Methylation of histone H3 K79 by Dot1L is a hallmark of actively transcribed genes that depends on monoubiquitination of H2B K120 (H2B-Ub) and is an example of histone modification cross-talk that is conserved from yeast to humans. We report here cryo-EM structures of Dot1L bound to ubiquitinated nucleosome that show how H2B-Ub stimulates Dot1L activity and reveal a role for the histone H4 tail in positioning Dot1L. We find that contacts mediated by Dot1L and the H4 tail induce a conformational change in the globular core of histone H3 that reorients K79 from an inaccessible position, thus enabling this side chain to insert into the active site in a position primed for catalysis. Our study provides a comprehensive mechanism of cross-talk between histone ubiquitination and methylation and reveals structural plasticity in histones that makes it possible for histone-modifying enzymes to access residues within the nucleosome core.
The enzyme 3-hydroxy-3-methylglutaryl
coenzyme A (HMG-CoA) reductase
(HMGR), in most organisms, catalyzes the four-electron reduction of
the thioester (S)-HMG-CoA to the primary alcohol
(R)-mevalonate, utilizing NADPH as the hydride donor.
In some organisms, including the opportunistic lung pathogen Burkholderia cenocepacia, it catalyzes the reverse reaction,
utilizing NAD+ as a hydride acceptor in the oxidation of
mevalonate. B. cenocepacia HMGR has been previously
shown to exist as an ensemble of multiple non-additive oligomeric
states, each with different levels of enzymatic activity, suggesting
that the enzyme exhibits characteristics of the morpheein model of
allostery. We have characterized a number of factors, including pH,
substrate concentration, and enzyme concentration, that modulate the
structural transitions that influence the interconversion among the
multiple oligomers. We have also determined the crystal structure
of B. cenocepacia HMGR in the hexameric state bound
to coenzyme A and ADP. This hexameric assembly provides important
clues about how the transition among oligomers might occur, and why B. cenocepacia HMGR, unique among characterized HMGRs, exhibits
morpheein-like behavior.
Methylation of histone H3, lysine 79 (H3K79), by Dot1L is a hallmark of actively transcribed genes that depends on monoubiquitination of H2B at lysine 120 (H2B-Ub), and is a well-characterized example of histone modification cross-talk that is conserved from yeast to humans. The mechanism by which H2B-Ub stimulates Dot1L to methylate the relatively inaccessible histone core H3K79 residue is unknown. The 3.0 Å resolution cryo-EM structure of Dot1L bound to ubiquitinated nucleosome reveals that Dot1L contains binding sites for both ubiquitin and the histone H4 tail, which establish two regions of contact that stabilize a catalytically competent state and positions the Dot1L active site over H3K79. We unexpectedly find that contacts mediated by both Dot1L and the H4 tail induce a conformational change in the globular core of histone H3 that reorients K79 from an inaccessible position, thus enabling this side chain to project deep into the active site in a position primed for catalysis. Our study provides a comprehensive mechanism of cross-talk between histone ubiquitination and methylation and reveals an unexpected structural plasticity in histones that makes it possible for histone-modifying enzymes to access residues within the nucleosome core.
The enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase is expressed in members of all three kingdoms of life. Its most well-known role is in the reductive biosynthesis of mevalonate from HMG-CoA as part of the mevalonate pathway for the biosynthesis of isopentenyl diphosphate (IPP) and subsequent isoprenoid derivatives. However, a number of bacteria have been shown to utilize this enzyme in the oxidation of mevalonate to HMG-CoA, presumably as a source of acetyl-CoA. One of these bacteria, Burkholderia cenocepacia, has been shown to express an oxidative HMG-CoA reductase but appears to utilize the nonmevalonate pathway for the biosynthesis of isoprenoids. As such, the physiological role of B. cenocepacia HMG-CoA reductase (BcHMGR) is not entirely clear. Current evidence from a number of kinetic, spectroscopic and chromatographic techniques strongly suggest that BcHMGR is regulated via the morpheein model of allostery. In this model, nonadditive quaternary forms of different levels of activity interconvert in response to changes in substrate concentration, pH, and enzyme concentration. Evidence of BcHMGR's morpheein characteristics will be presented, including unusual kinetic behavior, the presence of multiple oligomeric states of differing activities, a possible alternate function for the enzyme involving GTP hydrolysis, and reversible aggregation in solution. Emerging crystallographic and molecular dynamics simulation studies will also be presented, suggesting possible mechanisms by which this dynamic shapeshifting enzyme responds to changes in ligand and substrate concentrations.
Monoubiquitination of histone H2BK120/123 plays multiple roles in regulating transcription, DNA replication and the DNA damage response. The structure of a nucleosome in complex with the dimeric RING E3 ligase, Bre1, reveals that one RING domain binds to the nucleosome acidic patch, where it can position the Rad6 E2, while the other RING domain contacts the DNA. Comparisons with H2A-specific E3 ligases suggests a general mechanism of tuning histone specificity via the non-E2-binding RING domain.
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