2OD2 image
Entry Detail
PDB ID:
2OD2
Keywords:
Title:
Crystal Structure of yHst2 I117F mutant bound to carba-NAD+ and an acetylated H4 peptide
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2006-12-21
Release Date:
2007-02-20
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.23
R-Value Work:
0.22
R-Value Observed:
0.11
Space Group:
P 32 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:NAD-dependent deacetylase HST2
Mutations:I117F
Chain IDs:A
Chain Length:308
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Acetylated H4 peptide
Chain IDs:B
Chain Length:14
Number of Molecules:1
Biological Source:
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ALY B LYS N(6)-ACETYLLYSINE
Primary Citation
Structural basis for nicotinamide inhibition and base exchange in sir2 enzymes.
Mol.Cell 25 463 472 (2007)
PMID: 17289592 DOI: 10.1016/j.molcel.2006.12.022

Abstact

The Sir2 family of proteins consists of broadly conserved NAD(+)-dependent deacetylases that are implicated in diverse biological processes, including DNA regulation, metabolism, and longevity. Sir2 proteins are regulated in part by the cellular concentrations of a noncompetitive inhibitor, nicotinamide, that reacts with a Sir2 reaction intermediate via a base-exchange reaction to reform NAD(+) at the expense of deacetylation. To gain a mechanistic understanding of nicotinamide inhibition in Sir2 enzymes, we captured the structure of nicotinamide bound to a Sir2 homolog, yeast Hst2, in complex with its acetyl-lysine 16 histone H4 substrate and a reaction intermediate analog, ADP-HPD. Together with related biochemical studies and structures, we identify a nicotinamide inhibition and base-exchange site that is distinct from the so-called "C pocket" binding site for the nicotinamide group of NAD(+). These results provide insights into the Sir2 mechanism of nicotinamide inhibition and have important implications for the development of Sir2-specific effectors.

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Primary Citation of related structures