2N5D | pdb_00002n5d

NMR structure of PKS domains

• PDB DOI: https://doi.org/10.2210/pdb2N5D/pdb
• BMRB: 25706

• Classification: PROTEIN BINDING
• Organism(s): Streptomyces virginiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-14 Released: 2016-03-23 
• Deposition Author(s): Dorival, J., Annaval, T., Risser, F., Collin, S., Roblin, P., Jacob, C., Gruez, A., Chagot, B., Weissman, K.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Characterization of Intersubunit Communication in the Virginiamycin trans-Acyl Transferase Polyketide Synthase.

Dorival, J., Annaval, T., Risser, F., Collin, S., Roblin, P., Jacob, C., Gruez, A., Chagot, B., Weissman, K.J.

(2016) J Am Chem Soc 138: 4155-4167

• PubMed: 26982529 
• DOI: https://doi.org/10.1021/jacs.5b13372
• Primary Citation Related Structures: 
  2N5D


• PubMed Abstract: 
  

  Modular polyketide synthases (PKSs) direct the biosynthesis of clinically valuable secondary metabolites in bacteria. The fidelity of chain growth depends on specific recognition between successive subunits in each assembly line: interactions mediated by C- and N-terminal "docking domains" (DDs). We have identified a new family of DDs in trans-acyl transferase PKSs, exemplified by a matched pair from the virginiamycin (Vir) system. In the absence of C-terminal partner (VirA (C)DD) or a downstream catalytic domain, the N-terminal DD (VirFG (N)DD) exhibits multiple characteristics of an intrinsically disordered protein. Fusion of the two docking domains results in a stable fold for VirFG (N)DD and an overall protein-protein complex of unique topology whose structure we support by site-directed mutagenesis. Furthermore, using small-angle X-ray scattering (SAXS), the positions of the flanking acyl carrier protein and ketosynthase domains have been identified, allowing modeling of the complete intersubunit interface.

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Organizational Affiliation: 
• UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine , Campus Biologie Santé, 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France.
Synchrotron SOLEIL, L'Orme des Merisiers , Saint-Aubin BP 48, 91192 Gif-sur-Yvette CEDEX, France.
UR1268 Biopolymères, Interactions Assemblages (BIA), INRA , Rue de la Géraudière BP 71627, 44316 Nantes CEDEX 3, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.46 kDa 
• Atom Count: 593 
• Modeled Residue Count: 84 
• Deposited Residue Count: 84 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
fusion protein of two PKS domains	A	84	Streptomyces virginiae	Mutation(s): 0  Gene Names: virA
UniProt
Find proteins for A4PHN0 (Streptomyces virginiae) Explore A4PHN0  Go to UniProtKB:  A4PHN0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Dorival, J., Annaval, T., Risser, F., Collin, S., Roblin, P., Jacob, C., Gruez, A., Chagot, B., Weissman, K.J.

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 1.1: 2016-05-11
  Changes: Database references
• Version 1.2: 2016-12-07
  Changes: Database references
• Version 1.3: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.4: 2024-05-15
  Changes: Data collection, Database references