4TWI

The structure of Sir2Af1 bound to a succinylated histone peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Alternate deacylating specificities of the archaeal sirtuins Sir2Af1 and Sir2Af2.

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

(2014) Protein Sci 23: 1686-1697

  • 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 mu ...

    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
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Succinylated H4 Peptide (aa8-20)B14Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HHF1YBR009CYBR0122HHF2YNL030WN2752
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02309 
Go to UniProtKB:  P02309
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent protein deacylase 1A245Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: cobB1AF_1676
EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
Find proteins for O28597 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Explore O28597 
Go to UniProtKB:  O28597
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SLL
Query on SLL
BL-PEPTIDE LINKINGC10 H18 N2 O5LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.61α = 90
b = 51.362β = 101.85
c = 57.687γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-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, Structure summary
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence