2YOR

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/pdb2YOR/pdb

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

Deposited: 2012-10-26 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: 2.19 Å
R-Value Free: 0.237
R-Value Work: 0.169
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 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 Biol Chem 288: 34767

PubMed: 24126915 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1074/jbc.M113.514521
Primary Citation of 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: 80.35 kDa
Atom Count: 6,261
Modelled Residue Count: 648
Deposited Residue Count: 650
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AROMATIC PEROXYGENASE	A, B	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B9W4V6
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	D	5		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	8		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G61846BY GlyCosmos: G61846BY GlyGen: G61846BY

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I, J	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain V [auth B] MOL2 format, chain K [auth A] MOL2 format, chain V [auth B] mmCIF format, chain K [auth A] mmCIF format, chain V [auth B]	K [auth A], V [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain K [auth A] Focus chain V [auth B] Interactions & Density Focus chain K [auth A] Focus chain V [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Y [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Y [auth B]	AA [auth B], N [auth A], O [auth A], P [auth A], Y [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Y [auth B]
BMA Query on BMA Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain Z [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain Z [auth B]	Q [auth A], Z [auth B]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain Q [auth A] Focus chain Z [auth B] Interactions & Density Focus chain Q [auth A] Focus chain Z [auth B]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain BA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain BA [auth B]	BA [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain BA [auth B] Interactions & Density Focus chain BA [auth B]
MZ0 Query on MZ0 Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain X [auth B] MOL2 format, chain M [auth A] MOL2 format, chain X [auth B] mmCIF format, chain M [auth A] mmCIF format, chain X [auth B]	M [auth A], X [auth B]	1H-imidazol-5-ylmethanol C₄ H₆ N₂ O QDYTUZCWBJRHKK-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain X [auth B] Interactions & Density Focus chain M [auth A] Focus chain X [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A]	DA [auth B] FA [auth B] GA [auth B] R [auth A] T [auth A] DA [auth B], FA [auth B], GA [auth B], R [auth A], T [auth A], U [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain R [auth A] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain DA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain R [auth A] Focus chain T [auth A] Focus chain U [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain EA [auth B] SDF format, chain HA [auth B] SDF format, chain S [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain S [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain S [auth A]	CA [auth B], EA [auth B], HA [auth B], S [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth B] Focus chain EA [auth B] Focus chain HA [auth B] Focus chain S [auth A] Interactions & Density Focus chain CA [auth B] Focus chain EA [auth B] Focus chain HA [auth B] Focus chain S [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain W [auth B] MOL2 format, chain L [auth A] MOL2 format, chain W [auth B] mmCIF format, chain L [auth A] mmCIF format, chain W [auth B]	L [auth A], W [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain W [auth B] Interactions & Density Focus chain L [auth A] Focus chain W [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.237
R-Value Work: 0.169
R-Value Observed: 0.172
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.29	α = 90
b = 95.03	β = 90
c = 127.2	γ = 90

Software Package:

Software Name	Purpose
SOLOMON	model building
XDS	data scaling
SHELXD	phasing
SHELXE	phasing
autoSHARP	phasing
SOLOMON	phasing
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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

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2YOR

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

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

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)