4ZOQ

Crystal Structure of a Lanthipeptide Protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Applications of the class II lanthipeptide protease LicP for sequence-specific, traceless peptide bond cleavage.

Tang, W.Dong, S.H.Repka, L.M.He, C.Nair, S.K.van der Donk, W.A.

(2015) Chem Sci 6: 6270-6279

  • DOI: https://doi.org/10.1039/c5sc02329g
  • Primary Citation of Related Structures:  
    4ZOQ

  • PubMed Abstract: 

    The final step of lanthipeptide biosynthesis involves the removal of leader peptides by dedicated proteases. In vitro characterization of LicP, a class II LanP protease involved in the biosynthesis of the lantibiotic lichenicidin, revealed a self-cleavage step that removes 100 amino acids from the N-terminus. The 2.35 Å resolution crystal structure provides insights into the active site geometry and substrate specificity, and unveiled an unusual calcium-independent maturation mechanism of a subtilisin family member. LicP processes LicA2 peptides with or without post-translational modifications, but dehydrated and cyclized LicA2 is favored. Investigation of its substrate specificity demonstrated that LicP can serve as an efficient sequence-specific traceless protease and may have great utility in basic research and biotechnology. Encouraged by these findings for LicP, we identified 13 other class II LanPs, ten of which were previously unknown, and suggest that these proteins may serve as a pool of proteases with diverse recognition sequences for general traceless tag removal applications, expanding the current toolbox of proteases.


  • Organizational Affiliation

    Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , 600 S. Mathews Ave. , Urbana , IL 61801 , USA . Email: vddonk@illinois.edu ; ; Tel: +1 217 244 5360.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Intracellular serine protease100Bacillus licheniformisMutation(s): 0 
UniProt
Find proteins for Q65DC7 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46))
Explore Q65DC7 
Go to UniProtKB:  Q65DC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ65DC7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Intracellular serine protease343Bacillus licheniformisMutation(s): 0 
UniProt
Find proteins for Q65DC7 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46))
Explore Q65DC7 
Go to UniProtKB:  Q65DC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ65DC7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.04α = 82.17
b = 112.78β = 89.68
c = 114.77γ = 82.85
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references