8CAR | pdb_00008car

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

• PDB DOI: https://doi.org/10.2210/pdb8CAR/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Thermomonospora curvata
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-24 Released: 2023-06-14 
• Deposition Author(s): Martins, B.M., Sigurdsson, A., Duettmann, A.A., Jasyk, M., Dimos-Roehl, B., Schoepf, F., Gemander, M., Knittel, C.H., Schegotzki, R., Schmid, B., Kosol, S., Pommerening, L., Gonzalez-Viegas, M., Seidel, M., Huegelland, M., Leimkuehler, S., Dobbek, H., Mainz, A., Suessmuth, R.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 
  0.337 (Depositor), 0.337 (DCC) 
• R-Value Work: 
  0.297 (Depositor), 0.297 (DCC) 
• R-Value Observed: 
  0.298 (Depositor) 

Starting Model: other

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

• PubMed: 37014271 
• DOI: https://doi.org/10.1002/anie.202302490
• Primary Citation 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.

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Organizational Affiliation: 
• Fakultät II-Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany.
Institut für Biologie-Strukturbiologie/Biochemie, Humboldt Universität zu Berlin, Philippstraße 13, 10115, Berlin, Germany.
Institut für Biochemie und Biologie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 93.59 kDa 
• Atom Count: 6,318 
• Modeled Residue Count: 830 
• Deposited Residue Count: 865 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine protein kinase	A	865	Thermomonospora curvata	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NO3	C [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free:  0.337 (Depositor), 0.337 (DCC) 
• R-Value Work:  0.297 (Depositor), 0.297 (DCC) 
• R-Value Observed: 0.298 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.651	α = 90
b = 135.651	β = 90
c = 335.436	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoXDS	data processing
SHELX	phasing
Coot	model building
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Martins, B.M., Sigurdsson, A., Duettmann, A.A., Jasyk, M., Dimos-Roehl, B., Schoepf, F., Gemander, M., Knittel, C.H., Schegotzki, R., Schmid, B., Kosol, S., Pommerening, L., Gonzalez-Viegas, M., Seidel, M., Huegelland, M., Leimkuehler, S., Dobbek, H., Mainz, A., Suessmuth, R.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	EXC 2008 390540038

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection
• Version 2.1: 2024-11-20
  Changes: Structure summary