3ZOF

Crystal structure of FMN-binding protein (YP_005476) from Thermus thermophilus with bound benzene-1,4-diol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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:  
    3ZOC, 3ZOD, 3ZOE, 3ZOF, 3ZOG, 3ZOH

  • 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 enzymes based on three-dimensional constellations of functional groups in active sites ('catalophores') ...

    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 Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FLAVOREDOXINA, B178Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_C1507
UniProt
Find proteins for Q72HI0 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72HI0 
Go to UniProtKB:  Q72HI0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72HI0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
HQE
Query on HQE

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
benzene-1,4-diol
C6 H6 O2
QIGBRXMKCJKVMJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.524α = 90
b = 74.618β = 90
c = 77.743γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references