6ZYL | pdb_00006zyl

non-heme monooxygenase; ThoJ apo


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.207 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Non-Heme Monooxygenase ThoJ Catalyzes Thioholgamide beta-Hydroxylation.

Sikandar, A.Lopatniuk, M.Luzhetskyy, A.Koehnke, J.

(2020) ACS Chem Biol 15: 2815-2819

  • DOI: https://doi.org/10.1021/acschembio.0c00637
  • Primary Citation Related Structures: 
    6ZYK, 6ZYL

  • PubMed Abstract: 

    Thioviridamide-like compounds, including thioholgamides, are ribosomally synthesized and post-translationally modified peptide natural products with potent anticancer cell activity and an unprecedented structure. Very little is known about their biosynthesis, and we were intrigued by the β-hydroxy-N1, N3-dimethylhistidinium moiety found in these compounds. Here we report the construction of a heterologous host capable of producing thioholgamide with a 15-fold increased yield compared to the wild-type strain. A knockout of thoJ , encoding a predicted nonheme monooxygenase, shows that ThoJ is essential for thioholgamide β-hydroxylation. The crystal structure of ThoJ exhibits a typical mono/dioxygenase fold with conserved key active-site residues. Yet, ThoJ possesses a very large substrate binding pocket that appears suitable to receive a cyclic thioholgamide intermediate for hydroxylation. The improved production of the heterologous host will enable the dissection of the individual biosynthetic steps involved in biosynthesis of this exciting RiPP family.


  • 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.

Macromolecule Content 

  • Total Structure Weight: 33.73 kDa 
  • Atom Count: 2,247 
  • Modeled Residue Count: 260 
  • Deposited Residue Count: 310 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein310Streptomyces malaysienseMutation(s): 0 
Gene Names: VT52_024865
UniProt
Find proteins for A0A1J4PXK4 (Streptomyces malaysiense)
Explore A0A1J4PXK4 
Go to UniProtKB:  A0A1J4PXK4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1J4PXK4
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on TLA



Download:Ideal Coordinates CCD File
B [auth A]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.207 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.517α = 90
b = 80.517β = 90
c = 130.144γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
SCALAdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyKO4116_3_1

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description