6ISO

Human SIRT3 Recognizing H3K4cr

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Identification of 'erasers' for lysine crotonylated histone marks using a chemical proteomics approach.

Bao, X., Wang, Y., Li, X., Li, X.M., Liu, Z., Yang, T., Wong, C.F., Zhang, J., Hao, Q., Li, X.D.

(2014) Elife 3: --

  • DOI: 10.7554/eLife.02999
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Posttranslational modifications (PTMs) play a crucial role in a wide range of biological processes. Lysine crotonylation (Kcr) is a newly discovered histone PTM that is enriched at active gene promoters and potential enhancers in mammalian cell genom ...

    Posttranslational modifications (PTMs) play a crucial role in a wide range of biological processes. Lysine crotonylation (Kcr) is a newly discovered histone PTM that is enriched at active gene promoters and potential enhancers in mammalian cell genomes. However, the cellular enzymes that regulate the addition and removal of Kcr are unknown, which has hindered further investigation of its cellular functions. Here we used a chemical proteomics approach to comprehensively profile 'eraser' enzymes that recognize a lysine-4 crotonylated histone H3 (H3K4Cr) mark. We found that Sirt1, Sirt2, and Sirt3 can catalyze the hydrolysis of lysine crotonylated histone peptides and proteins. More importantly, Sirt3 functions as a decrotonylase to regulate histone Kcr dynamics and gene transcription in living cells. This discovery not only opens opportunities for examining the physiological significance of histone Kcr, but also helps to unravel the unknown cellular mechanisms controlled by Sirt3, that have previously been considered solely as a deacetylase.

    Organizational Affiliation: 

    Department of Chemistry, University of Hong Kong, Hong Kong, Hong Kong.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent protein deacetylase sirtuin-3, mitochondrial
A, B, E, G, I, K
275Homo sapiensMutation(s): 0 
Gene Names: SIRT3 (SIR2L3)
EC: 3.5.1.-
Find proteins for Q9NTG7 (Homo sapiens)
Go to Gene View: SIRT3
Go to UniProtKB:  Q9NTG7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ARG-THR-LYS-GLN-THR-ALA-ARG
C, D, F, H, L, J
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, E, G, I
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CRD
Query on CRD
Download SDF File 
Download CCD File 
C, D, F, H, J, L
(2E)-BUT-2-ENAL
CROTONALDEHYDE
C4 H6 O
MLUCVPSAIODCQM-NSCUHMNNSA-N
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
B, E, G, K
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.221 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 138.085α = 90.00
b = 138.085β = 90.00
c = 225.342γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-11-17 
  • Released Date: 2019-01-23 
  • Deposition Author(s): Wang, Y., Hao, Q.
  • This entry supersedes: 4V1C
Funding OrganizationLocationGrant Number
Hong KongGRF766510

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release