1 and class 2 histone deacetylases Hildmann, Christian; Wegener, Dennis; Riester, Daniel Journal of Biotechnology, Vol. 124, Issue 1 https://doi.org/10.1016/j.jbiotec.2006.01.030	journal	June 2006
UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine Deacetylase Functions through a General Acid-Base Catalyst Pair Mechanism Hernick, Marcy; Gennadios, Heather A.; Whittington, Douglas A. Journal of Biological Chemistry, Vol. 280, Issue 17 https://doi.org/10.1074/jbc.M413560200	journal	April 2005
Crystal structure of LpxC, a zinc-dependent deacetylase essential for endotoxin biosynthesis Whittington, Douglas A.; Rusche, Kristin M.; Shin, Hyunshun Proceedings of the National Academy of Sciences, Vol. 100, Issue 14 https://doi.org/10.1073/pnas.1432990100	journal	June 2003
Binding to thermolysin of phenolate-containing inhibitors necessitates a revised mechanism of catalysis Mock, W. L.; Aksamawati, M. Biochemical Journal, Vol. 302, Issue 1 https://doi.org/10.1042/bj3020057	journal	August 1994
Catalytic Mechanism and Molecular Recognition of E . coli UDP-3- O -( R -3-Hydroxymyristoyl)- N -acetylglucosamine Deacetylase Probed by Mutagenesis ^† Hernick, Marcy; Fierke, Carol A. Biochemistry, Vol. 45, Issue 51 https://doi.org/10.1021/bi061405k	journal	December 2006
Differences in transition state stabilization between thermolysin (EC 3.4.24.27) and neprilysin (EC 3.4.24.11) Marie-Claire, Cynthia; Ruffet, Emmanuel; Tiraboschi, Gilles FEBS Letters, Vol. 438, Issue 3 https://doi.org/10.1016/S0014-5793(98)01267-8	journal	November 1998
A Correlation of Reaction Rates Hammond, George S. Journal of the American Chemical Society, Vol. 77, Issue 2 https://doi.org/10.1021/ja01607a027	journal	January 1955
Unexpected Deacetylation Mechanism Suggested by a Density Functional Theory QM/MM Study of Histone-Deacetylase-Like Protein Corminboeuf, Clémence; Hu, Po; Tuckerman, Mark E. Journal of the American Chemical Society, Vol. 128, Issue 14 https://doi.org/10.1021/ja0600882	journal	April 2006
A Proton-Shuttle Reaction Mechanism for Histone Deacetylase 8 and the Catalytic Role of Metal Ions Wu, Ruibo; Wang, Shenglong; Zhou, Nengjie Journal of the American Chemical Society, Vol. 132, Issue 27 https://doi.org/10.1021/ja103932d	journal	July 2010
Inhibition and Mechanism of HDAC8 Revisited Chen, Kai; Zhang, Xiaoxiao; Wu, Yun-Dong Journal of the American Chemical Society, Vol. 136, Issue 33 https://doi.org/10.1021/ja501548p	journal	August 2014

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Regulation of Histone Deacetylase 3 by Metal Cations and 10-Hydroxy-2E-DecenoicAcid: Possible Molecular Epigenetic Mechanisms of Queen-Worker Bee Differentiation Polsinelli, Gregory A.; Yu, Hongwei D. bioRxiv https://doi.org/10.1101/415364	posted_content	September 2018
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Histone deacetylase 6 structure and molecular basis of catalysis and inhibition Hai, Yang; Christianson, David W. Nature Chemical Biology, Vol. 12, Issue 9 https://doi.org/10.1038/nchembio.2134	journal	July 2016
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