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Decroos C, Bowman CM, Moser JAS, Christianson KE, Deardorff MA, Christianson DW. Compromised structure and function of HDAC8 mutants identified in Cornelia de Lange Syndrome spectrum disorders. ACS Chem Biol 2014; 9:2157-64. [PMID: 25075551 PMCID: PMC4168803 DOI: 10.1021/cb5003762] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
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Cornelia
de Lange Syndrome (CdLS) is a multiple congenital anomaly
disorder resulting from mutations in genes that encode the core components
of the cohesin complex, SMC1A, SMC3, and RAD21, or two of its regulatory
proteins, NIPBL and HDAC8. HDAC8 is the human SMC3 lysine deacetylase
required for cohesin recycling in the cell cycle. To date, 16 different
missense mutations in HDAC8 have recently been identified in children
diagnosed with CdLS. To understand the molecular effects of these
mutations in causing CdLS and overlapping phenotypes, we have fully
characterized the structure and function of five HDAC8 mutants: C153F,
A188T, I243N, T311M, and H334R. X-ray crystal structures reveal that
each mutation causes local structural changes that compromise catalysis
and/or thermostability. For example, the C153F mutation triggers conformational
changes that block acetate product release channels, resulting in
only 2% residual catalytic activity. In contrast, the H334R mutation
causes structural changes in a polypeptide loop distant from the active
site and results in 91% residual activity, but the thermostability
of this mutant is significantly compromised. Strikingly, the catalytic
activity of these mutants can be partially or fully rescued in vitro by the HDAC8 activator N-(phenylcarbamothioyl)benzamide.
These results suggest that HDAC8 activators might be useful leads
in the search for new therapeutic strategies in managing CdLS.
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Affiliation(s)
- Christophe Decroos
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323 United States
| | - Christine M. Bowman
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323 United States
| | - Joe-Ann S. Moser
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323 United States
| | - Karen E. Christianson
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323 United States
| | - Matthew A. Deardorff
- Division
of Human Genetics and Molecular Biology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 United States
- Department
of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104 United States
| | - David W. Christianson
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323 United States
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Kaiser FJ, Ansari M, Braunholz D, Concepción Gil-Rodríguez M, Decroos C, Wilde JJ, Fincher CT, Kaur M, Bando M, Amor DJ, Atwal PS, Bahlo M, Bowman CM, Bradley JJ, Brunner HG, Clark D, Del Campo M, Di Donato N, Diakumis P, Dubbs H, Dyment DA, Eckhold J, Ernst S, Ferreira JC, Francey LJ, Gehlken U, Guillén-Navarro E, Gyftodimou Y, Hall BD, Hennekam R, Hudgins L, Hullings M, Hunter JM, Yntema H, Innes AM, Kline AD, Krumina Z, Lee H, Leppig K, Lynch SA, Mallozzi MB, Mannini L, McKee S, Mehta SG, Micule I, Mohammed S, Moran E, Mortier GR, Moser JAS, Noon SE, Nozaki N, Nunes L, Pappas JG, Penney LS, Pérez-Aytés A, Petersen MB, Puisac B, Revencu N, Roeder E, Saitta S, Scheuerle AE, Schindeler KL, Siu VM, Stark Z, Strom SP, Thiese H, Vater I, Willems P, Williamson K, Wilson LC, Hakonarson H, Quintero-Rivera F, Wierzba J, Musio A, Gillessen-Kaesbach G, Ramos FJ, Jackson LG, Shirahige K, Pié J, Christianson DW, Krantz ID, Fitzpatrick DR, Deardorff MA. Loss-of-function HDAC8 mutations cause a phenotypic spectrum of Cornelia de Lange syndrome-like features, ocular hypertelorism, large fontanelle and X-linked inheritance. Hum Mol Genet 2014; 23:2888-900. [PMID: 24403048 DOI: 10.1093/hmg/ddu002] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a multisystem genetic disorder with distinct facies, growth failure, intellectual disability, distal limb anomalies, gastrointestinal and neurological disease. Mutations in NIPBL, encoding a cohesin regulatory protein, account for >80% of cases with typical facies. Mutations in the core cohesin complex proteins, encoded by the SMC1A, SMC3 and RAD21 genes, together account for ∼5% of subjects, often with atypical CdLS features. Recently, we identified mutations in the X-linked gene HDAC8 as the cause of a small number of CdLS cases. Here, we report a cohort of 38 individuals with an emerging spectrum of features caused by HDAC8 mutations. For several individuals, the diagnosis of CdLS was not considered prior to genomic testing. Most mutations identified are missense and de novo. Many cases are heterozygous females, each with marked skewing of X-inactivation in peripheral blood DNA. We also identified eight hemizygous males who are more severely affected. The craniofacial appearance caused by HDAC8 mutations overlaps that of typical CdLS but often displays delayed anterior fontanelle closure, ocular hypertelorism, hooding of the eyelids, a broader nose and dental anomalies, which may be useful discriminating features. HDAC8 encodes the lysine deacetylase for the cohesin subunit SMC3 and analysis of the functional consequences of the missense mutations indicates that all cause a loss of enzymatic function. These data demonstrate that loss-of-function mutations in HDAC8 cause a range of overlapping human developmental phenotypes, including a phenotypically distinct subgroup of CdLS.
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Affiliation(s)
- Frank J Kaiser
- Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Lübeck 23538, Germany
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Genshaft A, Moser JAS, D'Antonio EL, Bowman CM, Christianson DW. Energetically unfavorable amide conformations for N6-acetyllysine side chains in refined protein structures. Proteins 2013; 81:1051-7. [PMID: 23401043 DOI: 10.1002/prot.24262] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 01/14/2013] [Accepted: 01/21/2013] [Indexed: 11/07/2022]
Abstract
The reversible acetylation of lysine to form N6-acetyllysine in the regulation of protein function is a hallmark of epigenetics. Acetylation of the positively charged amino group of the lysine side chain generates a neutral N-alkylacetamide moiety that serves as a molecular "switch" for the modulation of protein function and protein-protein interactions. We now report the analysis of 381 N6-acetyllysine side chain amide conformations as found in 79 protein crystal structures and 11 protein NMR structures deposited in the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics. We find that only 74.3% of N6-acetyllysine residues in protein crystal structures and 46.5% in protein NMR structures contain amide groups with energetically preferred trans or generously trans conformations. Surprisingly, 17.6% of N6-acetyllysine residues in protein crystal structures and 5.3% in protein NMR structures contain amide groups with energetically unfavorable cis or generously cis conformations. Even more surprisingly, 8.1% of N6-acetyllysine residues in protein crystal structures and 48.2% in NMR structures contain amide groups with energetically prohibitive twisted conformations that approach the transition state structure for cis-trans isomerization. In contrast, 109 unique N-alkylacetamide groups contained in 84 highly accurate small molecule crystal structures retrieved from the Cambridge Structural Database exclusively adopt energetically preferred trans conformations. Therefore, we conclude that cis and twisted N6-acetyllysine amides in protein structures deposited in the PDB are erroneously modeled due to their energetically unfavorable or prohibitive conformations.
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Affiliation(s)
- Alexander Genshaft
- Department of Chemistry, Roy and Diana Vagelos Laboratories, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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