8BXL

Patulin Synthase from Penicillium expansum

PDB DOI: https://doi.org/10.2210/pdb8BXL/pdb

Classification: FLAVOPROTEIN
Organism(s): Penicillium expansum
Expression System: Aspergillus niger
Mutation(s): No

Deposited: 2022-12-09 Released: 2023-09-06
Deposition Author(s): Tjallinks, G., Boverio, A., Rozeboom, H.J., Fraaije, M.W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.222
R-Value Work: 0.182
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure elucidation and characterization of patulin synthase, insights into the formation of a fungal mycotoxin.

Tjallinks, G., Boverio, A., Maric, I., Rozeboom, H., Arentshorst, M., Visser, J., Ram, A.F.J., Mattevi, A., Fraaije, M.W.

(2023) FEBS J 290: 5114-5126

PubMed: 37366079 Search on PubMed
DOI: https://doi.org/10.1111/febs.16804
Primary Citation of Related Structures:
8BXL

PubMed Abstract:
Patulin synthase (PatE) from Penicillium expansum is a flavin-dependent enzyme that catalyses the last step in the biosynthesis of the mycotoxin patulin. This secondary metabolite is often present in fruit and fruit-derived products, causing postharvest losses. The patE gene was expressed in Aspergillus niger allowing purification and characterization of PatE. This confirmed that PatE is active not only on the proposed patulin precursor ascladiol but also on several aromatic alcohols including 5-hydroxymethylfurfural. By elucidating its crystal structure, details on its catalytic mechanism were revealed. Several aspects of the active site architecture are reminiscent of that of fungal aryl-alcohol oxidases. Yet, PatE is most efficient with ascladiol as substrate confirming its dedicated role in biosynthesis of patulin.

Organizational Affiliation

Molecular Enzymology, University of Groningen, The Netherlands.

