8HLY

Crystal structure of SIRT3 in complex with H3K23la peptide

Summary for 8HLY

• Entry DOI: 10.2210/pdb8hly/pdb
• Descriptor: NAD-dependent protein deacetylase sirtuin-3, mitochondrial, H3K23la peptide, GLYCEROL, ... (7 entities in total)
• Functional Keywords: sirt3, lysine lactylation eraser, hydrolase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 32365.57

Authors

Zhuming, F.,Hao, Q. (deposition date: 2022-12-01, release date: 2023-09-27, Last modification date: 2023-11-15)

Primary citation

Fan, Z.,Liu, Z.,Zhang, N.,Wei, W.,Cheng, K.,Sun, H.,Hao, Q.
Identification of SIRT3 as an eraser of H4K16la.
Iscience, 26:107757-107757, 2023

PubMed Abstract: Lysine lactylation (Kla) is a novel histone post-translational modification discovered in late 2019. Later, HDAC1-3, were identified as the robust Kla erasers. While the Sirtuin family proteins showed weak eraser activities toward Kla, as reported. However, the catalytic mechanisms and physiological functions of HDACs and Sirtuins are not identical. In this study, we observed that SIRT3 exhibits a higher eraser activity against the H4K16la site than the other human Sirtuins. Crystal structures revealed the detailed binding mechanisms between lactyl-lysine peptides and SIRT3. Furthermore, a chemical probe, p-H4K16laAlk, was developed to capture potential Kla erasers from cell lysates. SIRT3 was captured by this probe and detected via proteomic analysis. And another chemical probe, p-H4K16la-NBD, was developed to detect the eraser-Kla delactylation processes directly via fluorescence indication. Our findings and chemical probes provide new directions for further investigating Kla and its roles in gene transcription regulation.

PubMed: 37720100
DOI: 10.1016/j.isci.2023.107757

Experimental method

X-RAY DIFFRACTION (2 Å)