4KXQ

Structure of NAD-dependent protein deacetylase sirtuin-1 (closed state, 1.85 A)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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This is version 1.2 of the entry. See complete history. 


Literature

Structural and Functional Analysis of Human SIRT1.

Davenport, A.M., Huber, F.M., Hoelz, A.

(2014) J Mol Biol 426: 526-541

  • DOI: 10.1016/j.jmb.2013.10.009
  • Primary Citation of Related Structures:  
    4IG9, 4KXQ

  • PubMed Abstract: 

    • SIRT1 is a NAD(+)-dependent deacetylase that plays important roles in many cellular processes. SIRT1 activity is uniquely controlled by a C-terminal regulatory segment (CTR). Here we present crystal structures of the catalytic domain of human SIRT1 in complex with the CTR in an open apo form and a closed conformation in complex with a cofactor and a pseudo-substrate peptide ...

    SIRT1 is a NAD(+)-dependent deacetylase that plays important roles in many cellular processes. SIRT1 activity is uniquely controlled by a C-terminal regulatory segment (CTR). Here we present crystal structures of the catalytic domain of human SIRT1 in complex with the CTR in an open apo form and a closed conformation in complex with a cofactor and a pseudo-substrate peptide. The catalytic domain adopts the canonical sirtuin fold. The CTR forms a β hairpin structure that complements the β sheet of the NAD(+)-binding domain, covering an essentially invariant hydrophobic surface. The apo form adopts a distinct open conformation, in which the smaller subdomain of SIRT1 undergoes a rotation with respect to the larger NAD(+)-binding subdomain. A biochemical analysis identifies key residues in the active site, an inhibitory role for the CTR, and distinct structural features of the CTR that mediate binding and inhibition of the SIRT1 catalytic domain.

    Organizational Affiliation: 

    Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. Electronic address: hoelz@caltech.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-1A281Homo sapiensMutation(s): 0 
Gene Names: SIRT1, SIR2L1
EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EB6 (Homo sapiens)
Explore Q96EB6 
Go to UniProtKB:  Q96EB6
PHAROS:  Q96EB6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EB6
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-1B30Homo sapiensMutation(s): 0 
Gene Names: SIRT1, SIR2L1
EC: 2.3.1.286 (UniProt), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EB6 (Homo sapiens)
Explore Q96EB6 
Go to UniProtKB:  Q96EB6
PHAROS:  Q96EB6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EB6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APR
Query on APR
Download Ideal Coordinates CCD File 
D [auth A]ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
BME
Query on BME
Download Ideal Coordinates CCD File 
E [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.714α = 90
b = 92.714β = 90
c = 97.745γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-11-06
    Changes: Database references, Structure summary
  • Version 1.2: 2014-02-05
    Changes: Database references