PDBsum entry 2od2

Hydrolase

PDB id: 2od2

Contents

Protein chain

291 a.a. *

Ligands

LYS-GLY-GLY-ALA-ALY-ARG-HIS

CNA

GOL ×4

Metals

_ZN

Waters ×166

* Residue conservation analysis

PDB id:

2od2

Name:

Hydrolase

Title:

Crystal structure of yhst2 i117f mutant bound to carba-NAD+ and an acetylated h4 peptide

Structure:

NAD-dependent deacetylase hst2. Chain: a. Fragment: hst2 catalytic core domain, residues 1-294. Synonym: homologous to sir2 protein 2. Engineered: yes. Mutation: yes. Acetylated h4 peptide. Chain: b. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: hst2. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: this sequence occurs naturally in homo sapiens (humans)

Resolution:

2.00Å R-factor: 0.225 R-free: 0.233

Authors:

B.D.Sanders

Key ref:

B.D.Sanders et al. (2007). Structural basis for nicotinamide inhibition and base exchange in Sir2 enzymes. Mol Cell, 25, 463-472. PubMed id: 17289592 DOI: 10.1016/j.molcel.2006.12.022

Date:

21-Dec-06 Release date: 20-Feb-07

Protein chain

P53686  (HST2_YEAST) -  NAD-dependent protein deacetylase HST2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 357 a.a.

Struc: 291 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.3.1.286 - protein acetyllysine N-acetyltransferase.
• Reaction: N₆-acetyl-L-lysyl-[protein] + NAD⁺ + H2O = 2''-O-acetyl-ADP-D-ribose + nicotinamide + L-lysyl-[protein]

N(6)-acetyl-L-lysyl-[protein] + NAD(+) + H2O (Bound ligand (Het Group name = CNA) matches with 95.56% similarity) = 2''-O-acetyl-ADP-D-ribose + nicotinamide + L-lysyl-[protein] (Bound ligand (Het Group name = ALY) matches with 61.54% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.molcel.2006.12.022

Mol Cell 25:463-472 (2007)

PubMed id: 17289592

Structural basis for nicotinamide inhibition and base exchange in Sir2 enzymes.

B.D.Sanders, K.Zhao, J.T.Slama, R.Marmorstein.

ABSTRACT

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.

Selected figure(s)

Figure 1.
Figure 1. Structures of the Free yHst2/ADP-HPD/Histone H4 Complex
(A) Ternary yHst2 (gray) complex, highlighting strictly conserved (red) and conserved (pink) residues; the binding sites of acetyl-lysine (green), carba-NAD^+ (cyan), and ADP-ribose (yellow); and the conserved C and D pockets.
Hydrogen bonds between the acetyl-lysine and carba-NAD^+ are shown as yellow dotted lines. Residues 43–48 of the flexible loop and residue 64 were omitted for clarity.
(B) Superimposition of the yHst2/ADP-ribose/H4 complex (magenta) with the yHst2/ADP-HPD/H4 complex (cyan) and the yHst2/ADP-HPD/H4 complex bound to nicotinamide (blue). The intermediate analog, acetylated histone H4 ligands, and nicotinamide are shown in green for the ADP-ribose complex, yellow for the free ADP-HPD complex, and orange for the nicotinamide-bound ADP-HDP complex.
(C) Simulated annealing omit density contoured at 1.0 σ showing density for the protein (blue) and ADP-HPD (atoms individually colored). Water molecules are shown as blue spheres.
(D) yHst2 bound to ADP-HPD (atoms individually colored) and highlighting residues that make hydrogen bonds (red dashed lines) or van der Waals contacts with ADP-HPD. Hydrogen bonding residues are colored pink, residues that make van der Waals interactions are colored cyan, and residues that make both interactions are colored purple.

Figure 4.
Figure 4. The Overall Structure of yHst2 I117F Bound to Carba-NAD^+ and Acetyl-Lysine
(A) Simulated annealing omit density contoured at 1.0 σ showing density for the protein (gray), carba-NAD^+ (cyan), acetyl-lysine (magenta), and the mutated I117F residue (yellow).
(B) The superposition of the nicotinamide-bound yHst2/ADP-HPD/H4 and the yHst2 I117F/carba-NAD^+/H4 structures. The yHst2 protein is shown in blue, and the mutated I117F side chain (yellow) and the nicotinamide molecule (red) are shown both in stick and modeled in terms of the van der Waals radius of each atom of the molecules.

The above figures are reprinted by permission from Cell Press: Mol Cell (2007, 25, 463-472) copyright 2007.

Figures were selected by an automated process.