6VGT

Solution NMR structure of enterococcal cytolysin L (CylLL") produced by Enterococcus faecalis


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Structural determinants of macrocyclization in substrate-controlled lanthipeptide biosynthetic pathways.

Bobeica, S.C.Zhu, L.Acedo, J.Z.Tang, W.van der Donk, W.A.

(2020) Chem Sci 11: 12854-12870

  • DOI: https://doi.org/10.1039/d0sc01651a
  • Primary Citation of Related Structures:  
    6VE9, 6VGT, 6VHJ, 6VJQ, 6VLJ, 7JU9, 7JVF

  • PubMed Abstract: 

    Lanthipeptides are characterized by thioether crosslinks formed by post-translational modifications. The cyclization process that favors a single ring pattern over many other possible ring patterns has been the topic of much speculation. Recent studies suggest that for some systems the cyclization pattern and stereochemistry is determined not by the enzyme, but by the sequence of the precursor peptide. However, the factors that govern the outcome of the cyclization process are not understood. This study presents the three-dimensional structures of seven lanthipeptides determined by nuclear magnetic resonance spectroscopy, including five prochlorosins and the two peptides that make up cytolysin, a virulence factor produced by Enterococcus faecalis that is directly linked to human disease. These peptides were chosen because their substrate sequence determines either the ring pattern (prochlorosins) or the stereochemistry of cyclization (cytolysins). We present the structures of prochlorosins 1.1, 2.1, 2.8, 2.10 and 2.11, the first three-dimensional structures of prochlorosins. Our findings provide insights into the molecular determinants of cyclization as well as why some prochlorosins may be better starting points for library generation than others. The structures of the large and small subunits of the enterococcal cytolysin show that these peptides have long helical stretches, a rare observation for lanthipeptides characterized to date. These helices may explain their pore forming activity and suggest that the small subunit may recognize a molecular target followed by recruitment of the large subunit to span the membrane.


  • Organizational Affiliation

    Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana Illinois 61801 USA vddonk@illinois.edu +1-217-244-8533 +1-217-244-5360.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cytolysin L38Enterococcus faecalisMutation(s): 0 
UniProt
Find proteins for H7C7B0 (Enterococcus faecalis (strain ATCC 700802 / V583))
Explore H7C7B0 
Go to UniProtKB:  H7C7B0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH7C7B0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
ABA
Query on ABA
A
L-PEPTIDE LINKINGC4 H9 N O2ALA
DBU
Query on DBU
A
PEPTIDE LINKINGC4 H7 N O2THR
DHA
Query on DHA
A
PEPTIDE LINKINGC3 H5 N O2SER
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • 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 StatesR37GM058822

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 2.0: 2020-09-09
    Type: Coordinate replacement
    Reason: Chirality error
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2021-07-14
    Changes: Database references
  • Version 2.2: 2023-06-14
    Changes: Database references, Other