7ULF

l-glutamate/GTP complex of F420-gamma glutamyl ligase (CofE) from Archaeoglobus fulgidus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 
    0.212 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Poly-gamma-glutamylation of biomolecules.

Bashiri, G.Bulloch, E.M.M.Bramley, W.R.Davidson, M.Stuteley, S.M.Young, P.G.Harris, P.W.R.Naqvi, M.S.H.Middleditch, M.J.Schmitz, M.Chang, W.C.Baker, E.N.Squire, C.J.

(2024) Nat Commun 15: 1310-1310

  • DOI: https://doi.org/10.1038/s41467-024-45632-1
  • Primary Citation of Related Structures:  
    7ULD, 7ULE, 7ULF, 8G8P

  • PubMed Abstract: 

    Poly-γ-glutamate tails are a distinctive feature of archaeal, bacterial, and eukaryotic cofactors, including the folates and F 420 . Despite decades of research, key mechanistic questions remain as to how enzymes successively add glutamates to poly-γ-glutamate chains while maintaining cofactor specificity. Here, we show how poly-γ-glutamylation of folate and F 420 by folylpolyglutamate synthases and γ-glutamyl ligases, non-homologous enzymes, occurs via processive addition of L-glutamate onto growing γ-glutamyl chain termini. We further reveal structural snapshots of the archaeal γ-glutamyl ligase (CofE) in action, crucially including a bulged-chain product that shows how the cofactor is retained while successive glutamates are added to the chain terminus. This bulging substrate model of processive poly-γ-glutamylation by terminal extension is arguably ubiquitous in such biopolymerisation reactions, including addition to folates, and demonstrates convergent evolution in diverse species from archaea to humans.


  • Organizational Affiliation

    School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand. g.bashiri@auckland.ac.nz.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coenzyme F420:L-glutamate ligase251Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: cofEAF_2256
EC: 6.3.2.31 (PDB Primary Data), 6.3.2.34 (PDB Primary Data)
UniProt
Find proteins for O28028 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O28028 
Go to UniProtKB:  O28028
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO28028
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free:  0.212 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.71α = 90
b = 68.71β = 90
c = 92.45γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GTPClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Database references, Structure summary