General Base–General Acid Catalysis in Human Histone Deacetylase 8

[20] Processing of X-ray diffraction data collected in oscillation mode

Otwinowski, Z., & Minor, W. (1997) · Methods in Enzymology · doi:10.1016/s0076-6879(97)76066-x · Cited by 33,475 · see citing works

Features and development of Coot

Emsley, P., Lohkamp, B., Scott, W. G., & Cowtan, K. D. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910007493 · Cited by 27,510 · see citing works

<i>PHENIX</i> : a comprehensive Python-based system for macromolecular structure solution

Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909052925 · Cited by 23,716 · see citing works

A Correlation of Reaction Rates

Hammond, G. S. (1955) · Journal of the American Chemical Society · doi:10.1021/ja01607a027 · Cited by 3,590 · see citing works

ACETYLATION AND METHYLATION OF HISTONES AND THEIR POSSIBLE ROLE IN THE REGULATION OF RNA SYNTHESIS

Allfrey, V. G., Faulkner, R. D., & Mirsky, A. E. (1964) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.51.5.786 · Cited by 2,649 · see citing works

Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors

Finnin, M. S., Donigian, J. R., Cohen, A., Richon, V. M., Rifkind, R. A., Marks, P. A., Breslow, R., & Pavletich, N. P. (1999) · Nature · doi:10.1038/43710 · Cited by 1,714 · see citing works

Acetylation and deacetylation of non-histone proteins

Glozak, M. A., Sengupta, N., Zhang, X., & Seto, E. (2005) · Gene · doi:10.1016/j.gene.2005.09.010 · Cited by 1,584 · see citing works

Histone deacetylase inhibitors: molecular mechanisms of action

Xu, W. S., Parmigiani, R. B., & Marks, P. A. (2007) · Oncogene · doi:10.1038/sj.onc.1210620 · Cited by 1,542 · see citing works

Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis

Gregoretti, I., Lee, Y.-M., & Goodson, H. V. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.02.006 · Cited by 1,456 · see citing works

FDA Approval Summary: Vorinostat for Treatment of Advanced Primary Cutaneous T-Cell Lymphoma

Mann, B. S., Johnson, J. R., Cohen, M. H., Justice, R., & Pazdur, R. (2007) · The Oncologist · doi:10.1634/theoncologist.12-10-1247 · Cited by 1,365 · see citing works

Dimethyl sulfoxide to vorinostat: development of this histone deacetylase inhibitor as an anticancer drug

Marks, P. A., & Breslow, R. (2007) · Nature Biotechnology · doi:10.1038/nbt1272 · Cited by 1,198 · see citing works

Histone deacetylases and cancer

Glozak, M. A., & Seto, E. (2007) · Oncogene · doi:10.1038/sj.onc.1210610 · Cited by 1,031 · see citing works

The biochemistry of sirtuins

Sauve, A. A., Wolberger, C., Schramm, V. L., & Boeke, J. D. (2006) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.74.082803.133500 · Cited by 763 · see citing works

Untitled work

(2002) · PubMed · Cited by 732 · see citing works

Therapeutic application of histone deacetylase inhibitors for central nervous system disorders

Kazantsev, A. G., & Thompson, L. M. (2008) · Nature Reviews Drug Discovery · doi:10.1038/nrd2681 · Cited by 715 · see citing works

Structural Snapshots of Human HDAC8 Provide Insights into the Class I Histone Deacetylases

Somoza, J. R., Skene, R. J., Katz, B. A., Mol, C., Ho, J. D., Jennings, A. J., Luong, C., Arvai, A., Buggy, J. J., Chi, E., et al. (2004) · Structure · doi:10.1016/j.str.2004.04.012 · Cited by 710 · see citing works

Structural basis of the action of thermolysin and related zinc peptidases

Matthews, B. W. (1988) · Accounts of Chemical Research · doi:10.1021/ar00153a003 · Cited by 687 · see citing works

Crystal structure of a eukaryotic zinc-dependent histone deacetylase, human HDAC8, complexed with a hydroxamic acid inhibitor

Vannini, A., Volpari, C., Filocamo, G., Casavola, E. C., Brunetti, M., Renzoni, D., Chakravarty, P., Paolini, C., De Francesco, R., Gallinari, P., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404603101 · Cited by 638 · see citing works

Carboxypeptidase A

Christianson, D. W., & Lipscomb, W. N. (1989) · Accounts of Chemical Research · doi:10.1021/ar00158a003 · Cited by 606 · see citing works

FDA Approval: Belinostat for the Treatment of Patients with Relapsed or Refractory Peripheral T-cell Lymphoma

Lee, H.-Z., Kwitkowski, V. E., Valle, P. L. D., Ricci, M., Saber, H., Habtemariam, B. A., Bullock, J. M., Bloomquist, E. W., Shen, Y. L., Chen, X.-H., et al. (2015) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-14-3119 · Cited by 365 · see citing works

