6F74 | pdb_00006f74

Crystal structure of VAO-type flavoprotein MtVAO713 from Myceliophthora thermophila C1

• PDB DOI: https://doi.org/10.2210/pdb6F74/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Thermothelomyces thermophilus ATCC 42464
• Expression System: Thermothelomyces thermophilus ATCC 42464
• Mutation(s): No 


• Deposited: 2017-12-07 Released: 2018-01-10 
• Deposition Author(s): Rozeboom, H.J., Fraaije, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: other

Literature

Characterization of Two VAO-Type Flavoprotein Oxidases from Myceliophthora thermophila.

Ferrari, A.R., Rozeboom, H.J., Vugts, A.S.C., Koetsier, M.J., Floor, R., Fraaije, M.W.

(2018) Molecules 23

• PubMed: 29303991 
• DOI: https://doi.org/10.3390/molecules23010111
• Primary Citation Related Structures: 
  6F72, 6F73, 6F74


• PubMed Abstract: 
  

  The VAO flavoprotein family consists mostly of oxidoreductases harboring a covalently linked flavin cofactor. The linkage can be either monocovalent at position 8 with a histidine or tyrosine or bicovalent at position 8 with a histidine and at position 6 with a cysteine. Bicovalently bound flavoproteins show a preference for bulkier substrates such as oligosaccharides or secondary metabolites. The genome of the thermophilic fungus Myceliophthora thermophila C1 was found to be rich in genes encoding putative covalent VAO-type flavoproteins. Enzymes from this fungus have the advantage of being rather thermostable and homologous overexpression in M. thermophila C1 is feasible. Recently we discovered a new and VAO-type carbohydrate oxidase from this fungus: xylooligosaccharide oxidase. In this study, two other putative VAO-type oxidases, protein sequence XP_003663615 (MtVAO615) and XP_003665713 (MtVAO713), were expressed in M. thermophila C1, purified and characterized. Enzyme MtVAO615 was found to contain a bicovalently bound FAD, while enzyme MtVAO713 contained a monocovalent histidyl-bound FAD. The crystal structures of both proteins were obtained which revealed atypical active site architectures. It could be experimentally verified that both proteins, when reduced, rapidly react with molecular oxygen, a hallmark of flavoprotein oxidases. A large panel of alcohols, including carbohydrates, steroids and secondary alcohols were tested as potential substrates. For enzyme MtVAO713 low oxidase activity was discovered towards ricinoleic acid.

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Organizational Affiliation: 
• Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands. [e-mail].
Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands. [e-mail].
Dupont Industrial Biosciences, 6709PA Wageningen, The Netherlands. [e-mail].
Dupont Industrial Biosciences, 6709PA Wageningen, The Netherlands. [e-mail].
Dupont Industrial Biosciences, 6709PA Wageningen, The Netherlands. [e-mail].
Molecular Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 267.77 kDa 
• Atom Count: 19,546 
• Modeled Residue Count: 2,287 
• Deposited Residue Count: 2,392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol oxidase	A, B, C, D	598	Thermothelomyces thermophilus ATCC 42464	Mutation(s): 0  Gene Names: MYCTH_2309690
UniProt
Find proteins for G2QMS8 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799)) Explore G2QMS8  Go to UniProtKB:  G2QMS8
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	I [auth A], M [auth B], P [auth C], T [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAG	J [auth A], N [auth B], Q [auth C], U [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	K [auth A], L [auth A], O [auth B], R [auth C], S [auth C], V [auth D], W [auth D], X [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.195	α = 90
b = 108.506	β = 90
c = 135.989	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-10 
Deposition Author(s): Rozeboom, H.J., Fraaije, M.W.

Revision History  

• Version 1.0: 2018-01-10
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-05-01
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary