PDBsum entry 1j8f

Gene regulation, transferase

PDB id: 1j8f

Contents

Protein chain

312 a.a. *

Metals

_ZN ×3

Waters ×2598

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structure of the histone deacetylase sirt2.

Authors

M.S.Finnin, J.R.Donigian, N.P.Pavletich.

Ref.

Nat Struct Biol, 2001, 8, 621-625. [DOI no: 10.1038/89668]

PubMed id

11427894

Abstract

Sir2 is an NAD-dependent histone deacetylase that mediates transcriptional silencing at mating-type loci, telomeres and ribosomal gene clusters, and has a critical role in the determination of life span in yeast and Caenorhabditis elegans. The 1.7 A crystal structure of the 323 amino acid catalytic core of human SIRT2, a homolog of yeast Sir2, reveals an NAD-binding domain, which is a variant of the Rossmann fold, and a smaller domain composed of a helical module and a zinc-binding module. A conserved large groove at the interface of the two domains is the likely site of catalysis based on mutagenesis. Intersecting this large groove, there is a pocket formed by the helical module. The pocket is lined with hydrophobic residues conserved within each of the five Sir2 classes, suggesting that it is a class-specific protein-binding site.

Figure 3.
Figure 3. Conservation among Sir2-like enzymes. a, Surface representation of SIRT2 generated by the program GRASP39, with residues identical among all Sir2-like enzymes (yellow) and those identical among class I enzymes (magenta) mapped onto the surface. These residues are indicated as ball-and-stick representations in the black-rimmed expansion (right), which shows a close-up view of the potential NAD-binding site. b, An expanded surface representation of the area highlighted in (a) with the hydrophobic residues of the pocket mapped onto the surface in orange. The black-rimmed expansion shows a ribbon diagram of the helical module containing the hydrophobic pocket and ball-and-stick representation of the hydrophobic residues, which are labeled. c, Histone deacetylase activity of the SIRT2 point mutants. Reactions contained wild type or mutant SIRT2, 500 M NAD and 10 g of [3H]acetyl-labeled murine erythroleukemia histone preparation. Assays were performed in triplicate and error bars denote the standard deviation.

Figure 4.
Figure 4. Structural comparison between SIRT2 and Sir2-Af1. a, Superposition of SIRT2 Rossmann fold with Sir2-Af1 in stereo. SIRT2 is shown in cyan and positioned approximately in the same orientation as in Fig. 1 (right), and Sir2-Af1 is in gray. The zinc from SIRT2 is in magenta, whereas the zinc atom from Sir2-Af1 is in orange. The NAD molecule from the Sir2-Af1 -NAD complex is in red. The SIRT2 small pocket and the L-1B loop of Sir2-Af1 are labeled. Notice the increased size of the Sir2-Af1 acetyl-lysine binding site in SIRT2. b, A stereo, close-up view of the NAD binding sites of SIRT2 and Sir2-Af1. The view shows the molecules turned 90° along a horizontal axis in the plane of the paper. Conserved SIRT2 residues that are candidates for NAD-binding or catalysis are shown as ball-and-stick representations and are labeled.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 621-625) copyright 2001.