5GK9

Crystal structure of human HBO1 in complex with BRPF2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.260 

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Literature

Structural and mechanistic insights into regulation of HBO1 histone acetyltransferase activity by BRPF2.

Tao, Y.Zhong, C.Zhu, J.Xu, S.Ding, J.

(2017) Nucleic Acids Res 45: 5707-5719

  • DOI: 10.1093/nar/gkx142
  • Primary Citation of Related Structures:  
    5GK9

  • PubMed Abstract: 
  • HBO1, a member of the MYST family of histone acetyltransferases (HATs), is required for global acetylation of histone H3K14 and embryonic development. It functions as a catalytic subunit in multisubunit complexes comprising a BRPF1/2/3 or JADE1/2/3 scaffold protein, and two accessory proteins ...

    HBO1, a member of the MYST family of histone acetyltransferases (HATs), is required for global acetylation of histone H3K14 and embryonic development. It functions as a catalytic subunit in multisubunit complexes comprising a BRPF1/2/3 or JADE1/2/3 scaffold protein, and two accessory proteins. BRPF2 has been shown to be important for the HAT activity of HBO1 toward H3K14. Here we demonstrated that BRPF2 can regulate the HAT activity of HBO1 toward free H3 and H4, and nucleosomal H3. Particularly, a short N-terminal region of BRPF2 is sufficient for binding to HBO1 and can potentiate its activity toward H3K14. The crystal structure of the HBO1 MYST domain in complex with this segment of BRPF2 together with the biochemical and cell biological data revealed the key residues responsible for the HBO1-BRPF2 interaction. Our structural and functional data together indicate that the N-terminal region of BRPF2 plays an important role in the binding of HBO1 and a minor role in the binding of nucleosomes, which provide new mechanistic insights into the regulation of the HAT activity of HBO1 by BRPF2.


    Organizational Affiliation

    Collaborative Innovation Center for Genetics and Development, Fudan University, 2005 Songhu Road, Shanghai 200438, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone acetyltransferase KAT7A276Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95251
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BRD1 proteinB50Homo sapiensMutation(s): 0 
Gene Names: BRD1BRLBRPF2
UniProt & NIH Common Fund Data Resources
Find proteins for O95696 (Homo sapiens)
Explore O95696 
Go to UniProtKB:  O95696
PHAROS:  O95696
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95696
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACO
Query on ACO

Download Ideal Coordinates CCD File 
D [auth A]ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.260 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.47α = 90
b = 39.321β = 122.1
c = 87.666γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references