5BWN

Crystal Structure of SIRT3 with a H3K9 Peptide Containing a Myristoyl Lysine

Summary for 5BWN

• Entry DOI: 10.2210/pdb5bwn/pdb
• Related: 5BWL 5BWO 5BWP 5BWQ
• Descriptor: myristoyl H3K9 peptide, NAD-dependent protein deacetylase sirtuin-3, mitochondrial, ZINC ION, ... (4 entities in total)
• Functional Keywords: hydrolase, peptide-hydrolase complex, peptide/hydrolase
• Biological source: Homo sapiens (Human); More
• Cellular location: Mitochondrion matrix : Q9NTG7
• Total number of polymer chains: 2
• Total formula weight: 35770.40

Authors

Gai, W.,Liu, D. (deposition date: 2015-06-08, release date: 2016-07-13, Last modification date: 2023-11-08)

Primary citation

Gai, W.,Li, H.,Jiang, H.,Long, Y.,Liu, D.
Crystal structures of SIRT3 reveal that the alpha 2-alpha 3 loop and alpha 3-helix affect the interaction with long-chain acyl lysine.
Febs Lett., 590:3019-3028, 2016

PubMed Abstract: SIRT1-7 play important roles in many biological processes and age-related diseases. In addition to a NAD(+) -dependent deacetylase activity, they can catalyze several other reactions, including the hydrolysis of long-chain fatty acyl lysine. To study the binding modes of sirtuins to long-chain acyl lysines, we solved the crystal structures of SIRT3 bound to either a H3K9-myristoylated- or a H3K9-palmitoylated peptide. Interaction of SIRT3 with the palmitoyl group led to unfolding of the α3-helix. The myristoyl and palmitoyl groups bind to the C-pocket and an allosteric site near the α3-helix, respectively. We found that the residues preceding the α3-helix determine the size of the C-pocket. The flexibility of the α2-α3 loop and the plasticity of the α3-helix affect the interaction with long-chain acyl lysine.

PubMed: 27501476
DOI: 10.1002/1873-3468.12345

Experimental method

X-RAY DIFFRACTION (1.942 Å)