Direct transfer of extended groups from synthetic cofactors by DNA methyltransferases

Dalhoff, Christian; Lukinavičius, Gražvydas; Klimašauskas, Saulius; Weinhold, Elmar G.

doi:10.1038/nchembio754

Cited by 217 publications

(204 citation statements)

References 12 publications

Supporting

Mentioning

191

Contrasting

Unclassified

Order By: Relevance

“…Although several previous efforts show that the existence of sulfonium-β-sp 2 carbon is crucial for the SAM analogs to be active cofactors of PMT-mediated transalkylation (native PMTs or their variants) (25,33), the current structural and biochemical studies shed light on how such unsaturated moiety can play a role in enzyme catalysis. Prior structural analysis on native PMTs suggests that the highly conserved Tyr residues in SET-domain-containing PMTs (e.g., EuHMT1/2's Y1211/Y1154) facilitate the transmethylation reaction through the formation of nonclassical C-H. .…”

Section: Discussionmentioning

confidence: 99%

Defining efficient enzyme–cofactor pairs for bioorthogonal profiling of protein methylation

Islam¹,

Chen

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

116

View full text Add to dashboard Cite

Protein methyltransferase (PMT)-mediated posttranslational modification of histone and nonhistone substrates modulates stability, localization, and interacting partners of target proteins in diverse cellular contexts. These events play critical roles in normal biological processes and are frequently deregulated in human diseases. In the course of identifying substrates of individual PMTs, bioorthogonal profiling of protein methylation (BPPM) has demonstrated its merits. In this approach, specific PMTs are engineered to process S-adenosyl-L-methionine (SAM) analogs as cofactor surrogates and label their substrates with distinct chemical modifications for target elucidation. Despite the proof-of-concept advancement of BPPM, few efforts have been made to explore its generality. With two cancer-relevant PMTs, EuHMT1 (GLP1/KMT1D) and EuHMT2 (G9a/ KMT1C), as models, we defined the key structural features of engineered PMTs and matched SAM analogs that can render the orthogonal enzyme-cofactor pairs for efficient catalysis. Here we have demonstrated that the presence of sulfonium-β-sp 2 carbon and flexible, medium-sized sulfonium-δ-substituents are crucial for SAM analogs as BPPM reagents. The bulky cofactors can be accommodated by tailoring the conserved Y1211/Y1154 residues and nearby hydrophobic cavities of EuHMT1/2. Profiling proteomewide substrates with BPPM allowed identification of >500 targets of EuHMT1/2 with representative targets validated using native EuHMT1/2 and SAM. This finding indicates that EuHMT1/2 may regulate many cellular events previously unrecognized to be modulated by methylation. The present work, therefore, paves the way to a broader application of the BPPM technology to profile methylomes of diverse PMTs and elucidate their downstream functions.epigenetic | bump-hole | posttranslation | proteomics

show abstract

Section: Discussionmentioning

confidence: 99%

Defining efficient enzyme–cofactor pairs for bioorthogonal profiling of protein methylation

Islam¹,

Chen

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

116

View full text Add to dashboard Cite

show abstract

“…Both analogs have been shown as substrates for several DNA methyltransferases (Dalhoff et al 2006a), including the N 6 A methyltransferase M.TaqI, the C 5 C methyltransferase M.HhaI, and the N 4 C methyltransferase M.BcnIB, for transfer of the side chains to diverse DNA substrates. While these analogs were not accommodated by E. coli TrmD or M. jannaschii Trm5 for transfer of their side chains to tRNA (data not shown), they were competitive inhibitors of AdoMet, permitting the determination of whether steric bulk in the vicinity of the sulfonium ion might engender inhibition specificity.…”

Section: No Differentiation By Natural and Synthetic Adomet Analogsmentioning

confidence: 99%

Differentiating analogous tRNA methyltransferases by fragments of the methyl donor

Lahoud¹,

Goto-Ito²,

Yoshida³

et al. 2011

RNA

View full text Add to dashboard Cite

Bacterial TrmD and eukaryotic-archaeal Trm5 form a pair of analogous tRNA methyltransferase that catalyze methyl transfer from S-adenosyl methionine (AdoMet) to N 1 of G37, using catalytic motifs that share no sequence or structural homology. Here we show that natural and synthetic analogs of AdoMet are unable to distinguish TrmD from Trm5. Instead, fragments of AdoMet, adenosine and methionine, are selectively inhibitory of TrmD rather than Trm5. Detailed structural information of the two enzymes in complex with adenosine reveals how Trm5 escapes targeting by adopting an altered structure, whereas TrmD is trapped by targeting due to its rigid structure that stably accommodates the fragment. Free energy analysis exposes energetic disparities between the two enzymes in how they approach the binding of AdoMet versus fragments and provides insights into the design of inhibitors selective for TrmD.

show abstract

“…Unlike aziridine‐based labeling, mTAG is a truly catalytic process and does not require stoichiometric amounts of the MTase 17b. Even though multiple turnovers per minute can be achieved, the process is still typically an order of magnitude slower than the equivalent methyl transfer 17b…”

Section: Labeling Strategies Using Adomet‐dependent Mtasesmentioning

confidence: 99%

Methyltransferase‐Directed Labeling of Biomolecules and its Applications

et al. 2017

View full text Add to dashboard Cite

Methyltransferases (MTases) form a large family of enzymes that methylate a diverse set of targets, ranging from the three major biopolymers to small molecules. Most of these MTases use the cofactor S‐adenosyl‐l‐Methionine (AdoMet) as a methyl source. In recent years, there have been significant efforts toward the development of AdoMet analogues with the aim of transferring moieties other than simple methyl groups. Two major classes of AdoMet analogues currently exist: doubly‐activated molecules and aziridine based molecules, each of which employs a different approach to achieve transalkylation rather than transmethylation. In this review, we discuss the various strategies for labelling and functionalizing biomolecules using AdoMet‐dependent MTases and AdoMet analogues. We cover the synthetic routes to AdoMet analogues, their stability in biological environments and their application in transalkylation reactions. Finally, some perspectives are presented for the potential use of AdoMet analogues in biology research, (epi)genetics and nanotechnology.

show abstract

Direct transfer of extended groups from synthetic cofactors by DNA methyltransferases

Cited by 217 publications

References 12 publications

Defining efficient enzyme–cofactor pairs for bioorthogonal profiling of protein methylation

Defining efficient enzyme–cofactor pairs for bioorthogonal profiling of protein methylation

Differentiating analogous tRNA methyltransferases by fragments of the methyl donor

Methyltransferase‐Directed Labeling of Biomolecules and its Applications

Contact Info

Product

Resources

About