PDBsum entry 3d4b

Hydrolase

PDB id: 3d4b

Contents

Protein chain

233 a.a. *

Ligands

THR-SER-ARG-HIS-LYS-ALY-LEU-MET-ALA

DZD

Metals

_ZN

Waters ×142

* Residue conservation analysis

PDB id:

3d4b

Name:

Hydrolase

Title:

Crystal structure of sir2tm in complex with acetyl p53 peptide and dadme-NAD+

Structure:

NAD-dependent deacetylase. Chain: a. Synonym: regulatory protein sir2 homolog. Engineered: yes. Acetyl p53 peptide. Chain: d. Engineered: yes

Source:

Thermotoga maritima. Organism_taxid: 2336. Gene: npda, tm_0490. Expressed in: escherichia coli. Synthetic: yes

Resolution:

1.90Å R-factor: 0.197 R-free: 0.229

Authors:

W.F.Hawse,K.G.Hoff,D.Fatkins,A.Daines,O.V.Zubkova,V.L.Schramm, W.Zheng,C.Wolberger

Key ref:

W.F.Hawse et al. (2008). Structural insights into intermediate steps in the Sir2 deacetylation reaction. Structure, 16, 1368-1377. PubMed id: 18786399 DOI: 10.1016/j.str.2008.05.015

Date:

14-May-08 Release date: 30-Sep-08

Protein chain

Q9WYW0  (NPD_THEMA) -  NAD-dependent protein deacetylase from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 246 a.a.

Struc: 233 a.a.

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 = 2''-O-acetyl-ADP-D-ribose + nicotinamide + L-lysyl-[protein] (Bound ligand (Het Group name = ARG) matches with 66.67% similarity)

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

Added reference

DOI no: 10.1016/j.str.2008.05.015

Structure 16:1368-1377 (2008)

PubMed id: 18786399

Structural insights into intermediate steps in the Sir2 deacetylation reaction.

W.F.Hawse, K.G.Hoff, D.G.Fatkins, A.Daines, O.V.Zubkova, V.L.Schramm, W.Zheng, C.Wolberger.

ABSTRACT

Sirtuin enzymes comprise a unique class of NAD(+)-dependent protein deacetylases. Although structures of many sirtuin complexes have been determined, structural resolution of intermediate chemical steps are needed to understand the deacetylation mechanism. We report crystal structures of the bacterial sirtuin, Sir2Tm, in complex with an S-alkylamidate intermediate, analogous to the naturally occurring O-alkylamidate intermediate, and a Sir2Tm ternary complex containing a dissociated NAD(+) analog and acetylated peptide. The structures and biochemical studies reveal critical roles for the invariant active site histidine in positioning the reaction intermediate, and for a conserved phenylalanine residue in shielding reaction intermediates from base exchange with nicotinamide. The new structural and biochemical studies provide key mechanistic insight into intermediate steps of the Sir2 deacetylation reaction.

Selected figure(s)

Figure 1.
Figure 1. Sirtuin Deacetylation Reaction Mechanism
(A and B) (A) In the first step of the Sir2 deacetylation reaction (I), the ADP-ribose moiety of NAD^+ is transferred to acetyl-lysine, generating the O-alkylamidate intermediate. In this step (I), the nicotinamide-N-ribose bond is broken to generate free nicotinamide. Next, the N-ribose 2′OH group attacks the O-alkylamidate intermediate, generating a 1′,2′ bicyclic species (II). Subsequent hydrolysis of the 1′,2′ bicyclic species yields deacetylated lysine and 2′O-acetyl-ADP-ribose (III). The structure of the DADMe-NAD^+ analog, which represents a dissociated NAD^+ species, is depicted in (B).

Figure 5.
Figure 5. A Conserved Cluster of Phenylalanines Protects the Peptidyl-Imidate Intermediate from Hydrolysis and Base Exchange with Nicotinamide
(A) Cluster of phenylalanine side chains (red), Phe33, Phe48, and Phe162, that shield the S-alkylamidate intermediate from solvent. (B) Orientation of Phe33 side chain in the Michaelis complex (blue) and in the structure containing the S-alkylamidate intermediate (grey). (C) Conformation of Phe 33 in the Sir2Tm-S-alkylamidate intermediate (pink) as compared with its position in the structure of Sir2Tm bound to the deacetylation reaction product, nicotinamid (green; PDB ID code 2H4J).

The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 1368-1377) copyright 2008.

Figures were selected by an automated process.