How the “Marriage” between SET and MYND Domains Made SMYD Proteins So Special

A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (31 July 2022) | Viewed by 2539

Special Issue Editor

Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
Interests: SMYD proteins; structure and function relationships; data science
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

SMYD proteins are a special class of protein lysine methyltransferases with an MYND domain inserted into a SET domain. Structurally, these two functional domains are intimately bundled, with a conserved architecture, being integrated into a single coherent module in SMYD proteins. The evolutionary history of SMYD proteins dates back to more than 1 billion years ago at the beginning of multicellular life. They were found in the plant Arabidopsis thaliana, the yeast Saccharomyces cerevisiae, and Filastera, one of the closest unicellular relatives to animals. However, the nature of the selective pressure that has driven the “marriage” of the SET and MYND domains, and what specific function evolved at the time of this marriage remain unclear. From the time when SMYD1, the founding member of the SMYD protein family, was identified as being required for cardiomyocyte differentiation, our understanding of SMYD protein structure and function has been steadily increasing. We now know that not only are they involved in heart and skeletal muscle development, but they also play diverse other roles in both normal biology and disease states, ranging from tumor cell proliferation, cancer stemness and dormancy, and the immune response, to a very recent association with ciliogenesis via regulating microtubule dynamics.

While the scope of SMYD protein research has been broadened significantly over the past two decades, it is becoming increasingly clear to us that, the more we learn about the multifunctionality and multispecificity of the proteins, the more we realize that there are more yet to be discovered. With the thriving of functional genomics studies, new research ideas are emerging in uncharted areas, including but not limited to mitochondrial and nucleolar ribosome biogenesis, RNA biology in stress granules, intellectual disability, calcium-dependent signaling, and sperm chromatin remodeling at fertilization. The goal of this Special Issue is to promote new paradigms in SMYD protein research while further broadening our understanding of their functional diversity. As our knowledge develops and advances, we want to conclude that the marriage between the SET and MYND domains that made SMYD proteins so special is an ultimate rule governing their past, present and future.

Dr. Zhe Yang
Guest Editor

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Keywords

  • Chromatin remodeling and histone modifications
  • Immunity and inflammatory response
  • Intracellular trafficking and endocytosis
  • RNA processing and ribosome biogenesis
  • Structure and function relationships
  • Heart and skeletal muscle development and cardiovascular disease
  • Neurodegenerative disease and intellectual disability
  • Stress response and cellular signaling
  • Cell cycle regulation and telomere maintenance
  • Tumor growth and metastasis

Published Papers (1 paper)

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Research

24 pages, 13397 KiB  
Article
Unique SMYD5 Structure Revealed by AlphaFold Correlates with Its Functional Divergence
by Yingxue Zhang, Eid Alshammari, Jacob Sobota, Alexander Yang, Chunying Li and Zhe Yang
Biomolecules 2022, 12(6), 783; https://0-doi-org.brum.beds.ac.uk/10.3390/biom12060783 - 03 Jun 2022
Cited by 6 | Viewed by 2098
Abstract
SMYD5 belongs to a special class of protein lysine methyltransferases with an MYND (Myeloid-Nervy-DEAF1) domain inserted into a SET (Suppressor of variegation, Enhancer of Zeste, Trithorax) domain. Despite recent advances in its functional characterization, the lack of the crystal structure has hindered our [...] Read more.
SMYD5 belongs to a special class of protein lysine methyltransferases with an MYND (Myeloid-Nervy-DEAF1) domain inserted into a SET (Suppressor of variegation, Enhancer of Zeste, Trithorax) domain. Despite recent advances in its functional characterization, the lack of the crystal structure has hindered our understanding of the structure-and-function relationships of this most unique member of the SMYD protein family. Here, we demonstrate the reliability of using AlphaFold structures for understanding the structure and function of SMYD5 by comparing the AlphaFold structures to the known crystal structures of SMYD proteins, using an inter-residue distance maps-based metric. We found that the AlphaFold confidence scores are inversely associated with the refined B-factors and can serve as a structural indicator of conformational flexibility. We also found that the N-terminal sequence of SMYD5, predicted to be a mitochondrial targeting signal, contains a novel non-classical nuclear localization signal. This sequence is structurally flexible and does not have a well-defined conformation, which might facilitate its recognition for SMYD5’s cytonuclear transport. The structure of SMYD5 is unique in many aspects. The “crab”-like structure with a large negatively charged cleft provides a potential binding site for basic molecules such as protamines. The less positively charged MYND domain is associated with the undetectable DNA-binding ability. The most surprising feature is an incomplete target lysine access channel that lacks the evolutionarily conserved tri-aromatic arrangement, being associated with the low H3/H4 catalytic activity. This study expands our understanding of the SMYD protein family from a classical two-lobed structure to a structure of its own kind, being as a fundamental determinant of its functional divergence. Full article
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