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Unique SMYD5 Structure Revealed by AlphaFold Correlates with Its Functional Divergence.

Yingxue Zhang1, Eid Alshammari1, Jacob Sobota1

  • 1Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA.

Biomolecules
|June 24, 2022
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Summary

SMYD5 protein structure was predicted using AlphaFold, revealing unique features like a nuclear localization signal and an incomplete catalytic channel, explaining its distinct functions within the SMYD family.

Keywords:
AlphaFoldSET and MYND domain-containing proteinSMYD5nuclear localization signalstructure-and-function relationshipssubcellular localization

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Background:

  • SMYD5 is a unique protein lysine methyltransferase featuring an MYND domain within its SET domain.
  • Understanding SMYD5's structure-function relationship is crucial but limited by the absence of crystal structures.
  • Previous studies have advanced functional characterization but lacked detailed structural insights.

Purpose of the Study:

  • To validate AlphaFold structures for studying SMYD5's structure and function.
  • To investigate the structural basis for SMYD5's unique biochemical properties and cellular localization.
  • To expand the understanding of the SMYD protein family's structural diversity.

Main Methods:

  • Comparative analysis of AlphaFold-predicted SMYD5 structures against known SMYD protein crystal structures using inter-residue distance maps.
  • Evaluation of AlphaFold confidence scores as indicators of conformational flexibility by correlating them with B-factors.
  • Bioinformatic analysis to identify potential targeting signals and functional domains within the SMYD5 structure.

Main Results:

  • AlphaFold structures reliably represent SMYD protein structures, with confidence scores correlating with conformational flexibility.
  • SMYD5 possesses a novel non-classical nuclear localization signal within its N-terminal sequence, which is conformationally flexible.
  • The predicted SMYD5 structure exhibits a unique "crab"-like shape, a less charged MYND domain, and an incomplete catalytic channel, correlating with low H3/H4 methyltransferase activity.

Conclusions:

  • AlphaFold is a reliable tool for elucidating the structure and function of proteins lacking experimental structures, like SMYD5.
  • SMYD5's unique structural features, including its N-terminal signal and incomplete active site, dictate its distinct biological roles and low catalytic efficiency.
  • This study provides a structural foundation for understanding SMYD5's functional divergence within the broader SMYD protein family.