9F5Q | pdb_00009f5q

Crystal structure of selenomethionine-labelled kinetoplastid kinetochore protein KKT23 acetyltransferase domain from Trypanosoma brucei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.227 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

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This is version 1.3 of the entry. See complete history


Literature

The kinetoplastid kinetochore protein KKT23 acetyltransferase is a structural homolog of GCN5 that acetylates the histone H2A C-terminal tail.

Ludzia, P.Ishii, M.Deak, G.Spanos, C.Wilson, M.D.Redfield, C.Akiyoshi, B.

(2025) Structure 33: 123

  • DOI: https://doi.org/10.1016/j.str.2024.10.031
  • Primary Citation of Related Structures:  
    9EVQ, 9EVR, 9F5Q

  • PubMed Abstract: 

    The kinetochore is the macromolecular protein machine that drives chromosome segregation in eukaryotes. In an evolutionarily divergent group of organisms called kinetoplastids, kinetochores are built using a unique set of proteins (KKT1-25 and KKIP1-12). KKT23 is a constitutively localized kinetochore protein containing a C-terminal acetyltransferase domain of unknown function. Here, using X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, we have determined the structure and dynamics of the KKT23 acetyltransferase domain from Trypanosoma brucei and found that it is structurally similar to the GCN5 histone acetyltransferase domain. We find that KKT23 can acetylate the C-terminal tail of histone H2A and that knockdown of KKT23 results in decreased H2A acetylation levels in T. brucei. Finally, we have determined the crystal structure of the N-terminal region of KKT23 and shown that it interacts with KKT22. Our study provides important insights into the structure and function of the unique kinetochore acetyltransferase in trypanosomes.


  • Organizational Affiliation
    • Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acetyltransferase domain-containing protein
A, B
224Trypanosoma brucei brucei TREU927Mutation(s): 0 
Gene Names: Tb10.70.0180
UniProt
Find proteins for Q38AU6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q38AU6 
Go to UniProtKB:  Q38AU6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38AU6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.227 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.299α = 100.54
b = 44.528β = 103.17
c = 68.969γ = 101.33
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
CRANK2phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom210622/Z/18/Z/WT
Boehringer Ingelheim Fonds (BIF)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-28
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary
  • Version 1.2: 2024-12-04
    Changes: Database references
  • Version 1.3: 2025-01-15
    Changes: Database references