6F97 | pdb_00006f97

Crystal structure of the V465T mutant of 5-(Hydroxymethyl)furfural Oxidase (HMFO)

• PDB DOI: https://doi.org/10.2210/pdb6F97/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Methylovorus sp. MP688
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-12-14 Released: 2018-02-14 
• Deposition Author(s): Pickl, M., Swoboda, A., Romero, E., Winkler, C.K., Binda, C., Mattevi, A., Faber, K., Fraaije, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.231 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Kinetic Resolution of sec-Thiols by Enantioselective Oxidation with Rationally Engineered 5-(Hydroxymethyl)furfural Oxidase.

Pickl, M., Swoboda, A., Romero, E., Winkler, C.K., Binda, C., Mattevi, A., Faber, K., Fraaije, M.W.

(2018) Angew Chem Int Ed Engl 57: 2864-2868

• PubMed: 29384246 
• DOI: https://doi.org/10.1002/anie.201713189
• Primary Citation Related Structures: 
  6F97


• PubMed Abstract: 
  

  Various flavoprotein oxidases were recently shown to oxidize primary thiols. Herein, this reactivity is extended to sec-thiols by using structure-guided engineering of 5-(hydroxymethyl)furfural oxidase (HMFO). The variants obtained were employed for the oxidative kinetic resolution of racemic sec-thiols, thus yielding the corresponding thioketones and nonreacted R-configured thiols with excellent enantioselectivities (E≥200). The engineering strategy applied went beyond the classic approach of replacing bulky amino acid residues with smaller ones, as the active site was additionally enlarged by a newly introduced Thr residue. This residue established a hydrogen-bonding interaction with the substrates, as verified in the crystal structure of the variant. These strategies unlocked HMFO variants for the enantioselective oxidation of a range of sec-thiols.

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Organizational Affiliation: 
• Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria.
Department of Biotechnology, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands.
Austrian Centre of Industrial Biotechnology (ACIB GmbH), c/o Heinrichstrasse 28, 8010, Graz, Austria.
Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 115.73 kDa 
• Atom Count: 8,097 
• Modeled Residue Count: 1,007 
• Deposited Residue Count: 1,062 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-(hydroxymethyl)furfural oxidase	A, B	531	Methylovorus sp. MP688	Mutation(s): 1  Gene Names: MPQ_0130 EC: 1.1.3.47 (PDB Primary Data), 1.8.3 (PDB Primary Data)
UniProt
Find proteins for E4QP00 (Methylovorus sp. (strain MP688)) Explore E4QP00  Go to UniProtKB:  E4QP00

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], D [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.231 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.189	α = 90
b = 122.004	β = 91.63
c = 72.698	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-14 
Deposition Author(s): Pickl, M., Swoboda, A., Romero, E., Winkler, C.K., Binda, C., Mattevi, A., Faber, K., Fraaije, M.W.

Revision History  

• Version 1.0: 2018-02-14
  Type: Initial release
  
• Version 1.1: 2018-02-28
  Changes: Database references
• Version 1.2: 2018-03-14
  Changes: Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description