7B2B

Solution structure of a non-covalent extended docking domain complex of the Pax NRPS: PaxA T1-CDD/PaxB NDD


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cooperation between a T Domain and a Minimal C-Terminal Docking Domain to Enable Specific Assembly in a Multiprotein NRPS.

Watzel, J.Duchardt-Ferner, E.Sarawi, S.Bode, H.B.Wohnert, J.

(2021) Angew Chem Int Ed Engl 60: 14171-14178

  • DOI: https://doi.org/10.1002/anie.202103498
  • Primary Citation of Related Structures:  
    7B2B, 7B2F

  • PubMed Abstract: 

    Non-ribosomal peptide synthetases (NRPS) produce natural products from amino acid building blocks. They often consist of multiple polypeptide chains which assemble in a specific linear order via specialized N- and C-terminal docking domains ( N/C DDs). Typically, docking domains function independently from other domains in NRPS assembly. Thus, docking domain replacements enable the assembly of "designer" NRPS from proteins that normally do not interact. The multiprotein "peptide-antimicrobial-Xenorhabdus" (PAX) peptide-producing PaxS NRPS is assembled from the three proteins PaxA, PaxB and PaxC. Herein, we show that the small C DD of PaxA cooperates with its preceding thiolation (T 1 ) domain to bind the N DD of PaxB with very high affinity, establishing a structural and thermodynamical basis for this unprecedented docking interaction, and we test its functional importance in vivo in a truncated PaxS assembly line. Similar docking interactions are apparently present in other NRPS systems.


  • Organizational Affiliation

    Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amino acid adenylation domain-containing proteinA [auth B]31Xenorhabdus cabanillasiiMutation(s): 2 
Gene Names: BDD26_3339
UniProt
Find proteins for A0A3D9UGN9 (Xenorhabdus cabanillasii)
Explore A0A3D9UGN9 
Go to UniProtKB:  A0A3D9UGN9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3D9UGN9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide synthetase PaxAB [auth A]104Xenorhabdus cabanillasii JM26Mutation(s): 0 
Gene Names: paxAXCR1_180002
EC: 5.1.1.11
UniProt
Find proteins for W1J0W9 (Xenorhabdus cabanillasii JM26)
Explore W1J0W9 
Go to UniProtKB:  W1J0W9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW1J0W9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Database references, Other