Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 30.88 kDa 
• Atom Count: 2139 
• Residue Count: 246 
• Unique protein chains: 2

4TWJ

The structure of Sir2Af2 bound to a myristoylated histone peptide

• DOI: 10.2210/pdb4TWJ/pdb

• Classification: HYDROLASE
• Organism(s): Archaeoglobus fulgidus DSM 4304, Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-06-30 Released: 2014-12-03 
• Deposition Author(s): Ringel, A.E., Roman, C., Wolberger, C.
• Funding Organization(s): National Science Foundation (NSF, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.205 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Literature

Alternate deacylating specificities of the archaeal sirtuins Sir2Af1 and Sir2Af2.

Ringel, A.E., Roman, C., Wolberger, C.

(2014) Protein Sci 23: 1686-1697

• PubMed: 25200501 
• DOI: 10.1002/pro.2546
• Primary Citation of Related Structures:  
  4TWI, 4TWJ


• PubMed Abstract: 
  

Sirtuins were originally shown to regulate a wide array of biological processes such as transcription, genomic stability, and metabolism by catalyzing the NAD(+) -dependent deacetylation of lysine residues. Recent proteomic studies have revealed a much wider array of lysine acyl modifications in vivo than was previously known, which has prompted a reevaluation of sirtuin substrate specificity. Several sirtuins have now been shown to preferentially remove propionyl, succinyl, and long-chain fatty acyl groups from lysines, which has changed our understanding of sirtuin biology. In light of these developments, we revisited the acyl specificity of several well-studied archaeal and bacterial sirtuins. We find that the Archaeoglobus fulgidus sirtuins, Sir2Af1 and Sir2Af2, preferentially remove succinyl and myristoyl groups, respectively. Crystal structures of Sir2Af1 bound to a succinylated peptide and Sir2Af2 bound to a myristoylated peptide show how the active site of each enzyme accommodates a noncanonical acyl chain. As compared to its structure in complex with an acetylated peptide, Sir2Af2 undergoes a conformational change that expands the active site to accommodate the myristoyl group. These findings point to both structural and biochemical plasticity in sirtuin active sites and provide further evidence that sirtuins from all three domains of life catalyze noncanonical deacylation.

---

Organizational Affiliation: 

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205-2185.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacylase 2	A	253	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0  Gene Names: cobB2, Sir2Af2, AF_0112 EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
Find proteins for O30124 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)) Explore O30124  Go to UniProtKB:  O30124

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4 peptide	B	14	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02309  Go to UniProtKB:  P02309

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MYK	B	L-PEPTIDE LINKING	C20 H40 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.205 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.478	α = 90
b = 77.251	β = 110.74
c = 45.904	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-06-30 
• Released Date: 2014-12-03 
Deposition Author(s): Ringel, A.E., Roman, C., Wolberger, C.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-0920082

Revision History 

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence