3ZOF | pdb_00003zof

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

• PDB DOI: https://doi.org/10.2210/pdb3ZOF/pdb

• Classification: FMN-BINDING PROTEIN
• Organism(s): Thermus thermophilus HB27
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-21 Released: 2014-05-14 
• Deposition Author(s): Pavkov-Keller, T., Steinkellner, G., Gruber, C.C., Steiner, K., Winkler, C., Schwamberger, O., Schwab, H., Faber, K., Gruber, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.249 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

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

• PubMed: 24954722 
• DOI: https://doi.org/10.1038/ncomms5150
• Primary Citation 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'). 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.62 kDa 
• Atom Count: 3,000 
• Modeled Residue Count: 356 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FLAVOREDOXIN	A, B	178	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72HI0 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72HI0  Go to UniProtKB:  Q72HI0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	D [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
HQE	C [auth A], E [auth B]	benzene-1,4-diol C6 H6 O2 QIGBRXMKCJKVMJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.249 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.524	α = 90
b = 74.618	β = 90
c = 77.743	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-14 
Deposition Author(s): Pavkov-Keller, T., Steinkellner, G., Gruber, C.C., Steiner, K., Winkler, C., Schwamberger, O., Schwab, H., Faber, K., Gruber, K.

Revision History  

• Version 1.0: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2014-07-02
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description