8A90 | pdb_00008a90

Crystal structure of FrsH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 
    0.264 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8A90

This is version 1.3 of the entry. See complete history

Literature

Adenylation Domain-Guided Recruitment of Trans- Acting Nonheme Monooxygenases in Nonribosomal Peptide Biosynthesis.

Wirtz, D.A.Schneberger, N.Kloppel, S.Richarz, R.Geyer, M.Konig, G.M.Hagelueken, G.Crusemann, M.

(2023) ACS Chem Biol 18: 1748-1759

  • DOI: https://doi.org/10.1021/acschembio.3c00106
  • Primary Citation Related Structures: 
    8A90

  • PubMed Abstract: 

    Nonheme diiron monooxygenases (NHDMs) interact with nonribosomal peptide synthetase (NRPS) assembly lines to install β-hydroxylations at thiolation-domain-bound amino acids during nonribosomal peptide biosynthesis. The high potential of this enzyme family to diversify the products of engineered assembly lines is disproportionate to the currently small knowledge about their structures and mechanisms of substrate recognition. Here, we report the crystal structure of FrsH, the NHDM which catalyzes the β-hydroxylation of l-leucines during biosynthesis of the depsipeptide G protein inhibitor FR900359. Using biophysical approaches, we provide evidence that FrsH interacts with the cognate monomodular NRPS FrsA. By AlphaFold modeling and mutational studies, we detect and examine structural features within the assembly line crucial to recruit FrsH for leucine β-hydroxylation. These are, in contrast to cytochrome-dependent NRPS β-hydroxylases, not located on the thiolation domain, but on the adenylation domain. FrsH can be functionally substituted by homologous enzymes from biosyntheses of the cell-wall-targeting antibiotics lysobactin and hypeptin, indicating that these features are generally applicable to members of the family of trans- acting NHDMs. These insights give important directions for the construction of artificial assembly lines to yield bioactive and chemically complex peptide products.


  • Organizational Affiliation
    • Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany.

Macromolecule Content 

  • Total Structure Weight: 121.2 kDa 
  • Atom Count: 8,535 
  • Modeled Residue Count: 1,058 
  • Deposited Residue Count: 1,062 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Non-heme diiron monooxygenase
A, B
531Chromobacterium vacciniiMutation(s): 0 
Gene Names: frsH
UniProt
Find proteins for A0A7S9SWM2 (Chromobacterium vaccinii)
Explore A0A7S9SWM2 
Go to UniProtKB:  A0A7S9SWM2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7S9SWM2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
C [auth A],
F [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE
(Subject of Investigation/LOI)

Query on FE



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
L [auth B],
M [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
O

Query on O



Download:Ideal Coordinates CCD File
G [auth A],
K [auth B]
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free:  0.264 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.715α = 90
b = 117.715β = 90
c = 234.261γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Database references
  • Version 1.2: 2024-02-07
    Changes: Refinement description
  • Version 1.3: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary