2YOR | pdb_00002yor

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 (Depositor), 0.237 (DCC)
R-Value Work:
0.169 (Depositor), 0.170 (DCC)
R-Value Observed:
0.172 (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: 80.35 kDa
Atom Count: 6,261
Modeled Residue Count: 648
Deposited Residue Count: 650
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9W4V6
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
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	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	D 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	D 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	D 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 (Depositor), 0.237 (DCC)
R-Value Work: 0.169 (Depositor), 0.170 (DCC)
R-Value Observed: 0.172 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

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: 2024-11-13
Changes: Data collection, Database references, Structure summary