9KQO

cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome

Summary for 9KQO

• Entry DOI: 10.2210/pdb9kqo/pdb
• EMDB information: 62509
• Descriptor: E3 ubiquitin-protein ligase BRE1B, Ubiquitin-conjugating enzyme E2 A, ZINC ION, ... (12 entities in total)
• Functional Keywords: rnf20, rnf40, h2bs112glcnac, o-glcnacylation, ubiquitination, h2bk120ub, nuclear protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 14
• Total formula weight: 239802.24

Authors

Deng, Z.H.,Ai, H.S.,Liu, L. (deposition date: 2024-11-26, release date: 2025-12-31, Last modification date: 2026-02-04)

Primary citation

Deng, Z.,Tao, S.,Du, Y.,Li, Y.,Zhang, L.,Shi, Q.,Du, X.,Sun, M.,Tong, Z.,Pan, M.,Liu, L.,Ai, H.
Allosteric activation of RNF20/RNF40-RAD6A-mediated H2BK120 monoubiquitylation by H2BS112 GlcNAcylation.
Nat.Chem.Biol., 2026

PubMed Abstract: The activation of H2B K120 monoubiquitylation (H2BK120ub) by H2B S112 GlcNAcylation (H2BS112GlcNAc) has an important role in regulating transcriptional activation, yet its mechanism remains unclear. Here we chemically synthesized H2BS112GlcNAc-modified nucleosomes and quantitatively evaluated how H2BS112GlcNAc stimulates ubiquitylation by RNF20/RNF40-RAD6A E3-E2 enzymes. Cryo-electron microscopy determination of a chemically trapped RNF20/RNF40-RAD6A-Ub-H2BS112GlcNAc nucleosome complex revealed that the H2BS112GlcNAc moiety interacts with the E2 enzyme RAD6A but not the E3 ligase RNF20/RNF40. Mutagenesis and kinetics analyses demonstrated that H2BS112GlcNAc allosterically stimulates ubiquitin transfer from the RAD6A~Ub thioester to H2B K120 by enhancing the nucleophilicity of H2B K120. Structure‒activity relationship analysis further identified the essential roles of the C2 N-acetyl group and the β-configuration of C1 on the H2BS112GlcNAc moiety. These findings provide the structural evidence of histone posttranslational modification crosstalk involving O-GlcNAcylation and reveal how O-GlcNAcylation can allosterically stimulate enzyme activity through substrate modification.

PubMed: 41495224
DOI: 10.1038/s41589-025-02109-6

Experimental method

ELECTRON MICROSCOPY (3.48 Å)