6B5W | pdb_00006b5w

Benenodin-1-dC5, state 2


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 6B5W

This is version 1.3 of the entry. See complete history

Literature

Lasso Peptide Benenodin-1 Is a Thermally Actuated [1]Rotaxane Switch

Zong, C.Wu, M.J.Qin, J.Z.Link, A.J.

(2017) J Am Chem Soc 139 (30): 10403-10409

  • DOI: https://doi.org/10.1021/jacs.7b04830
  • Primary Citation Related Structures: 
    5TJ1, 6B5W

  • PubMed Abstract: 

    Mechanically interlocked molecules that change their conformation in response to stimuli have been developed by synthetic chemists as building blocks for molecular machines. Here we describe a natural product, the lasso peptide benenodin-1, which exhibits conformational switching between two distinct threaded conformers upon actuation by heat. We have determined the structures of both conformers and have characterized the kinetics and energetics of the conformational switch. Single amino acid substitutions to benenodin-1 generate peptides that are biased to a single conformer, showing that the switching behavior is potentially an evolvable trait in these peptides. Lasso peptides such as benenodin-1 can be recognized and cleaved by enzymes called lasso peptide isopeptidases. We show that only the native conformer of benenodin-1 is cleaved by its cognate isopeptidase. Thus, thermally induced conformational switching of benenodin-1 may also be relevant to the biological function of these molecules.


  • Organizational Affiliation
    • Department of Chemistry, ‡Department of Molecular Biology, and §Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States.

Macromolecule Content 

  • Total Structure Weight: 2.03 kDa 
  • Atom Count: 141 
  • Modeled Residue Count: 19 
  • Deposited Residue Count: 19 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Benenodin-119Asticcacaulis benevestitus DSM 16100 = ATCC BAA-896Mutation(s): 0 
Gene Names: ABENE_08090
UniProt
Find proteins for V4RMX4 (Asticcacaulis benevestitus DSM 16100 = ATCC BAA-896)
Explore V4RMX4 
Go to UniProtKB:  V4RMX4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV4RMX4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM107036

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2023-06-14
    Changes: Database references, Other
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Structure summary