7ABB

The truncated structure of the Bottromycin biosynthetic protein SalCYP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Characterization of the Stereoselective P450 Enzyme BotCYP Enables the In Vitro Biosynthesis of the Bottromycin Core Scaffold.

Adam, S.Franz, L.Milhim, M.Bernhardt, R.Kalinina, O.V.Koehnke, J.

(2020) J Am Chem Soc 142: 20560-20565

  • DOI: https://doi.org/10.1021/jacs.0c10361
  • Primary Citation of Related Structures:  
    7ABA, 7ABB

  • PubMed Abstract: 

    Bottromycins are ribosomally synthesized and post-translationally modified peptide natural product antibiotics that are effective against high-priority human pathogens such as methicillin-resistant Staphylococcus aureus . The total synthesis of bottromycins involves at least 17 steps, with a poor overall yield. Here, we report the characterization of the cytochrome P450 enzyme BotCYP from a bottromycin biosynthetic gene cluster. We determined the structure of a close BotCYP homolog and used our data to conduct the first large-scale survey of P450 enzymes associated with RiPP biosynthetic gene clusters. We demonstrate that BotCYP converts a C-terminal thiazoline to a thiazole via an oxidative decarboxylation reaction and provides stereochemical resolution for the pathway. Our data enable the two-pot in vitro production of the bottromycin core scaffold and may allow the rapid generation of bottromycin analogues for compound development.


  • Organizational Affiliation

    Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus Geb. E8.1, 66123 Saarbrücken, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SalCYP truncation388Salinispora tropicaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
B [auth A]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.538α = 90
b = 96.538β = 90
c = 49.999γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
Cootmodel building
XDSdata reduction
SCALAdata scaling
AutoSolphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyKO 4116/3-2

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description