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 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


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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:  
    6ISO

  • 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 genomes. However, the cellular enzymes that regulate the addition and removal of Kcr are unknown, which has hindered further investigation of its cellular functions ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-3, mitochondrial275Homo sapiensMutation(s): 0 
Gene Names: SIRT3, SIR2L3
EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTG7 (Homo sapiens)
Explore Q9NTG7 
Go to UniProtKB:  Q9NTG7
PHAROS:  Q9NTG7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NTG7
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ARG-THR-LYS-GLN-THR-ALA-ARG7synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
AA [auth K],
O [auth B],
R [auth E],
V [auth G]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CRD
Query on CRD
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N [auth C],
Q [auth D],
T [auth F],
U [auth H],
X [auth L],
N [auth C],
Q [auth D],
T [auth F],
U [auth H],
X [auth L],
Z [auth J]
(2E)-BUT-2-ENAL
C4 H6 O
MLUCVPSAIODCQM-NSCUHMNNSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
M [auth A],
P [auth B],
S [auth E],
W [auth G],
Y [auth I]		ZINC ION
Zn
PTFCDOFLOPIGGS-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 
  • R-Value Observed: 0.224 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.085α = 90
b = 138.085β = 90
c = 225.342γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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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  (Full details and data files)

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