5LHK

Bottromycin maturation enzyme BotP in complex with Mn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.147 

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 Mn2+ 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

    School of Chemistry and Biomedical Sciences Research Centre, University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, UK.




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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

Download SDF File 
Download CCD File 
A
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.147 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 151.510α = 90.00
b = 151.510β = 90.00
c = 101.190γ = 120.00
Software Package:
Software NamePurpose
xia2data reduction
REFMACrefinement
xia2data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-07-12 
  • Released Date: 2016-10-05 
  • Deposition Author(s): Koehnke, J., Adam, S.

Funding OrganizationLocationGrant Number
DFGGermanyKO4116/3-1

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-12-14
    Type: Database references