4H12

The crystal structure of methyltransferase domain of human SET domain-containing protein 2 in complex with S-adenosyl-L-homocysteine

Replaces:  3H6L

Summary for 4H12

• Entry DOI: 10.2210/pdb4h12/pdb
• Descriptor: Histone-lysine N-methyltransferase SETD2, ZINC ION, S-ADENOSYL-L-HOMOCYSTEINE, ... (5 entities in total)
• Functional Keywords: methyltransferase, set domain-containing protein 2, s-adenosyl-l-homocysteine, structural genomics, structural genomics consortium, sgc, activator, chromatin regulator, dna-binding, methylation, nucleus, phosphoprotein, transcription, transcription regulation, transferase
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus (Probable): Q9BYW2
• Total number of polymer chains: 1
• Total formula weight: 32571.58

Authors

Amaya, M.F.,Dong, A.,Zeng, H.,Mackenzie, F.,Bunnage, M.,Weigelt, J.,Bountra, C.,Arrowsmith, C.H.,Edwards, A.M.,Min, J.,Wu, H.,Structural Genomics Consortium (SGC) (deposition date: 2012-09-10, release date: 2012-10-03, Last modification date: 2023-09-13)

Primary citation

Zheng, W.,Ibanez, G.,Wu, H.,Blum, G.,Zeng, H.,Dong, A.,Li, F.,Hajian, T.,Allali-Hassani, A.,Amaya, M.F.,Siarheyeva, A.,Yu, W.,Brown, P.J.,Schapira, M.,Vedadi, M.,Min, J.,Luo, M.
Sinefungin Derivatives as Inhibitors and Structure Probes of Protein Lysine Methyltransferase SETD2.
J.Am.Chem.Soc., 134:18004-18014, 2012

PubMed Abstract: Epigenetic regulation is involved in numerous physiological and pathogenic processes. Among the key regulators that orchestrate epigenetic signaling are over 50 human protein lysine methyltransferases (PKMTs). Interrogation of the functions of individual PKMTs can be facilitated by target-specific PKMT inhibitors. Given the emerging need for such small molecules, we envisioned an approach to identify target-specific methyltransferase inhibitors by screening privileged small-molecule scaffolds against diverse methyltransferases. In this work, we demonstrated the feasibility of such an approach by identifying the inhibitors of SETD2. N-propyl sinefungin (Pr-SNF) was shown to interact preferentially with SETD2 by matching the distinct transition-state features of SETD2's catalytically active conformer. With Pr-SNF as a structure probe, we further revealed the dual roles of SETD2's post-SET loop in regulating substrate access through a distinct topological reconfiguration. Privileged sinefungin scaffolds are expected to have broad use as structure and chemical probes of methyltransferases.

PubMed: 23043551
DOI: 10.1021/ja307060p

Experimental method

X-RAY DIFFRACTION (2.06 Å)