3PKI

Human SIRT6 crystal structure in complex with ADP ribose

Summary for 3PKI

• Entry DOI: 10.2210/pdb3pki/pdb
• Related: 3PKJ
• Descriptor: NAD-dependent deacetylase sirtuin-6, UNKNOWN ATOM OR ION, ZINC ION, ... (6 entities in total)
• Functional Keywords: sirt6, adp ribose, structural genomics, structural genomics consortium, sgc, hydrolase
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus, nucleoplasm : Q8N6T7
• Total number of polymer chains: 6
• Total formula weight: 240598.04

Authors

Pan, P.W.,Dong, A.,Qiu, W.,Loppnau, P.,Wang, J.,Ravichandran, M.,Bochkarev, A.,Bountra, C.,Weigelt, J.,Arrowsmith, C.H.,Min, J.,Edwards, A.M.,Structural Genomics Consortium (SGC) (deposition date: 2010-11-11, release date: 2011-01-26, Last modification date: 2023-09-06)

Primary citation

Pan, P.W.,Feldman, J.L.,Devries, M.K.,Dong, A.,Edwards, A.M.,Denu, J.M.
Structure and biochemical functions of SIRT6.
J.Biol.Chem., 286:14575-14587, 2011

PubMed Abstract: SIRT6 is a member of the evolutionarily conserved sirtuin family of NAD(+)-dependent protein deacetylases and functions in genomic stability and transcriptional control of glucose metabolism. Early reports suggested that SIRT6 performs ADP-ribosylation, whereas more recent studies have suggested that SIRT6 functions mainly as a histone deacetylase. Thus, the molecular functions of SIRT6 remain uncertain. Here, we perform biochemical, kinetic, and structural studies to provide new mechanistic insight into the functions of SIRT6. Utilizing three different assays, we provide biochemical and kinetic evidence that SIRT6-dependent histone deacetylation produces O-acetyl-ADP-ribose but at a rate ∼1,000 times slower than other highly active sirtuins. To understand the molecular basis for such low deacetylase activity, we solved the first crystal structures of this class IV sirtuin in complex with ADP-ribose and the non-hydrolyzable analog of O-acetyl-ADP-ribose, 2'-N-acetyl-ADP-ribose. The structures revealed unique features of human SIRT6, including a splayed zinc-binding domain and the absence of a helix bundle that in other sirtuin structures connects the zinc-binding motif and Rossmann fold domain. SIRT6 also lacks the conserved, highly flexible, NAD(+)-binding loop and instead contains a stable single helix. These differences led us to hypothesize that SIRT6, unlike all other studied sirtuins, would be able to bind NAD(+) in the absence of an acetylated substrate. Indeed, we found that SIRT6 binds NAD(+) with relatively high affinity (K(d) = 27 ± 1 μM) in the absence of an acetylated substrate. Isothermal titration calorimetry and tryptophan fluorescence binding assays suggested that ADP-ribose and NAD(+) induce different structural perturbations and that NADH does not bind to SIRT6. Collectively, these new insights imply a unique activating mechanism and/or the possibility that SIRT6 could act as an NAD(+) metabolite sensor.

PubMed: 21362626
DOI: 10.1074/jbc.M111.218990

Experimental method

X-RAY DIFFRACTION (2.04 Å)