7BIO | pdb_00007bio

Crystal structure of monooxygenase RslO4 from Streptomyces bottropensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 
    0.204 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.183 (Depositor) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7BIO

This is version 1.3 of the entry. See complete history

Literature

Biosynthesis of the Tricyclic Aromatic Type II Polyketide Rishirilide: New Potential Third Ring Oxygenation after Three Cyclization Steps.

Alali, A.Zhang, L.Li, J.Zuo, C.Wassouf, D.Yan, X.Schwarzer, P.Gunther, S.Einsle, O.Bechthold, A.

(2021) Mol Biotechnol 63: 502-514

  • DOI: https://doi.org/10.1007/s12033-021-00314-x
  • Primary Citation Related Structures: 
    7BIO, 7BIP

  • PubMed Abstract: 

    Rishirilides are a group of PKS II secondary metabolites produced by Streptomyces bottropensis Gö C4/4. Biosynthetic studies in the past have elucidated early and late steps of rishirilide biosynthesis. This work is aiming to solve the remaining steps in the rishirilide biosynthesis. Inactivation of the cyclase gene rslC3 in Streptomyces bottropensis resulted in an interruption of rishirilide production. Instead, accumulation of the tricyclic aromatic galvaquinones was observed. Similar results were observed after deletion of rslO4. Closer inspection into RslO4 crystal structure in addition to site-directed mutagenesis and molecular dynamic simulations revealed that RslO4 might be responsible for quinone formation on the third ring. The RslO1 three-dimensional structure shows a high similarity to FMN-dependent luciferase-like monooxygenases such as the epoxy-forming MsnO8 which acts with the flavin reductase MsnO3 in mensacarcin biosynthesis in the same strain. The high sequence similarity between RslO2 and MsnO3 suggests that RslO2 provides RslO1 with reduced FMN to form an epoxide that serves as substrate for RslO5.


  • Organizational Affiliation
    • Institute of Pharmaceutical Biology and Biotechnology, Albert-Ludwigs-Universität, Stefan-Meier-Straße 19, 79104, Freiburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 26.77 kDa 
  • Atom Count: 1,935 
  • Modeled Residue Count: 217 
  • Deposited Residue Count: 228 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Monooxygenase/putative anthronoxygenase
A, B
114Streptomyces bottropensisMutation(s): 0 
Gene Names: rslO4
UniProt
Find proteins for W8QLE0 (Streptomyces bottropensis)
Explore W8QLE0 
Go to UniProtKB:  W8QLE0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW8QLE0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
E [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT

Query on ACT



Download:Ideal Coordinates CCD File
F [auth B],
G [auth B],
H [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
EOH

Query on EOH



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
I [auth B],
J [auth B]
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free:  0.204 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.183 (Depositor) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.681α = 90
b = 83.681β = 90
c = 82.346γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyRTG1976

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-04-07
    Changes: Database references
  • Version 1.2: 2021-05-12
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Database references, Refinement description