8F91 | pdb_00008f91

OxyB, a cytochrome P450 involved in keratinimicin biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.283 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.242 (Depositor) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Robust Chemoenzymatic Synthesis of Keratinimicin Aglycone Analogues Facilitated by the Structure and Selectivity of OxyB.

Hauser, N.Ireland, K.A.Chioti, V.T.Forneris, C.C.Davis, K.M.Seyedsayamdost, M.R.

(2023) ACS Chem Biol 18: 1473-1479

  • DOI: https://doi.org/10.1021/acschembio.3c00192
  • Primary Citation Related Structures: 
    8F91

  • PubMed Abstract: 

    The emergence of multidrug-resistant pathogens poses a threat to public health and requires new antimicrobial agents. As the archetypal glycopeptide antibiotic (GPA) used against drug-resistant Gram-positive pathogens, vancomycin provides a promising starting point. Peripheral alterations to the vancomycin scaffold have enabled the development of new GPAs. However, modifying the core remains challenging due to the size and complexity of this compound family. The recent successful chemoenzymatic synthesis of vancomycin suggests that such an approach can be broadly applied. Herein, we describe the expansion of chemoenzymatic strategies to encompass type II GPAs bearing all aromatic amino acids through the production of the aglycone analogue of keratinimicin A, a GPA that is 5-fold more potent than vancomycin against Clostridioides difficile . In the course of these studies, we found that the cytochrome P450 enzyme OxyB ker boasts both broad substrate tolerance and remarkable selectivity in the formation of the first aryl ether cross-link on the linear peptide precursors. The X-ray crystal structure of OxyB ker , determined to 2.8 Å, points to structural features that may contribute to these properties. Our results set the stage for using OxyB ker broadly as a biocatalyst toward the chemoenzymatic synthesis of diverse GPA analogues.


  • Organizational Affiliation
    • Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.

Macromolecule Content 

  • Total Structure Weight: 47.04 kDa 
  • Atom Count: 2,610 
  • Modeled Residue Count: 366 
  • Deposited Residue Count: 419 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
OxyB419Amycolatopsis keratiniphilaMutation(s): 0 
UniProt
Find proteins for A0A385L3H2 (Amycolatopsis keratiniphila)
Explore A0A385L3H2 
Go to UniProtKB:  A0A385L3H2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A385L3H2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SMC
Query on SMC
A
L-PEPTIDE LINKINGC4 H9 N O2 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.283 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.242 (Depositor) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.05α = 90
b = 179.05β = 90
c = 179.05γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/John E. Fogarty International Center (NIH/FIC)United StatesGM129460
National Science Foundation (NSF, United States)United States1937971

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary