4I51

Methyltransferase domain of HUMAN EUCHROMATIC HISTONE METHYLTRANSFERASE 1, mutant Y1211A

Replaces:  4H4H

Summary for 4I51

• Entry DOI: 10.2210/pdb4i51/pdb
• Descriptor: Histone-lysine N-methyltransferase EHMT1, H3K9 NE-ALLYL PEPTIDE, UNKNOWN PEPTIDE, ... (8 entities in total)
• Functional Keywords: ne-allyl peptide, structural genomics consortium, transferase-peptide complex, sgc, transferase/peptide
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: Q9H9B1
• Total number of polymer chains: 5
• Total formula weight: 70383.53

Authors

Dong, A.,Zeng, H.,Walker, J.R.,Islam, K.,Bountra, C.,Arrowsmith, C.H.,Edwards, A.M.,Lou, M.,Min, J.,Wu, H.,Structural Genomics Consortium (SGC) (deposition date: 2012-11-28, release date: 2012-12-19, Last modification date: 2023-12-06)

Primary citation

Islam, K.,Chen, Y.,Wu, H.,Bothwell, I.R.,Blum, G.J.,Zeng, H.,Dong, A.,Zheng, W.,Min, J.,Deng, H.,Luo, M.
Defining efficient enzyme-cofactor pairs for bioorthogonal profiling of protein methylation.
Proc.Natl.Acad.Sci.USA, 110:16778-16783, 2013

PubMed Abstract: 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 proteome-wide 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.

PubMed: 24082136
DOI: 10.1073/pnas.1216365110

Experimental method

X-RAY DIFFRACTION (1.9 Å)