5LHJ

Bottromycin maturation enzyme BotP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and Substrate Recognition of the Bottromycin Maturation Enzyme BotP.

Mann, G.Huo, L.Adam, S.Nardone, B.Vendome, J.Westwood, N.J.Muller, R.Koehnke, J.

(2016) Chembiochem 17: 2286-2292

  • DOI: 10.1002/cbic.201600406
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The bottromycins are a family of highly modified peptide natural products, which display potent antimicrobial activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus. Bottromycins have recently been shown to be ...

    The bottromycins are a family of highly modified peptide natural products, which display potent antimicrobial activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus. Bottromycins have recently been shown to be ribosomally synthesized and post-translationally modified peptides (RiPPs). Unique amongst RiPPs, the precursor peptide BotA contains a C-terminal "follower" sequence, rather than the canonical N-terminal "leader" sequence. We report herein the structural and biochemical characterization of BotP, a leucyl-aminopeptidase-like enzyme from the bottromycin pathway. We demonstrate that BotP is responsible for the removal of the N-terminal methionine from the precursor peptide. Determining the crystal structures of both apo BotP and BotP in complex with Mn 2+ allowed us to model a BotP/substrate complex and to rationalize substrate recognition. Our data represent the first step towards targeted compound modification to unlock the full antibiotic potential of bottro- mycin.


    Organizational Affiliation

    Howard Hughes Medical Institute, Columbia University, New York, NY, 10032, USA.,Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research, Saarland University, Universitätscampus E8 1, 66123, Saarbrücken, Germany.,School of Chemistry and Biomedical Sciences Research Centre, University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, UK.,Roger Adams Laboratory 156, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.,Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research, Saarland University, 66123, Saarbrücken, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Leucine aminopeptidase 2, chloroplastic
A
504Streptomyces sp. BC16019Mutation(s): 0 
Gene Names: botP
Find proteins for K4MHW2 (Streptomyces sp. BC16019)
Go to UniProtKB:  K4MHW2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
A
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.176 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 152.420α = 90.00
b = 152.420β = 90.00
c = 100.896γ = 120.00
Software Package:
Software NamePurpose
xia2data scaling
PHASERphasing
xia2data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-07-12 
  • Released Date: 2016-10-12 
  • Deposition Author(s): Koehnke, J., Mann, G.

Funding OrganizationLocationGrant Number
DFGGermanyKO4116/3-1
Wellcome TrustUnited Kingdom086036

Revision History 

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2016-12-14
    Type: Database references