8OOM | pdb_00008oom

Structural and functional studies of geldanamycin amide synthase ShGdmF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 
    0.196 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure and function of the geldanamycin amide synthase from Streptomyces hygroscopicus.

Ewert, W.Bartens, C.Ongouta, J.Holmes, M.Heutling, A.Kishore, A.Urbansky, T.Zeilinger, C.Preller, M.Kirschning, A.

(2025) Nat Commun 16: 2464-2464

  • DOI: https://doi.org/10.1038/s41467-025-57013-3
  • Primary Citation of Related Structures:  
    8BTM, 8OOM, 8OSV, 8OSZ

  • PubMed Abstract: 

    Amide synthases catalyze the formation of macrolactam rings from aniline-containing polyketide-derived seco-acids as found in the important class of ansamycin antibiotics. One of these amide synthases is the geldanamycin amide synthase GdmF, which we recombinantly expressed, purified and studied in detail both functionally as well as structurally. Here we show that purified GdmF catalyzes the amide formation using synthetically derived substrates. The atomic structures of the ligand-free enzyme and in complex with simplified substrates reveal distinct structural features of the substrate binding site and a putative role of the flexible interdomain region for the catalysis reaction.


  • Organizational Affiliation

    Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GdmF263Streptomyces hygroscopicusMutation(s): 0 
Gene Names: gdmF
UniProt
Find proteins for Q84G21 (Streptomyces hygroscopicus)
Explore Q84G21 
Go to UniProtKB:  Q84G21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84G21
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free:  0.196 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.874α = 90
b = 96.184β = 90
c = 86.754γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
Cootmodel building
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Structure summary
  • Version 1.2: 2025-04-02
    Changes: Database references