8OSV | pdb_00008osv

Structural and functional studies of geldanamycin amide synthase ShGdmF

• PDB DOI: https://doi.org/10.2210/pdb8OSV/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces hygroscopicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-20 Released: 2024-05-01 
• Deposition Author(s): Ewert, W., Zeilinger, C., Kirschning, A., Preller, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 
  0.180 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

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

• PubMed: 40075103 
• DOI: https://doi.org/10.1038/s41467-025-57013-3
• Primary Citation 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.

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Organizational Affiliation: 
• Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany.
Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany.
Center of Biomolecular Drug Research (BMWZ) Leibniz University Hannover, Hannover, Germany.
Institute for Functional Gene Analytics (IFGA), University of Applied Sciences Bonn-Rhein-Sieg, Rheinbach, Germany.
Center of Biomolecular Drug Research (BMWZ) Leibniz University Hannover, Hannover, Germany. [e-mail].
Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany. [e-mail].
Institute for Functional Gene Analytics (IFGA), University of Applied Sciences Bonn-Rhein-Sieg, Rheinbach, Germany. [e-mail].
Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany. [e-mail]-hannover.
Uppsala Biomedical Center (BMC), University Uppsala, Uppsala, Sweden. [e-mail]-hannover.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.2 kDa 
• Atom Count: 2,292 
• Modeled Residue Count: 248 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GdmF	A	263	Streptomyces hygroscopicus	Mutation(s): 0  Gene Names: gdmF
UniProt
Find proteins for Q84G21 (Streptomyces hygroscopicus) Explore Q84G21  Go to UniProtKB:  Q84G21

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W0K (Subject of Investigation/LOI)	B [auth A]	~{N}-(2-sulfanylethyl)ethanamide C4 H9 N O S AXFZADXWLMXITO-UHFFFAOYSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free:  0.180 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.304	α = 90
b = 95.288	β = 90
c = 86.591	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
Aimless	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Ewert, W., Zeilinger, C., Kirschning, A., Preller, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-05-01
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary
• Version 1.2: 2025-04-02
  Changes: Database references