4FVT

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

• PDB DOI: https://doi.org/10.2210/pdb4FVT/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 0.249 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

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

• PubMed: 22849721 
• DOI: https://doi.org/10.1021/jo301067e
• Primary Citation of Related Structures:  
  4FVT, 4G1C


• 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 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.

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Organizational Affiliation: 

Sirtris, a GSK Company, 200 Technology Square, Cambridge, Massachusetts 02139, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.21 kDa 
• Atom Count: 2,310 
• Modelled Residue Count: 279 
• Deposited Residue Count: 279 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-3, mitochondrial	A	274	Homo sapiens	Mutation(s): 0  EC: 3.5.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTG7 (Homo sapiens) Explore Q9NTG7  Go to UniProtKB:  Q9NTG7
PHAROS:  Q9NTG7 GTEx:  ENSG00000142082

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylated ACS2 peptide	B	5	N/A	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CNA	C [auth A]	CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE C22 H30 N7 O13 P2 DGPLSUKWXXSBCU-VGXGLJSLSA-O
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	B	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS
NLE	B	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 0.249 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.43	α = 90
b = 131.05	β = 90
c = 77.32	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references