8HN9

Human SIRT3 Recognizing CCNE2K348la peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.233 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

SIRT3-dependent delactylation of cyclin E2 prevents hepatocellular carcinoma growth.

Jin, J.Bai, L.Wang, D.Ding, W.Cao, Z.Yan, P.Li, Y.Xi, L.Wang, Y.Zheng, X.Wei, H.Ding, C.Wang, Y.

(2023) EMBO Rep 24: e56052-e56052

  • DOI: https://doi.org/10.15252/embr.202256052
  • Primary Citation of Related Structures:  
    8HN9

  • PubMed Abstract: 

    Lysine lactylation (Kla) is a recently discovered histone mark derived from metabolic lactate. The NAD + -dependent deacetylase SIRT3, which can also catalyze removal of the lactyl moiety from lysine, is expressed at low levels in hepatocellular carcinoma (HCC) and has been suggested to be an HCC tumor suppressor. Here we report that SIRT3 can delactylate non-histone proteins and suppress HCC development. Using SILAC-based quantitative proteomics, we identify cyclin E2 (CCNE2) as one of the lactylated substrates of SIRT3 in HCC cells. Furthermore, our crystallographic study elucidates the mechanism of CCNE2 K348la delactylation by SIRT3. Our results further suggest that lactylated CCNE2 promotes HCC cell growth, while SIRT3 activation by Honokiol induces HCC cell apoptosis and prevents HCC outgrowth in vivo by regulating Kla levels of CCNE2. Together, our results establish a physiological function of SIRT3 as a delactylase that is important for suppressing HCC, and our structural data could be useful for the future design of activators.


  • Organizational Affiliation

    Division of Life Sciences and Medicine, Department of Hepatobiliary Surgery, The First Affiliated Hospital of USTC, University of Science and Technology of China, Heifei, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-3, mitochondrial
A, B
274Homo sapiensMutation(s): 0 
Gene Names: SIRT3
EC: 2.3.1.286
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTG7 (Homo sapiens)
Explore Q9NTG7 
Go to UniProtKB:  Q9NTG7
PHAROS:  Q9NTG7
GTEx:  ENSG00000142082 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NTG7
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CCNE2 peptide13Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O96020 (Homo sapiens)
Explore O96020 
Go to UniProtKB:  O96020
PHAROS:  O96020
GTEx:  ENSG00000175305 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96020
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.233 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 235.676α = 90
b = 235.676β = 90
c = 235.676γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21977121

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-05-17
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations