Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2008 Dec 10;130(49):16721-8.
doi: 10.1021/ja807269j.

Highly dissociative and concerted mechanism for the nicotinamide cleavage reaction in Sir2Tm enzyme suggested by ab initio QM/MM molecular dynamics simulations

Po Hu  1 , Shenglong Wang, Yingkai Zhang
Affiliations

Highly dissociative and concerted mechanism for the nicotinamide cleavage reaction in Sir2Tm enzyme suggested by ab initio QM/MM molecular dynamics simulations

Po Hu et al. J Am Chem Soc. .

Abstract

Sir2 enzymes catalyze the NAD+-dependent protein deacetylation and play critical roles in epigenetics, cell death, and lifespan regulation. In spite of a current flurry of experimental studies, the catalytic mechanism for this unique and important class of enzymes remains elusive. Employing on-the-fly Born-Oppenheimer molecular dynamics simulations with the B3LYP/6-31G(d) QM/MM potential and the umbrella sampling method, we have characterized the initial step of the Sir2Tm-catalyzed reaction, which is also the most controversial portion of its mechanism. Our results indicate that the nicotinamide cleavage reaction employs a highly dissociative and concerted displacement mechanism: the cleavage of the glycosidic bond is facilitated by the nucleophilic participation of the acetyl-lysine, and the dissociative transition state has a significant oxocarbenium ion character. During this step of the reaction, the Sir2Tm enzyme strongly stabilizes the covalent O-alkylamidate intermediate whereas its effect on the transition state is quite minimal. In addition, functional roles of key residues and motifs have been elucidated. This work further demonstrates the feasibility and applicability of the state-of-the-art ab initio QM/MM molecular dynamics approach in simulating enzyme reactions.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Illustration of SN1-like step-wise and SN2-like concerted mechanisms. In SN1-like mechanism, glycosidic bond is cleaved prior to the attack of carbonyl oxygen, whereas these two steps are synchronous in SN2-like mechanism.
Figure 2
Figure 2
Illustration of the QM/MM partition. Color notations: black (MM subsystem); red (boundary carbon atoms in the QM subsystem described by improved pseudobond parameters62); blue (all other atoms in the QM subsystem).
Figure 3
Figure 3
Two-dimensional minimum energy surface along C1′ - N1 and O - C1′ bonds. The reactant is on the lower left corner, the intermediate is on the upper right corner, and the transition state is located in the middle. The pink cycle line represents the minimum reaction path determined by employing dC1′-N1 - dO-C1′ as the reaction coordinate.
Figure 4
Figure 4
Potential of mean force for the Sir2Tm catalyzed nicotinamide cleavage reaction determined with B3LYP/6-31G(d) QM/MM MD simulations. Geometries at reactant, transition state, and intermediate in schematic representation and bond lengths are also shown.
Figure 5
Figure 5
Computed group partial charges of acetyl-lysine, nicotinamide, and ribose ring at reactant, transition state, and intermediate.
Figure 6
Figure 6
Calculated electrostatic + van der Waals interaction energies between the QM subsystem and its environment at the reactant, the transition state and the intermediate. Note that the average energy distribution at the reactant is shifted to zero and the corresponding values are shifted for the transition state and the intermediate.
Figure 7
Figure 7
Individual residue contribution to the intermediate stabilization. Negative value indicates that a residue stabilizes the intermediate, and vice versa. Note that the electrostatic interaction is dominant in the residue contribution.
Figure 8
Figure 8
Three dimensional enzyme-substrate complex structure. Some key motifs which significantly contribute to the substrate binding and enzyme catalysis are shown in color.
Figure 9
Figure 9
The interactions of key residues with the NAD+ and the substrate acetyl-lysine. The left panel is shown in schematic representation, and the right is in actual three dimensional structure.
Figure 10
Figure 10
Superimposition of the active sites of wild-type Sir2Tm (in blue) and its D101N mutant (in yellow, simulation I). Both snapshots are taken at 5 ns in MD simulations after equilibration.
Figure 11
Figure 11
Time dependent trajectories of torsion angle of the glycosidic bond in NAD+ and some of the key hydrogen bonds in the nicotinamide binding pocket during 25 ns MD simulations in both wild-type Sir2Tm and its D101N mutant ( Simulation II), respectively.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Blander G, Guarente L. Annu. Rev. Biochem. 2004;73:417–435. - PubMed
    1. Marmorstein R. Biochem. Soc. Trans. 2004;32:904–909. - PubMed
    1. Denu JM. Curr. Opin. Chem. biol. 2005;9:431–440. - PubMed
    1. Sauve AA, Wolberger C, Schramm VL, Boeke JD. Annu. Rev. Biochem. 2006;75:435–465. - PubMed
    1. Braunstein M, Rose AB, Holmes SG, Allis CD, Broach JR. Genes Dev. 1993;7:592–604. - PubMed

Publication types