7Z94

Crystal structure of Variovorax paradoxus indole monooxygenase (VpIndA1) in complex with indole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural and Mechanistic Studies on Substrate and Stereoselectivity of the Indole Monooxygenase VpIndA1: New Avenues for Biocatalytic Epoxidations and Sulfoxidations.

Kratky, J.Eggerichs, D.Heine, T.Hofmann, S.Sowa, P.Weisse, R.H.Tischler, D.Strater, N.

(2023) Angew Chem Int Ed Engl 62: e202300657-e202300657

  • DOI: https://doi.org/10.1002/anie.202300657
  • Primary Citation of Related Structures:  
    7Z4X, 7Z94, 7Z97, 7Z98, 7Z99, 7ZCA

  • PubMed Abstract: 

    Flavoprotein monooxygenases are a versatile group of enzymes for biocatalytic transformations. Among these, group E monooxygenases (GEMs) catalyze enantioselective epoxidation and sulfoxidation reactions. Here, we describe the crystal structure of an indole monooxygenase from the bacterium Variovorax paradoxus EPS, a GEM designated as VpIndA1. Complex structures with substrates reveal productive binding modes that, in conjunction with force-field calculations and rapid mixing kinetics, reveal the structural basis of substrate and stereoselectivity. Structure-based redesign of the substrate cavity yielded variants with new substrate selectivity (for sulfoxidation of benzyl phenyl sulfide) or with greatly enhanced stereoselectivity (from 35.1 % to 99.8 % ee for production of (1S,2R)-indene oxide). This first determination of the substrate binding mode of GEMs combined with structure-function relationships opens the door for structure-based design of these powerful biocatalysts.


  • Organizational Affiliation

    Institute of Bioanalytical Chemistry, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative dehydrogenase/oxygenase subunit (Flavoprotein)433Variovorax paradoxus EPSMutation(s): 0 
Gene Names: Varpa_4903
UniProt
Find proteins for E6V140 (Variovorax paradoxus (strain EPS))
Explore E6V140 
Go to UniProtKB:  E6V140
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE6V140
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
IND (Subject of Investigation/LOI)
Query on IND

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C [auth A]
D [auth A]
E [auth A]
H [auth A]
I [auth A]
C [auth A],
D [auth A],
E [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
INDOLE
C8 H7 N
SIKJAQJRHWYJAI-UHFFFAOYSA-N
SO4
Query on SO4

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F [auth A],
M [auth A],
N [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS
Query on DMS

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G [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NA
Query on NA

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L [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.938α = 90
b = 93.938β = 90
c = 110.867γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description