9CBS | pdb_00009cbs

Crystal structure of Chaetomium thermophilum Gcn2 HisRS-like domain, catalytic domain

  • Classification: TRANSLATION
  • Organism(s): Thermochaetoides thermophila
  • Expression System: Escherichia coli B
  • Mutation(s): No 

  • Deposited: 2024-06-20 Released: 2024-08-21 
  • Deposition Author(s): Zhang, J.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 9CBS

This is version 1.4 of the entry. See complete history

Literature

Gcn2 structurally mimics and functionally repurposes the HisRS enzyme for the integrated stress response.

Bou-Nader, C.Gaikwad, S.Bahmanjah, S.Zhang, F.Hinnebusch, A.G.Zhang, J.

(2024) Proc Natl Acad Sci U S A 121: e2409628121-e2409628121

  • DOI: https://doi.org/10.1073/pnas.2409628121
  • Primary Citation Related Structures: 
    9C9Q, 9C9R, 9CBS

  • PubMed Abstract: 

    Protein kinase Gcn2 attenuates protein synthesis in response to amino acid starvation while stimulating translation of a transcriptional activator of amino acid biosynthesis. Gcn2 activation requires a domain related to histidyl-tRNA synthetase (HisRS), the enzyme that aminoacylates tRNA His . While evidence suggests that deacylated tRNA binds the HisRS domain for kinase activation, ribosomal P-stalk proteins have been implicated as alternative activating ligands on stalled ribosomes. We report crystal structures of the HisRS domain of Chaetomium thermophilum Gcn2 that reveal structural mimicry of both catalytic (CD) and anticodon-binding (ABD) domains, which in authentic HisRS bind the acceptor stem and anticodon loop of tRNA His . Elements for forming histidyl adenylate and aminoacylation are lacking, suggesting that Gcn2 HisRS was repurposed for kinase activation, consistent with mutations in the CD that dysregulate yeast Gcn2 function. Substituting conserved ABD residues well positioned to contact the anticodon loop or that form a conserved ABD-CD interface impairs Gcn2 function in starved cells. Mimicry in Gcn2 HisRS of two highly conserved structural domains for binding both ends of tRNA-each crucial for Gcn2 function-supports that deacylated tRNAs activate Gcn2 and exemplifies how a metabolic enzyme is repurposed to host new local structures and sequences that confer a novel regulatory function.


  • Organizational Affiliation
    • Laboratory of Molecular Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.

Macromolecule Content 

  • Total Structure Weight: 150.43 kDa 
  • Atom Count: 10,191 
  • Modeled Residue Count: 1,283 
  • Deposited Residue Count: 1,320 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
non-specific serine/threonine protein kinase
A, B, C, D
330Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0028700
EC: 2.7.11.1
UniProt
Find proteins for G0S7T0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S7T0 
Go to UniProtKB:  G0S7T0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S7T0
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.091α = 90
b = 132.554β = 90
c = 138.961γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2024-08-21 
  • Deposition Author(s): Zhang, J.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-21
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Database references
  • Version 1.2: 2024-09-11
    Changes: Database references
  • Version 1.3: 2024-09-18
    Changes: Database references
  • Version 1.4: 2024-10-23
    Changes: Structure summary