6EWU

Solution Structure of Rhabdopeptide NRPS Docking Domain Kj12C-NDD


Experimental Data Snapshot

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure-based redesign of docking domain interactions modulates the product spectrum of a rhabdopeptide-synthesizing NRPS.

Hacker, C.Cai, X.Kegler, C.Zhao, L.Weickhmann, A.K.Wurm, J.P.Bode, H.B.Wohnert, J.

(2018) Nat Commun 9: 4366-4366

  • DOI: https://doi.org/10.1038/s41467-018-06712-1
  • Primary Citation of Related Structures:  
    6EWS, 6EWT, 6EWU, 6EWV

  • PubMed Abstract: 

    Several peptides in clinical use are derived from non-ribosomal peptide synthetases (NRPS). In these systems multiple NRPS subunits interact with each other in a specific linear order mediated by specific docking domains (DDs), whose structures are not known yet, to synthesize well-defined peptide products. In contrast to classical NRPSs, single-module NRPS subunits responsible for the generation of rhabdopeptide/xenortide-like peptides (RXPs) can act in different order depending on subunit stoichiometry thereby producing peptide libraries. To define the basis for their unusual interaction patterns, we determine the structures of all N-terminal DDs ( N DDs) as well as of an N DD- C DD complex and characterize all putative DD interactions thermodynamically for such a system. Key amino acid residues for DD interactions are identified that upon their exchange change the DD affinity and result in predictable changes in peptide production. Recognition rules for DD interactions are identified that also operate in other megasynthase complexes.


  • Organizational Affiliation

    Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NRPS Kj12C-NDD63Xenorhabdus stockiaeMutation(s): 0 
UniProt
Find proteins for A0A173DW42 (Xenorhabdus stockiae)
Explore A0A173DW42 
Go to UniProtKB:  A0A173DW42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A173DW42
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 100 
  • 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: 2018-10-31
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection
  • Version 1.2: 2021-06-23
    Changes: Data collection
  • Version 1.3: 2024-06-19
    Changes: Data collection, Database references