6T6H

Apo structure of the Bottromycin epimerase BotH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The bottromycin epimerase BotH defines a group of atypical alpha / beta-hydrolase-fold enzymes.

Sikandar, A.Franz, L.Adam, S.Santos-Aberturas, J.Horbal, L.Luzhetskyy, A.Truman, A.W.Kalinina, O.V.Koehnke, J.

(2020) Nat Chem Biol 16: 1013-1018

  • DOI: 10.1038/s41589-020-0569-y
  • Primary Citation of Related Structures:  
    6T6H, 6T6X, 6T6Y, 6T6Z, 6T70

  • PubMed Abstract: 
  • D-amino acids endow peptides with diverse, desirable properties, but the post-translational and site-specific epimerization of L-amino acids into their D-counterparts is rare and chemically challenging. Bottromycins are ribosomally synthesized and post-translationally modified peptides that have overcome this challenge and feature a D-aspartate (D-Asp), which was proposed to arise spontaneously during biosynthesis ...

    D-amino acids endow peptides with diverse, desirable properties, but the post-translational and site-specific epimerization of L-amino acids into their D-counterparts is rare and chemically challenging. Bottromycins are ribosomally synthesized and post-translationally modified peptides that have overcome this challenge and feature a D-aspartate (D-Asp), which was proposed to arise spontaneously during biosynthesis. We have identified the highly unusual α/β-hydrolase (ABH) fold enzyme BotH as a peptide epimerase responsible for the post-translational epimerization of L-Asp to D-Asp during bottromycin biosynthesis. The biochemical characterization of BotH combined with the structures of BotH and the BotH-substrate complex allowed us to propose a mechanism for this reaction. Bioinformatic analyses of BotH homologs show that similar ABH enzymes are found in diverse biosynthetic gene clusters. This places BotH as the founding member of a group of atypical ABH enzymes that may be able to epimerize non-Asp stereocenters across different families of secondary metabolites.


    Related Citations: 
    • Towards automated crystallographic structure refinement with phenix.refine.
      Afonine, P.V., Grosse-Kunstleve, R.W., Echols, N., Headd, J.J., Moriarty, N.W., Mustyakimov, M., Terwilliger, T.C., Urzhumtsev, A., Zwart, P.H., Adams, P.D.
      (2012) Acta Crystallogr D Biol Crystallogr 68: 352

    Organizational Affiliation

    School of Chemistry, University of Glasgow, Glasgow, UK. jesko.koehnke@glasgow.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BotHA310Streptomyces sp. BC16019Mutation(s): 0 
Gene Names: botH
UniProt
Find proteins for K4MHV9 (Streptomyces sp. BC16019)
Explore K4MHV9 
Go to UniProtKB:  K4MHV9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK4MHV9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.683α = 90
b = 80.133β = 90
c = 88.699γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
XDSdata scaling
AutoSolphasing
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyKO 4116/3-1

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2020-08-26
    Changes: Database references