5U3H | pdb_00005u3h

Solution structure of apo PCP1 from yersiniabactin synthetase

• PDB DOI: https://doi.org/10.2210/pdb5U3H/pdb
• BMRB: 30205

• Classification: LIGASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-02 Released: 2017-02-08 
• Deposition Author(s): Harden, B.J., Frueh, D.P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Molecular Cross-Talk between Nonribosomal Peptide Synthetase Carrier Proteins and Unstructured Linker Regions.

Harden, B.J., Frueh, D.P.

(2017) Chembiochem 18: 629-632

• PubMed: 28120469 
• DOI: https://doi.org/10.1002/cbic.201700030
• Primary Citation Related Structures: 
  5U3H


• PubMed Abstract: 
  

  Nonribosomal peptide synthetases (NRPSs) employ multiple domains separated by linker regions to incorporate substrates into natural products. During synthesis, substrates are covalently tethered to carrier proteins that translocate between catalytic partner domains. The molecular parameters that govern translocation and associated linker remodeling remain unknown. Here, we used NMR to characterize the structure, dynamics, and invisible states of a peptidyl carrier protein flanked by its linkers. We showed that the N-terminal linker stabilizes and interacts with the protein core while modulating dynamics at specific sites involved in post-translational modifications and/or domain interactions. The results detail the molecular communication between peptidyl carrier proteins and their linkers and could guide efforts in engineering NRPSs to obtain new pharmaceuticals.

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Organizational Affiliation: 
• Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.35 kDa 
• Atom Count: 873 
• Modeled Residue Count: 111 
• Deposited Residue Count: 111 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HMWP2 nonribosomal peptide synthetase	A	111	Yersinia pestis	Mutation(s): 0  Gene Names: irp2, y2399, YPO1911
UniProt
Find proteins for A0A2S9PH42 (Yersinia pestis) Explore A0A2S9PH42  Go to UniProtKB:  A0A2S9PH42

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-02-08 
Deposition Author(s): Harden, B.J., Frueh, D.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM 104257

Revision History  

• Version 1.0: 2017-02-08
  Type: Initial release
  
• Version 1.1: 2017-04-19
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2023-06-14
  Changes: Database references, Other
• Version 1.5: 2024-05-15
  Changes: Data collection, Database references