6O9N | pdb_00006o9n

Structural insights on a new fungal aryl-alcohol oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.251 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history

Literature

Enzymatic versatility and thermostability of a new aryl-alcohol oxidase from Thermothelomyces thermophilus M77.

Kadowaki, M.A.S.Higasi, P.M.R.de Godoy, M.O.de Araujo, E.A.Godoy, A.S.Prade, R.A.Polikarpov, I.

(2020) Biochim Biophys Acta Gen Subj 1864: 129681-129681

  • DOI: https://doi.org/10.1016/j.bbagen.2020.129681
  • Primary Citation Related Structures: 
    6O9N

  • PubMed Abstract: 

    Background Fungal aryl-alcohol oxidases (AAOx) are extracellular flavoenzymes that belong to glucose-methanol-choline oxidoreductase family and are responsible for the selective conversion of primary aromatic alcohols into aldehydes and aromatic aldehydes to their corresponding acids, with concomitant production of hydrogen peroxide (H 2 O 2 ) as by-product. The H 2 O 2 can be provided to lignin degradation pathway, a biotechnological property explored in biofuel production. In the thermophilic fungus Thermothelomyces thermophilus (formerly Myceliophthora thermophila), just one AAOx was identified in the exo-proteome. Methods The glycosylated and non-refolded crystal structure of an AAOx from T. thermophilus at 2.6 Å resolution was elucidated by X-ray crystallography combined with small-angle X-ray scattering (SAXS) studies. Moreover, biochemical analyses were carried out to shed light on enzyme substrate specificity and thermostability. Results This flavoenzyme harbors a flavin adenine dinucleotide as a cofactor and is able to oxidize aromatic substrates and 5-HMF. Our results also show that the enzyme has similar oxidation rates for bulky or simple aromatic substrates such as cinnamyl and veratryl alcohols. Moreover, the crystal structure of MtAAOx reveals an open active site, which might explain observed specificity of the enzyme. Conclusions MtAAOx shows previously undescribed structural differences such as a fully accessible catalytic tunnel, heavy glycosylation and Ca 2+ binding site providing evidences for thermostability and activity of the enzymes from AA3_2 subfamily. General significance Structural and biochemical analyses of MtAAOx could be important for comprehension of aryl-alcohol oxidases structure-function relationships and provide additional molecular tools to be used in future biotechnological applications.


  • Organizational Affiliation
    • São Carlos Institute of Physics, University of São Paulo, Av. Trabalhador São-carlense, 400, São Carlos, SP 13566-590, Brazil. Electronic address: marcokadowaki@gmail.com.

Macromolecule Content 

  • Total Structure Weight: 143.39 kDa 
  • Atom Count: 10,140 
  • Modeled Residue Count: 1,226 
  • Deposited Residue Count: 1,294 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aryl-alcohol oxidase
A, B
647Thermothelomyces thermophilusMutation(s): 0 
Gene Names: MYCTH_2299749
EC: 1.1.3.7
UniProt
Find proteins for G2PZJ2 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799))
Explore G2PZJ2 
Go to UniProtKB:  G2PZJ2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2PZJ2
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
G [auth A],
N [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
B3P

Query on B3P



Download:Ideal Coordinates CCD File
L [auth A],
R [auth B]
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
O [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
144

Query on 144



Download:Ideal Coordinates CCD File
Q [auth B]TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
C4 H12 N O3
DRDCQJADRSJFFD-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
J [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
M [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
K [auth A],
P [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.251 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.854α = 90
b = 109.696β = 90
c = 220.258γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-09-30
    Changes: Database references, Structure summary
  • Version 2.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 2.3: 2024-11-20
    Changes: Structure summary