Lysine acetylation and the bromodomain: a new partnership for signaling

Yang, X. (2004) · BioEssays · doi:10.1002/bies.20104 · Cited by 359 · see citing works

Vorinostat: a new oral histone deacetylase inhibitor approved for cutaneous T-cell lymphoma

Duvic, M., & Vu, J. (2007) · Expert Opinion on Investigational Drugs · doi:10.1517/13543784.16.7.1111 · Cited by 345 · see citing works

Pharmacodynamic response and inhibition of growth of human tumor xenografts by the novel histone deacetylase inhibitor PXD101.

Plumb, J. A., Finn, P. W., Williams, R. J., Bandara, M. J., Romero, M., Watkins, C. J., Thangue, N. B. L., & Brown, R. E. (2003) · PubMed · Cited by 312 · see citing works

HDAC inhibitor‐based therapies: Can we interpret the code?

New, M. I., Olzscha, H., & Thangue, N. B. L. (2012) · Molecular Oncology · doi:10.1016/j.molonc.2012.09.003 · Cited by 310 · see citing works

Structure, mechanism, and inhibition of histone deacetylases and related metalloenzymes

Lombardi, P. M., Cole, K., Dowling, D., & Christianson, D. W. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.08.004 · Cited by 279 · see citing works

Human HDAC7 Harbors a Class IIa Histone Deacetylase-specific Zinc Binding Motif and Cryptic Deacetylase Activity

Schuetz, A., Min, J., Allali‐Hassani, A., Schapira, M., Shuen, M., Loppnau, P., Mazitschek, R., Kwiatkowski, N. P., Lewis, T. A., Maglathin, R. L., et al. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m707362200 · Cited by 261 · see citing works

Panobinostat for the Treatment of Multiple Myeloma

Laubach, J. P., Moreau, P., Miguel, J. F. S., & Richardson, P. G. G. (2015) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-0530 · Cited by 260 · see citing works

Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8–substrate complex

Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfí, A., De Francesco, R., Steinkühler, C., & Di Marco, S. (2007) · The EMBO Reports · doi:10.1038/sj.embor.7401047 · Cited by 256 · see citing works

Noncomplexing Tertiary Amines as “Better” Buffers Covering the Range of pH 3−11. Temperature Dependence of Their Acid Dissociation Constants

Kandegedara, A., & Rorabacher, D. B. (1999) · Analytical Chemistry · doi:10.1021/ac9902594 · Cited by 240 · see citing works

Epigenetic targeting of histone deacetylase: Therapeutic potential in Parkinson's disease?

Harrison, I. F., & Dexter, D. T. (2013) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2013.05.010 · Cited by 227 · see citing works

Structural Studies of Human Histone Deacetylase 8 and Its Site-Specific Variants Complexed with Substrate and Inhibitors^,

Dowling, D. P., Gantt, S. L., Gattis, S. G., Fierke, C. A., & Christianson, D. W. (2008) · Biochemistry · doi:10.1021/bi801610c · Cited by 200 · see citing works

Zinc hydrolases: the mechanisms of zinc-dependent deacetylases

Hernick, M., & Fierke, C. A. (2004) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2004.08.006 · Cited by 178 · see citing works

On the importance of orientation in general base catalysis by carboxylate

Gandour, R. D. (1981) · Bioorganic Chemistry · doi:10.1016/0045-2068(81)90020-1 · Cited by 173 · see citing works

Crystal structure of LpxC, a zinc-dependent deacetylase essential for endotoxin biosynthesis

Whittington, D. A., Rusche, K. M., Shin, H., Fierke, C. A., & Christianson, D. W. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1432990100 · Cited by 167 · see citing works

Carboxylate-histidine-zinc interactions in protein structure and function

Christianson, D. W., & Alexander, R. (1989) · Journal of the American Chemical Society · doi:10.1021/ja00198a065 · Cited by 165 · see citing works

Crystal Structure of a Bacterial Class 2 Histone Deacetylase Homologue

Nielsen, T. K., Hildmann, C., Dickmanns, A., Schwienhorst, A., & Ficner, R. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.09.065 · Cited by 157 · see citing works

Structural Basis of the Antiproliferative Activity of Largazole, a Depsipeptide Inhibitor of the Histone Deacetylases

Cole, K. E., Dowling, D. P., Boone, M. A., Phillips, A. J., & Christianson, D. W. (2011) · Journal of the American Chemical Society · doi:10.1021/ja205972n · Cited by 153 · see citing works

Catalytic Activity and Inhibition of Human Histone Deacetylase 8 Is Dependent on the Identity of the Active Site Metal Ion

Gantt, S. L., Gattis, S. G., & Fierke, C. A. (2006) · Biochemistry · doi:10.1021/bi060212u · Cited by 151 · see citing works

A Proton-Shuttle Reaction Mechanism for Histone Deacetylase 8 and the Catalytic Role of Metal Ions

Wu, R., Wang, S., Zhou, N., Cao, Z., & Zhang, Y. (2010) · Journal of the American Chemical Society · doi:10.1021/ja103932d · Cited by 135 · see citing works

Structure and activity of enzymes that remove histone modifications

Holbert, M. A., & Marmorstein, R. (2005) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2005.10.006 · Cited by 122 · see citing works

Unexpected Deacetylation Mechanism Suggested by a Density Functional Theory QM/MM Study of Histone-Deacetylase-Like Protein

Corminbœuf, C., Hu, P., Tuckerman, M. E., & Zhang, Y. (2006) · Journal of the American Chemical Society · doi:10.1021/ja0600882 · Cited by 108 · see citing works

The pKa values of two histidine residues in human haemoglobin, the Bohr effect, and the dipole moments of α-helices

Perutz, M. F., Gronenborn, A. M., Clore, G. M., Fogg, J. H., & Shih, D. (1985) · Journal of Molecular Biology · doi:10.1016/0022-2836(85)90016-6 · Cited by 103 · see citing works

Probing the elusive catalytic activity of vertebrate class IIa histone deacetylases

JONES, P. G., Altamura, S., Francesco, R. D., Gallinari, P., Lahm, A., Neddermann, P., Rowley, M., Serafini, S., & Steinkühler, C. (2008) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2008.02.025 · Cited by 100 · see citing works

Metabolic reprogramming by class I and II histone deacetylases

Mihaylova, M. M., & Shaw, R. J. (2012) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2012.09.003 · Cited by 95 · see citing works

Kinetics and Comparative Reactivity of Human Class I and Class IIb Histone Deacetylases

Schultz, B. E., Misialek, S., Wu, J., Tang, J., Conn, M. T., Tahilramani, R., & Wong, L. (2004) · Biochemistry · doi:10.1021/bi0494471 · Cited by 88 · see citing works

Activation and Inhibition of Histone Deacetylase 8 by Monovalent Cations

Gantt, S. L., Joseph, C. G., & Fierke, C. A. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.033399 · Cited by 87 · see citing works

Structures of Metal-Substituted Human Histone Deacetylase 8 Provide Mechanistic Inferences on Biological Function,

Dowling, D., Gattis, S. G., Fierke, C. A., & Christianson, D. W. (2010) · Biochemistry · doi:10.1021/bi1005046 · Cited by 81 · see citing works

Substrate and inhibitor specificity of class 1 and class 2 histone deacetylases

Hildmann, C., Wegener, D., Riester, D., Hempel, R., Schober, A., Merana, J., Giurato, L., Guccione, S., Nielsen, T. K., Ficner, R., et al. (2006) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2006.01.030 · Cited by 78 · see citing works

Members of the histone deacetylase superfamily differ in substrate specificity towards small synthetic substrates

Riester, D., Wegener, D., Hildmann, C., & Schwienhorst, A. (2004) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2004.09.155 · Cited by 68 · see citing works

Compromised Structure and Function of HDAC8 Mutants Identified in Cornelia de Lange Syndrome Spectrum Disorders

Decroos, C., Bowman, C. M., Moser, J. S., Christianson, K. E., Deardorff, M. A., & Christianson, D. W. (2014) · ACS Chemical Biology · doi:10.1021/cb5003762 · Cited by 67 · see citing works

UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine Deacetylase Functions through a General Acid-Base Catalyst Pair Mechanism

Hernick, M., Gennadios, H. A., Whittington, D. A., Rusche, K. M., Christianson, D. W., & Fierke, C. A. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m413560200 · Cited by 66 · see citing works

Inhibition and Mechanism of HDAC8 Revisited

Chen, K., Zhang, X., Wu, Y., & Wiest, O. (2014) · Journal of the American Chemical Society · doi:10.1021/ja501548p · Cited by 61 · see citing works

Variable Active Site Loop Conformations Accommodate the Binding of Macrocyclic Largazole Analogues to HDAC8

Decroos, C., Clausen, D. J., Haines, B. E., Wiest, O., Williams, R. M., & Christianson, D. W. (2015) · Biochemistry · doi:10.1021/acs.biochem.5b00010 · Cited by 58 · see citing works

Binding to thermolysin of phenolate-containing inhibitors necessitates a revised mechanism of catalysis

Mock, W. L., & Aksamawati, M. (1994) · Biochemical Journal · doi:10.1042/bj3020057 · Cited by 56 · see citing works

