PDBsum entry 2h4f

Hydrolase

PDB id: 2h4f

Contents

Protein chain

240 a.a. *

Ligands

SER-ARG-HIS-LYS-ALY-LEU-MET-PHE

NAD

Metals

_ZN

Waters ×70

* Residue conservation analysis

PDB id:

2h4f

Name:

Hydrolase

Title:

Sir2-p53 peptide-NAD+

Structure:

NAD-dependent deacetylase. Chain: a. Synonym: regulatory protein sir2 homolog. Engineered: yes. Cellular tumor antigen p53. Chain: d. Synonym: tumor suppressor p53, phosphoprotein p53, antigen ny-co-13. Engineered: yes

Source:

Thermotoga maritima. Organism_taxid: 2336. Gene: npda. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: f-moc synthetic construct

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.194 R-free: 0.228

Authors:

K.G.Hoff,J.L.Avalos,K.Sens,C.Wolberger

Key ref:

K.G.Hoff et al. (2006). Insights into the sirtuin mechanism from ternary complexes containing NAD+ and acetylated peptide. Structure, 14, 1231-1240. PubMed id: 16905097 DOI: 10.1016/j.str.2006.06.006

Date:

24-May-06 Release date: 05-Sep-06

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: 240 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 (Bound ligand (Het Group name = NAD) corresponds exactly) = 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.2006.06.006

Structure 14:1231-1240 (2006)

PubMed id: 16905097

Insights into the sirtuin mechanism from ternary complexes containing NAD+ and acetylated peptide.

K.G.Hoff, J.L.Avalos, K.Sens, C.Wolberger.

ABSTRACT

Sirtuin proteins comprise a unique class of NAD+-dependent protein deacetylases. Although several structures of sirtuins have been determined, the mechanism by which NAD+ cleavage occurs has remained unclear. We report the structures of ternary complexes containing NAD+ and acetylated peptide bound to the bacterial sirtuin Sir2Tm and to a catalytic mutant (Sir2Tm(H116Y)). NAD+ in these structures binds in a conformation different from that seen in previous structures, exposing the alpha face of the nicotinamide ribose to the carbonyl oxygen of the acetyl lysine substrate. The NAD+ conformation is identical in both structures, suggesting that proper coenzyme orientation is not dependent on contacts with the catalytic histidine. We also present the structure of Sir2Tm(H116A) bound to deacteylated peptide and 3'-O-acetyl ADP ribose. Taken together, these structures suggest a mechanism for nicotinamide cleavage in which an invariant phenylalanine plays a central role in promoting formation of the O-alkylamidate reaction intermediate and preventing nicotinamide exchange.

Selected figure(s)

Figure 1.
Figure 1. Structure of the Ternary Complex of Sir2Tm Bound to Acetylated Peptide and NAD^+
(A) Overall structure of Sir2Tm bound to an acetylated peptide corresponding to residues 372–389 of the p53 protein (yellow) and β-NAD^+ (gray). The Sir2Tm Rossmann fold domain, the α-helical subdomain and Zn binding subdomain, and the Zn atom are colored teal, blue, and gold, respectively.
(B) Electron density for the sirtuin substrates. The 2F[o] − F[c] electron density map contoured at 1σ is shown surrounding the acetylated p53 peptide (yellow) and β-NAD^+ bound to the active site of Sir2Tm.
(C) Stereodiagram of NAD^+ (white) in the active site of Sir2Tm (teal) bound to acetylated peptide (yellow). Active site residues that make contact with NAD^+ are shown as lines, the acetyl lysine substrate and NAD^+ are shown as sticks, and water contacts are shown as dashed, gray sticks.
(D) Schematic representation of Sir2Tm contacts with NAD^+ and acetyl lysine. Sir2Tm residues are shown as ovals containing the amino acid designation and number; invariant residues shaded in blue, waters are shown as red circles, and the acetyl lysine side chain is designated as Ac-K and shaded yellow. Hydrogen bonds between NAD^+ and backbone amides and carbonyls are shown as blue and red dashes, respectively. Hydrogen bonds to amino acid side chains are represented as green dashes, and van der Waals interactions are indicated by yellow semicircles.

Figure 2.
Figure 2. Comparison of NAD^+ and NAD^+-Analog Bound Sirtuin Structures
Structural alignment of Sir2Tm-acetylated p53 peptide-NAD^+ (blue), Hst2Sc-acetylated histone H4 peptide-carba-NAD^+ (green), and Sir2Af2-NAD^+ (pink) based on atoms in the adenine ring, adenine ribose, nicotinamide, and the catalytic histidine. Acetyl lysine and active site residues for the corresponding structures are indicated.

The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 1231-1240) copyright 2006.

Figures were selected by an automated process.