3ZOD

Crystal structure of FMN-binding protein (NP_142786.1) from Pyrococcus horikoshii with bound benzene-1,4-diol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification of Promiscuous Ene-Reductase Activity by Mining Structural Databases Using Active Site Constellations.

Steinkellner, G.Gruber, C.C.Pavkov-Keller, T.Binter, A.Steiner, K.Winkler, C.Lyskowski, A.Schwamberger, O.Oberer, M.Schwab, H.Faber, K.Macheroux, P.Gruber, K.

(2014) Nat.Commun. 5: 4150

  • DOI: 10.1038/ncomms5150
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. Here we describe a structural bioinformatic method for predicting catalytic activities of enzy ...

    The exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. Here we describe a structural bioinformatic method for predicting catalytic activities of enzymes based on three-dimensional constellations of functional groups in active sites ('catalophores'). As a proof-of-concept we identify two enzymes with predicted promiscuous ene-reductase activity (reduction of activated C-C double bonds) and compare them with known ene-reductases, that is, members of the Old Yellow Enzyme family. Despite completely different amino acid sequences, overall structures and protein folds, high-resolution crystal structures reveal equivalent binding modes of typical Old Yellow Enzyme substrates and ligands. Biochemical and biocatalytic data show that the two enzymes indeed possess ene-reductase activity and reveal an inverted stereopreference compared with Old Yellow Enzymes for some substrates. This method could thus be a tool for the identification of viable starting points for the development and engineering of novel biocatalysts.


    Organizational Affiliation

    1] ACIB GmbH, Petersgasse 14, 8010 Graz, Austria [2] Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria.,Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria.,1] ACIB GmbH, Petersgasse 14, 8010 Graz, Austria [2] Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria.,Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria.,ACIB GmbH, Petersgasse 14, 8010 Graz, Austria.,1] ACIB GmbH, Petersgasse 14, 8010 Graz, Austria [2] Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria.,1] ACIB GmbH, Petersgasse 14, 8010 Graz, Austria [2].,1] ACIB GmbH, Petersgasse 14, 8010 Graz, Austria [2] Institute of Biochemistry, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FMN-BINDING PROTEIN
A
191Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Mutation(s): 0 
Find proteins for O58586 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O58586
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
HQE
Query on HQE

Download SDF File 
Download CCD File 
A
benzene-1,4-diol
C6 H6 O2
QIGBRXMKCJKVMJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.213 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 46.395α = 90.00
b = 46.395β = 90.00
c = 269.637γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-07-02
    Type: Database references
  • Version 1.2: 2019-03-06
    Type: Data collection, Experimental preparation, Other