Unique SMYD5 Structure Revealed by AlphaFold Correlates with Its Functional Divergence

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 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.

Temporal and spatial assembly of inner ear hair cell ankle link condensate through phase separation

“…The prediction was obtained using the monomeric model of AlphaFold in default parameters. The predicted complex structure with the highest pLDDT value (87.86) was trusted with the highest confidence level and adopted for subsequent analyses 39 . And it was superimposed with the resolved complex structure of Cad23 NBM/Harmonin NTD (PDB ID: 2KBR ) for validation.…”

SMYD5 is a regulator of the mild hypothermia response

“…A caveat of our study is that our results are not fully transferable to neonatal hypoxic-ischemic brain injury as neuroprotection in that setting is achieved at 33.5°C and getting as low as 32°C is not recommended 10 . Another limitation of our study is that SMYD5 doesn´t have any known intrinsic DNA binding ability 45 , thus there must be another factor that recruits SMYD5 to the right sites. This could be addressed in future studies by exploring protein interactors of SMYD5 or with a more focused CRISPR-Cas9 library screening using a library only containing known transcriptional regulators.…”

Targeting Epigenetic Changes Mediated by Members of the SMYD Family of Lysine Methyltransferases

“…X-ray crystallographic studies have been carried out for SMYD1 [ 29 , 63 ], SMYD2 [ 29 , 45 , 64 , 65 , 66 , 67 ], and SMYD3 [ 29 , 31 , 68 , 69 ]. At this time, no structural studies have been reported for SMYD4, but some work is underway for SMYD5 [ 70 ].…”