8CAR

Discovery of the lanthipeptide Curvocidin and structural insights into its trifunctional synthetase CuvL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.298 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Discovery of the Lanthipeptide Curvocidin and Structural Insights into its Trifunctional Synthetase CuvL.

Sigurdsson, A.Martins, B.M.Duttmann, S.A.Jasyk, M.Dimos-Rohl, B.Schopf, F.Gemander, M.Knittel, C.H.Schnegotzki, R.Schmid, B.Kosol, S.Pommerening, L.Gonzales-Viegaz, M.Seidel, M.Hugelland, M.Leimkuhler, S.Dobbek, H.Mainz, A.Sussmuth, R.D.

(2023) Angew Chem Int Ed Engl 62: e202302490-e202302490

  • DOI: https://doi.org/10.1002/anie.202302490
  • Primary Citation of Related Structures:  
    8CAR, 8CAV

  • PubMed Abstract: 

    Lanthipeptides are ribosomally-synthesized natural products from bacteria featuring stable thioether-crosslinks and various bioactivities. Herein, we report on a new clade of tricyclic class-IV lanthipeptides with curvocidin from Thermomonospora curvata as its first representative. We obtained crystal structures of the corresponding lanthipeptide synthetase CuvL that showed a circular arrangement of its kinase, lyase and cyclase domains, forming a central reaction chamber for the iterative substrate processing involving nine catalytic steps. The combination of experimental data and artificial intelligence-based structural models identified the N-terminal subdomain of the kinase domain as the primary site of substrate recruitment. The ribosomal precursor peptide of curvocidin employs an amphipathic α-helix in its leader region as an anchor to CuvL, while its substrate core shuttles within the central reaction chamber. Our study thus reveals general principles of domain organization and substrate recruitment of class-IV and class-III lanthipeptide synthetases.


  • Organizational Affiliation

    Fakultät II-Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine protein kinase865Thermomonospora curvataMutation(s): 0 
Gene Names: Tcur_0376
UniProt
Find proteins for D1A2F7 (Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / KCTC 9072 / NBRC 15933 / NCIMB 10081 / Henssen B9))
Explore D1A2F7 
Go to UniProtKB:  D1A2F7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1A2F7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.298 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.651α = 90
b = 135.651β = 90
c = 335.436γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoXDSdata processing
SHELXphasing
Cootmodel building
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyEXC 2008 390540038

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection