Solution NMR structural bundle of the first cyclization domain from yersiniabactin synthetase (Cy1) impacted by dynamics

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Global protein dynamics as communication sensors in peptide synthetase domains.

Mishra, S.H.Kancherla, A.K.Marincin, K.A.Bouvignies, G.Nerli, S.Sgourakis, N.Dowling, D.P.Frueh, D.P.

(2022) Sci Adv 8: eabn6549-eabn6549

  • DOI: https://doi.org/10.1126/sciadv.abn6549
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Biological activity is governed by the timely redistribution of molecular interactions, and static structural snapshots often appear insufficient to provide the molecular determinants that choreograph communication. This conundrum applies to multidomain enzymatic systems called nonribosomal peptide synthetases (NRPSs), which assemble simple substrates into complex metabolites, where a dynamic domain organization challenges rational design to produce new pharmaceuticals. Using a nuclear magnetic resonance (NMR) atomic-level readout of biochemical transformations, we demonstrate that global structural fluctuations help promote substrate-dependent communication and allosteric responses, and impeding these global dynamics by a point-site mutation hampers allostery and molecular recognition. Our results establish global structural dynamics as sensors of molecular events that can remodel domain interactions, and they provide new perspectives on mechanisms of allostery, protein communication, and NRPS synthesis.

  • Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HMWP2 nonribosomal peptide synthetase453Yersinia pestisMutation(s): 0 
Gene Names: irp2y2399G4D66_03140NCTC144_00432
EC: 6.3.2
Find proteins for A0A2S9PH42 (Yersinia pestis)
Explore A0A2S9PH42 
Go to UniProtKB:  A0A2S9PH42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2S9PH42
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM104257

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2022-07-27
    Changes: Database references
  • Version 1.2: 2022-08-03
    Changes: Database references
  • Version 1.3: 2023-06-14
    Changes: Other
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references