1S7G

Structural Basis for the Mechanism and Regulation of Sir2 Enzymes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the mechanism and regulation of sir2 enzymes

Avalos, J.L.Boeke, J.D.Wolberger, C.

(2004) Mol Cell 13: 639-648

  • DOI: 10.1016/s1097-2765(04)00082-6
  • Primary Citation of Related Structures:  
    1S7G

  • PubMed Abstract: 
  • Sir2 proteins form a family of NAD(+)-dependent protein deacetylases required for diverse biological processes, including transcriptional silencing, suppression of rDNA recombination, control of p53 activity, regulation of acetyl-CoA synthetase, and aging ...

    Sir2 proteins form a family of NAD(+)-dependent protein deacetylases required for diverse biological processes, including transcriptional silencing, suppression of rDNA recombination, control of p53 activity, regulation of acetyl-CoA synthetase, and aging. Although structures of Sir2 enzymes in the presence and absence of peptide substrate or NAD(+) have been determined, the role of the enzyme in the mechanism of deacetylation and NAD(+) cleavage is still unclear. Here, we present additional structures of Sir2Af2 in several differently complexed states: in a productive complex with NAD(+), in a nonproductive NAD(+) complex with bound ADP-ribose, and in the unliganded state. We observe a new mode of NAD(+) binding that seems to depend on acetyl-lysine binding, in which the nicotinamide ring of NAD(+) is buried in the highly conserved "C" pocket of the enzyme. We propose a detailed structure-based mechanism for deacetylation and nicotinamide inhibition of Sir2 consistent with mutagenesis and enzymatic studies.


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205 USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent deacetylase 2A, B, C, D, E253Archaeoglobus fulgidusMutation(s): 0 
Gene Names: NPDA2AF0112
EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
UniProt
Find proteins for O30124 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Explore O30124 
Go to UniProtKB:  O30124
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
CA [auth C], L [auth A], U [auth B]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
APR (Subject of Investigation/LOI)
Query on APR

Download Ideal Coordinates CCD File 
LA [auth E]ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
 Ligand Interaction
2PE
Query on 2PE

Download Ideal Coordinates CCD File 
V [auth B]NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

Download Ideal Coordinates CCD File 
DA [auth C]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
M [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
EA [auth C], JA [auth D]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , H [auth A] , HA [auth D] , I [auth A] , IA [auth D] , J [auth A] , K [auth A] , 
AA [auth C],  BA [auth C],  H [auth A],  HA [auth D],  I [auth A],  IA [auth D],  J [auth A],  K [auth A],  Q [auth B],  R [auth B],  S [auth B],  T [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A] , FA [auth D] , G [auth A] , GA [auth D] , KA [auth E] , O [auth B] , P [auth B] , Y [auth C] , 
F [auth A],  FA [auth D],  G [auth A],  GA [auth D],  KA [auth E],  O [auth B],  P [auth B],  Y [auth C],  Z [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
N [auth A], W [auth B], X [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.85α = 90
b = 181.574β = 90
c = 78.921γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance