4FVT

Human SIRT3 bound to Ac-ACS peptide and Carba-NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Synthesis of Carba-NAD and the Structures of Its Ternary Complexes with SIRT3 and SIRT5.

Szczepankiewicz, B.G.Dai, H.Koppetsch, K.J.Qian, D.Jiang, F.Mao, C.Perni, R.B.

(2012) J.Org.Chem. 77: 7319-7329

  • DOI: 10.1021/jo301067e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Carba-NAD is a synthetic compound identical to NAD except for one substitution, where an oxygen atom adjacent to the anomeric linkage bearing nicotinamide is replaced with a methylene group. Because it is inert in nicotinamide displacement reactions, ...

    Carba-NAD is a synthetic compound identical to NAD except for one substitution, where an oxygen atom adjacent to the anomeric linkage bearing nicotinamide is replaced with a methylene group. Because it is inert in nicotinamide displacement reactions, carba-NAD is an unreactive substrate analogue for NAD-consuming enzymes. SIRT3 and SIRT5 are NAD-consuming enzymes that are potential therapeutic targets for the treatment of metabolic diseases and cancers. We report an improved carba-NAD synthesis, including a pyrophosphate coupling method that proceeds in approximately 60% yield. We also disclose the X-ray crystal structures of the ternary complexes of SIRT3 and SIRT5 bound to a peptide substrate and carba-NAD. These X-ray crystal structures provide critical snapshots of the mechanism by which human sirtuins function as protein deacylation catalysts.


    Organizational Affiliation

    Sirtris, a GSK Company, 200 Technology Square, Cambridge, Massachusetts 02139, USA. bruce.2.szczepankiewicz@gsk.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent protein deacetylase sirtuin-3, mitochondrial
A
274Homo sapiensMutation(s): 0 
Gene Names: SIRT3 (SIR2L3)
EC: 3.5.1.-
Find proteins for Q9NTG7 (Homo sapiens)
Go to Gene View: SIRT3
Go to UniProtKB:  Q9NTG7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Acetylated ACS2 peptide
B
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CNA
Query on CNA

Download SDF File 
Download CCD File 
A
CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C22 H30 N7 O13 P2
DGPLSUKWXXSBCU-VGXGLJSLSA-O
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
B
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
NLE
Query on NLE
B
L-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.202 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 77.430α = 90.00
b = 131.050β = 90.00
c = 77.320γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
PHASERphasing
HKL-2000data collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-06-29 
  • Released Date: 2012-08-15 
  • Deposition Author(s): Dai, H.

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2012-09-19
    Type: Database references