7D0S

Crystal structure of human HBO1-BRPF2 in complex with succinyl-coenzyme A

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2020-09-11 Released: 2021-07-07 
  • Deposition Author(s): Li, W., Ding, J.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

HBO1 is a versatile histone acyltransferase critical for promoter histone acylations.

Xiao, Y.Li, W.Yang, H.Pan, L.Zhang, L.Lu, L.Chen, J.Wei, W.Ye, J.Li, J.Li, G.Zhang, Y.Tan, M.Ding, J.Wong, J.

(2021) Nucleic Acids Res 49: 8037-8059

  • DOI: https://doi.org/10.1093/nar/gkab607
  • Primary Citation of Related Structures:  
    7D0O, 7D0P, 7D0Q, 7D0R, 7D0S

  • PubMed Abstract: 

    Recent studies demonstrate that histones are subjected to a series of short-chain fatty acid modifications that is known as histone acylations. However, the enzymes responsible for histone acylations in vivo are not well characterized. Here, we report that HBO1 is a versatile histone acyltransferase that catalyzes not only histone acetylation but also propionylation, butyrylation and crotonylation both in vivo and in vitro and does so in a JADE or BRPF family scaffold protein-dependent manner. We show that the minimal HBO1/BRPF2 complex can accommodate acetyl-CoA, propionyl-CoA, butyryl-CoA and crotonyl-CoA. Comparison of CBP and HBO1 reveals that they catalyze histone acylations at overlapping as well as distinct sites, with HBO1 being the key enzyme for H3K14 acylations. Genome-wide chromatin immunoprecipitation assay demonstrates that HBO1 is highly enriched at and contributes to bulk histone acylations on the transcriptional start sites of active transcribed genes. HBO1 promoter intensity highly correlates with the level of promoter histone acylation, but has no significant correlation with level of transcription. We also show that HBO1 is associated with a subset of DNA replication origins. Collectively our study establishes HBO1 as a versatile histone acyltransferase that links histone acylations to promoter acylations and selection of DNA replication origins.


  • Organizational Affiliation

    Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase KAT7276Homo sapiensMutation(s): 0 
Gene Names: KAT7HBO1HBOaMYST2
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for O95251 (Homo sapiens)
Explore O95251 
Go to UniProtKB:  O95251
PHAROS:  O95251
GTEx:  ENSG00000136504 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95251
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BRD1 protein50Homo sapiensMutation(s): 0 
Gene Names: BRD1
UniProt & NIH Common Fund Data Resources
Find proteins for O95696 (Homo sapiens)
Explore O95696 
Go to UniProtKB:  O95696
PHAROS:  O95696
GTEx:  ENSG00000100425 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95696
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY
A
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.098α = 90
b = 39.565β = 122.88
c = 88.328γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

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)China31800622

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references
  • Version 1.2: 2021-09-29
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary