1
|
Jiang Y, Trescott L, Holcomb J, Zhang X, Brunzelle J, Sirinupong N, Shi X, Yang Z. Structural insights into estrogen receptor α methylation by histone methyltransferase SMYD2, a cellular event implicated in estrogen signaling regulation. J Mol Biol 2014; 426:3413-25. [PMID: 24594358 DOI: 10.1016/j.jmb.2014.02.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 02/20/2014] [Accepted: 02/23/2014] [Indexed: 12/13/2022]
Abstract
Estrogen receptor (ER) signaling plays a pivotal role in many developmental processes and has been implicated in numerous diseases including cancers. We recently showed that direct ERα methylation by the multi-specificity histone lysine methyltransferase SMYD2 regulates estrogen signaling through repressing ERα-dependent transactivation. However, the mechanism controlling the specificity of the SMYD2-ERα interaction and the structural basis of SMYD2 substrate binding diversity are unknown. Here we present the crystal structure of SMYD2 in complex with a target lysine (Lys266)-containing ERα peptide. The structure reveals that ERα binds SMYD2 in a U-shaped conformation with the binding specificity determined mainly by residues C-terminal to the target lysine. The structure also reveals numerous intrapeptide contacts that ensure shape complementarity between the substrate and the active site of the enzyme, thereby likely serving as an additional structural determinant of substrate specificity. In addition, comparison of the SMYD2-ERα and SMYD2-p53 structures provides the first structural insight into the diverse nature of SMYD2 substrate recognition and suggests that the broad specificity of SMYD2 is achieved by multiple molecular mechanisms such as distinct peptide binding modes and the intrinsic dynamics of peptide ligands. Strikingly, a novel potentially SMYD2-specific polyethylene glycol binding site is identified in the CTD domain, implicating possible functions in extended substrate binding or protein-protein interactions. Our study thus provides the structural basis for the SMYD2-mediated ERα methylation, and the resulting knowledge of SMYD2 substrate specificity and target binding diversity could have important implications in selective drug design against a wide range of ERα-related diseases.
Collapse
Affiliation(s)
- Yuanyuan Jiang
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Laura Trescott
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Joshua Holcomb
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Xi Zhang
- Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joseph Brunzelle
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Nualpun Sirinupong
- Nutraceuticals and Functional Food Research and Development Center, Faculty of Agro-Industry, Prince of Songkla University, Hat-Yai, Songkhla 90112, Thailand
| | - Xiaobing Shi
- Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhe Yang
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| |
Collapse
|
2
|
Ragain CM, Newberry RW, Ritchie AW, Webb LJ. Role of Electrostatics in Differential Binding of RalGDS to Rap Mutations E30D and K31E Investigated by Vibrational Spectroscopy of Thiocyanate Probes. J Phys Chem B 2012; 116:9326-36. [DOI: 10.1021/jp303272y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Christina M. Ragain
- Department of Chemistry
and Biochemistry, Center for Nano- and Molecular Science
and Technology and Institute
for Cell and Molecular Biology, The University of Texas at Austin, 1 University Station, A5300, Austin, Texas
78712, United States
| | - Robert W. Newberry
- Department of Chemistry
and Biochemistry, Center for Nano- and Molecular Science
and Technology and Institute
for Cell and Molecular Biology, The University of Texas at Austin, 1 University Station, A5300, Austin, Texas
78712, United States
| | - Andrew W. Ritchie
- Department of Chemistry
and Biochemistry, Center for Nano- and Molecular Science
and Technology and Institute
for Cell and Molecular Biology, The University of Texas at Austin, 1 University Station, A5300, Austin, Texas
78712, United States
| | - Lauren J. Webb
- Department of Chemistry
and Biochemistry, Center for Nano- and Molecular Science
and Technology and Institute
for Cell and Molecular Biology, The University of Texas at Austin, 1 University Station, A5300, Austin, Texas
78712, United States
| |
Collapse
|
3
|
Lees JPB, Manlandro CM, Picton LK, Tan AZE, Casares S, Flanagan JM, Fleming KG, Hill RB. A designed point mutant in Fis1 disrupts dimerization and mitochondrial fission. J Mol Biol 2012; 423:143-58. [PMID: 22789569 DOI: 10.1016/j.jmb.2012.06.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 06/21/2012] [Accepted: 06/24/2012] [Indexed: 01/06/2023]
Abstract
Mitochondrial and peroxisomal fission are essential processes with defects resulting in cardiomyopathy and neonatal lethality. Central to organelle fission is Fis1, a monomeric tetratricopeptide repeat (TPR)-like protein whose role in assembly of the fission machinery remains obscure. Two nonfunctional, Saccharomyces cerevisiae Fis1 mutants (L80P or E78D/I85T/Y88H) were previously identified in genetic screens. Here, we find that these two variants in the cytosolic domain of Fis1 (Fis1ΔTM) are unexpectedly dimeric. A truncation variant of Fis1ΔTM that lacks an N-terminal regulatory domain is also found to be dimeric. The ability to dimerize is a property innate to the native Fis1ΔTM amino acid sequence as we find this domain is dimeric after transient exposure to elevated temperature or chemical denaturants and is kinetically trapped at room temperature. This is the first demonstration of a specific self-association in solution for the Fis1 cytoplasmic domain. We propose a three-dimensional domain-swapped model for dimerization that is validated by a designed mutation, A72P, which potently disrupts dimerization of wild-type Fis1. A72P also disrupts dimerization of nonfunctional variants, indicating a common structural basis for dimerization. The obligate monomer variant A72P, like the dimer-promoting variants, is nonfunctional in fission, consistent with a model in which Fis1 activity depends on its ability to interconvert between monomer and dimer species. These studies suggest a new functionally important manner in which TPR-containing proteins may reversibly self-associate.
Collapse
Affiliation(s)
- Jonathan P B Lees
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | | | | | | | | | | | | |
Collapse
|
4
|
Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T. The SWISS-MODEL Repository and associated resources. Nucleic Acids Res 2009; 37:D387-92. [PMID: 18931379 PMCID: PMC2686475 DOI: 10.1093/nar/gkn750] [Citation(s) in RCA: 1550] [Impact Index Per Article: 103.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 10/05/2008] [Indexed: 12/12/2022] Open
Abstract
SWISS-MODEL Repository (http://swissmodel.expasy.org/repository/) is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline. The aim of the SWISS-MODEL Repository is to provide access to an up-to-date collection of annotated 3D protein models generated by automated homology modelling for all sequences in Swiss-Prot and for relevant models organisms. Regular updates ensure that target coverage is complete, that models are built using the most recent sequence and template structure databases, and that improvements in the underlying modelling pipeline are fully utilised. As of September 2008, the database contains 3.4 million entries for 2.7 million different protein sequences from the UniProt database. SWISS-MODEL Repository allows the users to assess the quality of the models in the database, search for alternative template structures, and to build models interactively via SWISS-MODEL Workspace (http://swissmodel.expasy.org/workspace/). Annotation of models with functional information and cross-linking with other databases such as the Protein Model Portal (http://www.proteinmodelportal.org) of the PSI Structural Genomics Knowledge Base facilitates the navigation between protein sequence and structure resources.
Collapse
Affiliation(s)
- Florian Kiefer
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Konstantin Arnold
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Michael Künzli
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Lorenza Bordoli
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| |
Collapse
|