Assignment of proton NMR resonances of histidine and other aromatic residues in met-, cyano-, oxy-, and (carbon monoxy)myoglobins

Carver, J. A., & Bradbury, J. (1984) · Biochemistry · doi:10.1021/bi00316a012 · Cited by 43 · see citing works

Pyrrole Hydrogen Ionization of Imidazole Derivatives in Metal Ion Complexes and Carbonic Anhydrase

Martin, R. B. (1974) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.71.11.4346 · Cited by 36 · see citing works

Differences in transition state stabilization between thermolysin (EC 3.4.24.27) and neprilysin (EC 3.4.24.11)

Cynthia Marie-claire, A., Ruffet, E., Tiraboschi, G., et al. (1998) · FEBS Letters · doi:10.1016/s0014-5793(98)01267-8 · Cited by 34 · see citing works

Catalytic Mechanism and Molecular Recognition ofE.coliUDP-3-O-(R-3-Hydroxymyristoyl)-N-acetylglucosamine Deacetylase Probed by Mutagenesis

Hernick, M., & Fierke, C. A. (2006) · Biochemistry · doi:10.1021/bi061405k · Cited by 31 · see citing works

Stereoelectronic effects at carboxylate: a syn-oriented model for the histidine-aspartate couple in enzymes

Zimmerman, S. C., & Cramer, K. D. (1988) · Journal of the American Chemical Society · doi:10.1021/ja00225a056 · Cited by 31 · see citing works

Conformational differences between various myoglobin ligated states as monitored by proton NMR spectroscopy

Bradbury, J., & Carver, J. A. (1984) · Biochemistry · doi:10.1021/bi00316a013 · Cited by 17 · see citing works

Clinical development of histone deacetylase inhibitor romidepsin.

Guan, P. F., & Fang, H. (2010) · PubMed · Cited by 14 · see citing works

Histone deacetylase 6 structure and molecular basis of catalysis and inhibition

Hai, Y., & Christianson, D. W. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2134 · Cited by 521 · see citing works

Histone deacetylase 11 is a fatty-acid deacylase

Kutil, Z., Novakova, Z., Meleshin, M., Mikesova, J., Schutkowski, M., & Barinka, C. (2018) · ACS Chemical Biology · doi:10.1021/acschembio.7b00942 · Cited by 174 · see citing works

Structure, mechanism, and inhibition of the zinc-dependent histone deacetylases

Porter, N. J., & Christianson, D. W. (2019) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2019.01.004 · Cited by 146 · see citing works

Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants

Marek, M., Shaik, T. B., Heimburg, T., Chakrabarti, A., Lancelot, J., Ramos-Morales, E., Da Veiga, C., Kalinin, D., Melesina, J., Robaa, D., et al. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b01087 · Cited by 123 · see citing works

Innovative Strategies for Selective Inhibition of Histone Deacetylases

Maolanon, A. R., Madsen, A. S., & Olsen, C. A. (2016) · Cell Chemical Biology · doi:10.1016/j.chembiol.2016.06.011 · Cited by 72 · see citing works

Class I HDAC Inhibitors: Potential New Epigenetic Therapeutics for Alcohol Use Disorder (AUD)

Bourguet, E., Ozdarska, K., Moroy, G., Jeanblanc, J., & Naassila, M. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b00115 · Cited by 36 · see citing works

Identification of histidine residues at the active site of Megalobatrachus japonicus alkaline phosphatase by chemical modification

Ding, S., Li, Y., & Zhu, L. (2002) · Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology · doi:10.1016/s0167-4838(01)00288-6 · Cited by 9 · see citing works

Implication of histidine at the active site of hemerythrin

Fan, C., & York, J. L. (1969) · Biochemical and Biophysical Research Communications · doi:10.1016/0006-291x(69)90573-7 · Cited by 21 · see citing works

Design, Synthesis, and Biological Evaluation of New Urushiol Derivatives as Potent Class I Histone Deacetylase Inhibitors

Zhou, H., Qi, Z., Liu, D., Xue, X., & Wang, C. (2023) · ChemBioChem · doi:10.1002/cbic.202300238 · Cited by 2 · see citing works

Reassignment of the active site histidines in ribonuclease A by selective deuteration studies

Patel, D. J., Canuel, L. L., & BOVEY, F. A. (1975) · Biopolymers · doi:10.1002/bip.1975.360140508 · Cited by 55 · see citing works

Inhibitors of Human Histone Deacetylase: Synthesis and Enzyme Assay of Hydroxamates with Piperazine Linker

Chakrabarty, S., Jasmine, J., Bhadaliya, C., Sinha, B. N., Mahesh, A., Bai, H., Blond, S. Y., & Jayaprakash, V. (2010) · Archiv der Pharmazie · doi:10.1002/ardp.200900117 · Cited by 7 · see citing works