2YP1 | pdb_00002yp1

Crystallization of a 45 kDa peroxygenase- peroxidase from the mushroom Agrocybe aegerita and structure determination by SAD utilizing only the haem iron

PDB DOI: https://doi.org/10.2210/pdb2YP1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Cyclocybe aegerita
Mutation(s): No

Deposited: 2012-10-29 Released: 2013-10-23
Deposition Author(s): Piontek, K., Strittmatter, E., Ullrich, R., Plattner, D.A., Hofrichter, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free:
0.230 (Depositor), 0.236 (DCC)
R-Value Work:
0.177 (Depositor)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structural Basis of Substrate Conversion in a New Aromatic Peroxygenase: P450 Functionality with Benefits

Piontek, K., Strittmatter, E., Ullrich, R., Grobe, G., Pecyna, M.J., Kluge, M., Scheibner, K., Hofrichter, M., Plattner, D.A.

(2013) J Biological Chem 288: 34767

PubMed: 24126915 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M113.514521
Primary Citation Related Structures:
2YOR, 2YP1

PubMed Abstract:
Aromatic peroxygenases (APOs) represent a unique oxidoreductase sub-subclass of heme proteins with peroxygenase and peroxidase activity and were thus recently assigned a distinct EC classification (EC 1.11.2.1). They catalyze, inter alia, oxyfunctionalization reactions of aromatic and aliphatic hydrocarbons with remarkable regio- and stereoselectivities. When compared with cytochrome P450, APOs appear to be the choice enzymes for oxyfunctionalizations in organic synthesis due to their independence from a cellular environment and their greater chemical versatility. Here, the first two crystal structures of a heavily glycosylated fungal aromatic peroxygenase (AaeAPO) are described. They reveal different pH-dependent ligand binding modes. We model the fitting of various substrates in AaeAPO, illustrating the way the enzyme oxygenates polycyclic aromatic hydrocarbons. Spatial restrictions by a phenylalanine pentad in the active-site environment govern substrate specificity in AaeAPO.

Organizational Affiliation

From the Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, 79104 Freiburg.

Macromolecule Content

Total Structure Weight: 158.44 kDa
Atom Count: 12,290
Modeled Residue Count: 1,295
Deposited Residue Count: 1,300
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AROMATIC PEROXYGENASE	A, B, C, D	325	Cyclocybe aegerita	Mutation(s): 0 EC: 1.11.2.1
UniProt
Find proteins for B9W4V6 (Cyclocybe aegerita) Explore B9W4V6 Go to UniProtKB: B9W4V6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9W4V6
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	6		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, J	5		N-Glycosylation	Interactions Focus chain F Focus chain J Interactions & Density Focus chain F Focus chain J
Glycosylation Resources
GlyTouCan: G94626GC GlyCosmos: G94626GC GlyGen: G94626GC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, I, K, L, N G, I, K, L, N, P, Q, R, S	2		N-Glycosylation	Interactions Focus chain G Focus chain I Focus chain K Focus chain L Focus chain N Focus chain P Focus chain Q Focus chain R Focus chain S Interactions & Density Focus chain G Focus chain I Focus chain K Focus chain L Focus chain N Focus chain P Focus chain Q Focus chain R Focus chain S
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, M	8		N-Glycosylation	Interactions Focus chain H Focus chain M Interactions & Density Focus chain H Focus chain M
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O, T	3		N-Glycosylation	Interactions Focus chain O Focus chain T Interactions & Density Focus chain O Focus chain T
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain HA [auth C] SDF format, chain QA [auth D] SDF format, chain U [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain QA [auth D] MOL2 format, chain U [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain QA [auth D] mmCIF format, chain U [auth A]	BA [auth B], HA [auth C], QA [auth D], U [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain BA [auth B] Focus chain HA [auth C] Focus chain QA [auth D] Focus chain U [auth A] Interactions & Density Focus chain BA [auth B] Focus chain HA [auth C] Focus chain QA [auth D] Focus chain U [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain SA [auth D] SDF format, chain TA [auth D] SDF format, chain UA [auth D] SDF format, chain JA [auth C] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain JA [auth C] mmCIF format, chain SA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain UA [auth D] mmCIF format, chain JA [auth C]	JA [auth C], SA [auth D], TA [auth D], UA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain JA [auth C] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Interactions & Density Focus chain JA [auth C] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain WA [auth D] SDF format, chain X [auth A] SDF format, chain XA [auth D] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth D] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A] EA [auth B] FA [auth B] GA [auth B] LA [auth C] AA [auth A], EA [auth B], FA [auth B], GA [auth B], LA [auth C], MA [auth C], NA [auth C], OA [auth C], WA [auth D], X [auth A], XA [auth D], Y [auth A], Z [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth A] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain WA [auth D] Focus chain X [auth A] Focus chain XA [auth D] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain WA [auth D] Focus chain X [auth A] Focus chain XA [auth D] Focus chain Y [auth A] Focus chain Z [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain PA [auth C] SDF format, chain VA [auth D] SDF format, chain W [auth A] SDF format, chain KA [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth A] MOL2 format, chain KA [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain PA [auth C] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth A] mmCIF format, chain KA [auth C]	DA [auth B], KA [auth C], PA [auth C], VA [auth D], W [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth B] Focus chain KA [auth C] Focus chain PA [auth C] Focus chain VA [auth D] Focus chain W [auth A] Interactions & Density Focus chain DA [auth B] Focus chain KA [auth C] Focus chain PA [auth C] Focus chain VA [auth D] Focus chain W [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain RA [auth D] SDF format, chain V [auth A] SDF format, chain CA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain RA [auth D] MOL2 format, chain V [auth A] MOL2 format, chain CA [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain RA [auth D] mmCIF format, chain V [auth A] mmCIF format, chain CA [auth B]	CA [auth B], IA [auth C], RA [auth D], V [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain IA [auth C] Focus chain RA [auth D] Focus chain V [auth A] Interactions & Density Focus chain CA [auth B] Focus chain IA [auth C] Focus chain RA [auth D] Focus chain V [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.230 (Depositor), 0.236 (DCC)
R-Value Work: 0.177 (Depositor)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.75	α = 90
b = 144.88	β = 90
c = 134.46	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-10-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-23
Type: Initial release
Version 1.1: 2013-12-11
Changes: Database references
Version 1.2: 2015-04-01
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2024-10-23
Changes: Data collection, Database references, Structure summary

2YP1 | pdb_00002yp1

Crystallization of a 45 kDa peroxygenase- peroxidase from the mushroom Agrocybe aegerita and structure determination by SAD utilizing only the haem iron

Literature

Structural Basis of Substrate Conversion in a New Aromatic Peroxygenase: P450 Functionality with Benefits

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

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Oligosaccharides

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)