3ZG6

The novel de-long chain fatty acid function of human sirt6

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Sirt6 Regulates Tnf-Alpha Secretion Through Hydrolysis of Long-Chain Fatty Acyl Lysine

Jiang, H., Khan, S., Wang, Y., Charron, G., He, B., Sebastian, C., Du, J., Kim, R., Ge, E., Mostoslavsky, R., Hang, H.C., Hao, Q., Lin, H.

(2013) Nature 496: 110

  • DOI: 10.1038/nature12038
  • Primary Citation of Related Structures:  
    3ZG6

  • PubMed Abstract: 

    • The Sir2 family of enzymes or sirtuins are known as nicotinamide adenine dinucleotide (NAD)-dependent deacetylases and have been implicated in the regulation of transcription, genome stability, metabolism and lifespan. However, four of the seven mamm ...

    The Sir2 family of enzymes or sirtuins are known as nicotinamide adenine dinucleotide (NAD)-dependent deacetylases and have been implicated in the regulation of transcription, genome stability, metabolism and lifespan. However, four of the seven mammalian sirtuins have very weak deacetylase activity in vitro. Here we show that human SIRT6 efficiently removes long-chain fatty acyl groups, such as myristoyl, from lysine residues. The crystal structure of SIRT6 reveals a large hydrophobic pocket that can accommodate long-chain fatty acyl groups. We demonstrate further that SIRT6 promotes the secretion of tumour necrosis factor-α (TNF-α) by removing the fatty acyl modification on K19 and K20 of TNF-α. Protein lysine fatty acylation has been known to occur in mammalian cells, but the function and regulatory mechanisms of this modification were unknown. Our data indicate that protein lysine fatty acylation is a novel mechanism that regulates protein secretion. The discovery of SIRT6 as an enzyme that controls protein lysine fatty acylation provides new opportunities to investigate the physiological function of a protein post-translational modification that has been little studied until now.

    Organizational Affiliation: 

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-6A296Homo sapiensMutation(s): 0 
Gene Names: SIRT6, SIR2L6
EC: 3.5.1 (PDB Primary Data), 2.4.2.31 (PDB Primary Data), 2.3.1.286 (UniProt)
Find proteins for Q8N6T7 (Homo sapiens)
Explore Q8N6T7 
Go to UniProtKB:  Q8N6T7
NIH Common Fund Data Resources
PHAROS  Q8N6T7
GTEx  ENSG00000077463
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDEF12synthetic constructMutation(s): 0 
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431
GTEx  ENSG00000197409GTEx  ENSG00000197153GTEx  ENSG00000278828GTEx  ENSG00000275714GTEx  ENSG00000273983GTEx  ENSG00000274750GTEx  ENSG00000275379GTEx  ENSG00000277775
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APR
Query on APR
Download CCD File 
A
ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N		 Ligand Interaction
GOL
Query on GOL
Download CCD File 
A
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
MYK
Query on MYK		FL-PEPTIDE LINKINGC20 H40 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.891α = 90
b = 104.891β = 90
c = 231.492γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-12-15 
  • Released Date: 2013-04-03 
    • Deposition Author(s): Wang, Y., Hao, Q.

Revision History 

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2013-04-17
    Changes: Database references