Crystal structure of GAS41

Experimental Data Snapshot

  • Resolution: 2.61 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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Identification of the YEATS domain of GAS41 as a pH-dependent reader of histone succinylation

Wang, Y.Jin, J.Chung, M.W.H.Feng, L.Sun, H.Hao, Q.

(2018) Proc Natl Acad Sci U S A 115: 2365-2370

  • DOI: https://doi.org/10.1073/pnas.1717664115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Lysine succinylation is a newly discovered posttranslational modification with distinctive physical properties. However, to date rarely have studies reported effectors capable of interpreting this modification on histones. Following our previous study of SIRT5 as an eraser of succinyl-lysine (Ksuc), here we identified the GAS41 YEATS domain as a reader of Ksuc on histones. Biochemical studies showed that the GAS41 YEATS domain presents significant binding affinity toward H3K122suc upon a protonated histidine residue. Furthermore, cellular studies showed that GAS41 had prominent interaction with H3K122suc on histones and also demonstrated the coenrichment of GAS41 and H3K122suc on the p21 promoter. To investigate the binding mechanism, we solved the crystal structure of the YEATS domain of Yaf9, the GAS41 homolog, in complex with an H3K122suc peptide that demonstrated the presence of a salt bridge formed when a protonated histidine residue (His39) recognizes the carboxyl terminal of the succinyl group. We also solved the apo structure of GAS41 YEATS domain, in which the conserved His43 residue superimposes well with His39 in the Yaf9 structure. Our findings identified a reader of succinyl-lysine, and the binding mechanism will provide insight into the development of specific regulators targeting GAS41.

  • Organizational Affiliation

    School of Biomedical Sciences, University of Hong Kong, Hong Kong, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YEATS domain-containing protein 4A [auth B],
B [auth A],
140Homo sapiensMutation(s): 0 
Gene Names: YEATS4GAS41
UniProt & NIH Common Fund Data Resources
Find proteins for O95619 (Homo sapiens)
Explore O95619 
Go to UniProtKB:  O95619
PHAROS:  O95619
GTEx:  ENSG00000127337 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95619
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.61 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.467α = 90
b = 57.212β = 90
c = 205.854γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
HK-RGCHong KongC7037-14G

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description