9ISB | pdb_00009isb

Ligand bound AGD of enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 
    0.270 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural basis of the catalytic and allosteric mechanism of bacterial acetyltransferase PatZ.

Park, J.B.Lee, G.Han, Y.Y.Kim, D.Heo, K.Kim, J.Park, J.Yun, H.Lee, C.W.Cho, H.S.Kim, J.S.Steinegger, M.Seok, Y.J.Roh, S.H.

(2025) Proc Natl Acad Sci U S A 122: e2419096122-e2419096122

  • DOI: https://doi.org/10.1073/pnas.2419096122
  • Primary Citation of Related Structures:  
    9ISB, 9ISQ, 9IT0

  • PubMed Abstract: 

    GCN5-related N -acetyltransferases (GNATs) are essential for regulating bacterial metabolism by acetylating specific target proteins. Despite their importance in bacterial physiology, the mechanisms behind their enzymatic and regulatory functions remain poorly understood. In this study, we investigated the structures of Escherichia coli protein acetyltransferase Z (PatZ), a Type I GNAT, and examined its ligand interactions, catalytic mechanism, and allosteric regulation. PatZ functions as a homotetramer, with each subunit comprising a catalytic and a regulatory domain. Our results demonstrate that the regulatory domain is vital for acetyltransferase activity, as it triggers cooperative conformational changes in the catalytic domain and directly aids in the formation of substrate-binding pockets. Additionally, a protein structure-based evolutionary analysis of bacterial GNAT types revealed a distinct regulatory domain pattern across phyla, highlighting its crucial role in responding to cellular energy levels.


  • Organizational Affiliation
    • School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein acetyltransferase
A, B
234Escherichia coli BL21(DE3)Mutation(s): 2 
Gene Names: 
EC: 2.3.1
UniProt
Find proteins for P76594 (Escherichia coli (strain K12))
Explore P76594 
Go to UniProtKB:  P76594
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76594
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free:  0.270 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.05α = 90
b = 76.05β = 90
c = 199.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
pointlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Database references