4FVT | pdb_00004fvt

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free:
0.249 (Depositor), 0.241 (DCC)
R-Value Work:
0.202 (Depositor), 0.196 (DCC)
R-Value Observed:
0.204 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 22849721 Search on PubMed
DOI: https://doi.org/10.1021/jo301067e
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 (PDB Primary Data), 2.3.1 (UniProt), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTG7 (Homo sapiens) Explore Q9NTG7 Go to UniProtKB: Q9NTG7
PHAROS: Q9NTG7 GTEx: ENSG00000142082
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NTG7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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	3D Interactions
CNA Query on CNA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₂ H₃₀ N₇ O₁₃ P₂ DGPLSUKWXXSBCU-VGXGLJSLSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
CNA	BindingDB: 4FVT	Kd: min: 6600, max: 7300 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free: 0.249 (Depositor), 0.241 (DCC)
R-Value Work: 0.202 (Depositor), 0.196 (DCC)
R-Value Observed: 0.204 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-08-15

Deposition Author(s):

Dai, H.

Revision History (Full details and data files)

Version 1.0: 2012-08-15
Type: Initial release
Version 1.1: 2012-09-19
Changes: Database references
Version 1.2: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary