Abstract
Lysine methylation of cellular proteins is catalyzed by dozens of lysine methyltransferases (KMTs), occurs in thousands of different histone and nonhistone proteins, and regulates diverse biological processes. Dysregulation of KMT-mediated lysine methylations underlies many human diseases. A key unanswered question is how proteins, nonhistone proteins in particular, are specifically methylated by each KMT. Here, using several biochemical approaches, including analytical gel filtration chromatography, isothermal titration calorimetry, and in vitro methylation assays, we discovered that SET domain-containing 7 histone lysine methyltransferase (SETD7), a KMT capable of methylating both histone and nonhistone proteins, uses its N-terminal membrane occupation and recognition nexus (MORN) repeats to dock its substrates and subsequently juxtapose their Lys methylation motif for efficient and specific methylation by the catalytic SET domain. Such docking site-mediated methylation mechanism rationalizes binding and methylation of previously known substrates and predicts new SETD7 substrates. Our findings further suggest that other KMTs may also use docking-mediated substrate recognition mechanisms to achieve their catalytic specificity and efficiency.
Highlights
Lysine methylation of cellular proteins is catalyzed by dozens of lysine methyltransferases (KMTs), occurs in thousands of different histone and nonhistone proteins, and regulates diverse biological processes
Using several biochemical approaches, including analytical gel filtration chromatography, isothermal titration calorimetry, and in vitro methylation assays, we discovered that SET domain– containing 7 histone lysine methyltransferase (SETD7), a KMT capable of methylating both histone and nonhistone proteins, uses its N-terminal membrane occupation and recognition nexus (MORN) repeats to dock its substrates and subsequently juxtapose their Lys methylation motif for efficient and specific methylation by the catalytic SET domain
We recently discovered that the MORN repeats of MORN4 can bind to a segment in the tail cargo– binding domain of unconventional Myo3a [37], providing a direct clue suggesting that MORN repeats can be a protein– protein interaction module
Summary
SETD7 interacts with the DNA-binding domain of PDX1 through charge– charge interaction. For histone H3, we hypothesized that the highly positively charged sequence C-terminal to the Lys-4 methylation site can bind to the SETD7_MORN and serve to dock the histone protein to the full-length SETD7 for specific and efficient Lys-4 methylation (Fig. 2A). Our above studies on histone H3 and the TAF10-PDX1 chimera point to a possibility that an optimal substrate for SETD7 should contain a MORN repeat– binding docking sequence and a SET domain recognition methylation site (Fig. 4A). A specific DNA sequence can inhibit methylation of a transcription factor with a docking site, but not a peptide containing only a methylation site (Fig. S5, B and C), further demonstrating the critical role of the MORN repeat–mediated docking interaction in substrate methylation by SETD7
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