5H84 | pdb_00005h84

Human Gcn5 bound to propionyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.195 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Structural basis for acyl-group discrimination by human Gcn5L2.

Ringel, A.E.Wolberger, C.

(2016) Acta Crystallogr D Struct Biol 72: 841-848

  • DOI: https://doi.org/10.1107/S2059798316007907
  • Primary Citation Related Structures: 
    5H84, 5H86

  • PubMed Abstract: 

    Gcn5 is a conserved acetyltransferase that regulates transcription by acetylating the N-terminal tails of histones. Motivated by recent studies identifying a chemically diverse array of lysine acyl modifications in vivo, the acyl-chain specificity of the acetyltransferase human Gcn5 (Gcn5L2) was examined. Whereas Gcn5L2 robustly catalyzes lysine acetylation, the acyltransferase activity of Gcn5L2 becomes progressively weaker with increasing acyl-chain length. To understand how Gcn5 discriminates between different acyl-CoA molecules, structures of the catalytic domain of human Gcn5L2 bound to propionyl-CoA and butyryl-CoA were determined. Although the active site of Gcn5L2 can accommodate propionyl-CoA and butyryl-CoA without major structural rearrangements, butyryl-CoA adopts a conformation incompatible with catalysis that obstructs the path of the incoming lysine residue and acts as a competitive inhibitor of Gcn5L2 versus acetyl-CoA. These structures demonstrate how Gcn5L2 discriminates between acyl-chain donors and explain why Gcn5L2 has weak activity for acyl moieties that are larger than an acetyl group.


  • Organizational Affiliation
    • Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA.

Macromolecule Content 

  • Total Structure Weight: 20.48 kDa 
  • Atom Count: 1,507 
  • Modeled Residue Count: 164 
  • Deposited Residue Count: 168 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone acetyltransferase KAT2A168Homo sapiensMutation(s): 0 
Gene Names: KAT2AGCN5GCN5L2HGCN5
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92830 (Homo sapiens)
Explore Q92830 
Go to UniProtKB:  Q92830
PHAROS:  Q92830
GTEx:  ENSG00000108773 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92830
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.195 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.087α = 90
b = 38.087β = 90
c = 187.057γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM098522

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-07-13
    Changes: Database references
  • Version 1.2: 2016-07-20
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description