Macromolecule Content

Total Structure Weight: 425.34 kDa
Atom Count: 29,074
Modelled Residue Count: 3,540
Deposited Residue Count: 3,768
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Patulin synthase	A [auth B] B [auth C] C [auth D] D [auth A] E [auth F] A [auth B], B [auth C], C [auth D], D [auth A], E [auth F], F [auth E]	628	Penicillium expansum	Mutation(s): 0 Gene Names: patE, PEX2_082770 EC: 1.1
UniProt
Find proteins for A0A075TRK9 (Penicillium expansum) Explore A0A075TRK9 Go to UniProtKB: A0A075TRK9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A075TRK9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I, J, K	3		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L	2		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain JB [auth E] SDF format, chain M [auth B] SDF format, chain MA [auth A] SDF format, chain VA [auth F] SDF format, chain W [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain JB [auth E] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth A] MOL2 format, chain VA [auth F] MOL2 format, chain W [auth C]	EA [auth D] JB [auth E] M [auth B] MA [auth A] VA [auth F] EA [auth D], JB [auth E], M [auth B], MA [auth A], VA [auth F], W [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain EA [auth D] Focus chain JB [auth E] Focus chain M [auth B] Focus chain MA [auth A] Focus chain VA [auth F] Focus chain W [auth C] Interactions & Density Focus chain EA [auth D] Focus chain JB [auth E] Focus chain M [auth B] Focus chain MA [auth A] Focus chain VA [auth F] Focus chain W [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain FA [auth D] SDF format, chain GB [auth F] SDF format, chain HA [auth D] SDF format, chain KA [auth D] SDF format, chain KB [auth E] SDF format, chain LA [auth D] SDF format, chain N [auth B] SDF format, chain NA [auth A] SDF format, chain OB [auth E] SDF format, chain P [auth B] SDF format, chain PA [auth A] SDF format, chain PB [auth E] SDF format, chain QB [auth E] SDF format, chain S [auth B] SDF format, chain SA [auth A] SDF format, chain U [auth B] SDF format, chain UA [auth A] SDF format, chain WA [auth F] SDF format, chain X [auth C] SDF format, chain YA [auth F] SDF format, chain Z [auth C] MOL2 format, chain BB [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GB [auth F] MOL2 format, chain HA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth E] MOL2 format, chain LA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth A] MOL2 format, chain OB [auth E] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth E] MOL2 format, chain QB [auth E] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth A] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth A] MOL2 format, chain WA [auth F] MOL2 format, chain X [auth C] MOL2 format, chain YA [auth F] MOL2 format, chain Z [auth C]	BB [auth F] CA [auth C] DA [auth C] FA [auth D] GB [auth F] BB [auth F], CA [auth C], DA [auth C], FA [auth D], GB [auth F], HA [auth D], KA [auth D], KB [auth E], LA [auth D], N [auth B], NA [auth A], OB [auth E], P [auth B], PA [auth A], PB [auth E], QB [auth E], S [auth B], SA [auth A], U [auth B], UA [auth A], WA [auth F], X [auth C], YA [auth F], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BB [auth F] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FA [auth D] Focus chain GB [auth F] Focus chain HA [auth D] Focus chain KA [auth D] Focus chain KB [auth E] Focus chain LA [auth D] Focus chain N [auth B] Focus chain NA [auth A] Focus chain OB [auth E] Focus chain P [auth B] Focus chain PA [auth A] Focus chain PB [auth E] Focus chain QB [auth E] Focus chain S [auth B] Focus chain SA [auth A] Focus chain U [auth B] Focus chain UA [auth A] Focus chain WA [auth F] Focus chain X [auth C] Focus chain YA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain BB [auth F] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FA [auth D] Focus chain GB [auth F] Focus chain HA [auth D] Focus chain KA [auth D] Focus chain KB [auth E] Focus chain LA [auth D] Focus chain N [auth B] Focus chain NA [auth A] Focus chain OB [auth E] Focus chain P [auth B] Focus chain PA [auth A] Focus chain PB [auth E] Focus chain QB [auth E] Focus chain S [auth B] Focus chain SA [auth A] Focus chain U [auth B] Focus chain UA [auth A] Focus chain WA [auth F] Focus chain X [auth C] Focus chain YA [auth F] Focus chain Z [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CB [auth F] SDF format, chain EB [auth F] SDF format, chain FB [auth F] SDF format, chain GA [auth D] SDF format, chain HB [auth E] SDF format, chain IA [auth D] SDF format, chain IB [auth E] SDF format, chain LB [auth E] SDF format, chain MB [auth E] SDF format, chain O [auth B] SDF format, chain OA [auth A] SDF format, chain Q [auth B] SDF format, chain QA [auth A] SDF format, chain T [auth B] SDF format, chain TA [auth A] SDF format, chain V [auth B] SDF format, chain XA [auth F] SDF format, chain Y [auth C] SDF format, chain ZA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain CB [auth F] MOL2 format, chain EB [auth F] MOL2 format, chain FB [auth F] MOL2 format, chain GA [auth D] MOL2 format, chain HB [auth E] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth E] MOL2 format, chain LB [auth E] MOL2 format, chain MB [auth E] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth A] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth A] MOL2 format, chain V [auth B] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain ZA [auth F]	AA [auth C] CB [auth F] EB [auth F] FB [auth F] GA [auth D] AA [auth C], CB [auth F], EB [auth F], FB [auth F], GA [auth D], HB [auth E], IA [auth D], IB [auth E], LB [auth E], MB [auth E], O [auth B], OA [auth A], Q [auth B], QA [auth A], T [auth B], TA [auth A], V [auth B], XA [auth F], Y [auth C], ZA [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain CB [auth F] Focus chain EB [auth F] Focus chain FB [auth F] Focus chain GA [auth D] Focus chain HB [auth E] Focus chain IA [auth D] Focus chain IB [auth E] Focus chain LB [auth E] Focus chain MB [auth E] Focus chain O [auth B] Focus chain OA [auth A] Focus chain Q [auth B] Focus chain QA [auth A] Focus chain T [auth B] Focus chain TA [auth A] Focus chain V [auth B] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain CB [auth F] Focus chain EB [auth F] Focus chain FB [auth F] Focus chain GA [auth D] Focus chain HB [auth E] Focus chain IA [auth D] Focus chain IB [auth E] Focus chain LB [auth E] Focus chain MB [auth E] Focus chain O [auth B] Focus chain OA [auth A] Focus chain Q [auth B] Focus chain QA [auth A] Focus chain T [auth B] Focus chain TA [auth A] Focus chain V [auth B] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain ZA [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain BA [auth C] SDF format, chain DB [auth F] SDF format, chain JA [auth D] SDF format, chain NB [auth E] SDF format, chain R [auth B] SDF format, chain RA [auth A] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain JA [auth D] MOL2 format, chain NB [auth E] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth A]	AB [auth F] BA [auth C] DB [auth F] JA [auth D] NB [auth E] AB [auth F], BA [auth C], DB [auth F], JA [auth D], NB [auth E], R [auth B], RA [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain BA [auth C] Focus chain DB [auth F] Focus chain JA [auth D] Focus chain NB [auth E] Focus chain R [auth B] Focus chain RA [auth A] Interactions & Density Focus chain AB [auth F] Focus chain BA [auth C] Focus chain DB [auth F] Focus chain JA [auth D] Focus chain NB [auth E] Focus chain R [auth B] Focus chain RA [auth A]