8RNP

Unspecific peroxygenase from Marasmius wettsteinii (MweUPO-1) in complex with R-limonene

PDB DOI: https://doi.org/10.2210/pdb8RNP/pdb

Classification: OXIDOREDUCTASE
Organism(s): Marasmius wettsteinii
Expression System: Komagataella phaffii CBS 7435
Mutation(s): No

Deposited: 2024-01-10 Released: 2024-10-16
Deposition Author(s): Fernandez-Garcia, A., Sanz-Aparicio, J.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.256
R-Value Work: 0.199
R-Value Observed: 0.202

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural Insights and Reaction Profile of a New Unspecific Peroxygenase from Marasmius wettsteinii Produced in a Tandem-Yeast Expression System.

Sanchez-Moreno, I., Fernandez-Garcia, A., Mateljak, I., Gomez de Santos, P., Hofrichter, M., Kellner, H., Sanz-Aparicio, J., Alcalde, M.

(2024) ACS Chem Biol 19: 2240-2253

PubMed: 39367827 Search on PubMed
DOI: https://doi.org/10.1021/acschembio.4c00504
Primary Citation of Related Structures:
8RNJ, 8RNK, 8RNL, 8RNM, 8RNN, 8RNO, 8RNP, 8RNQ, 8RNR

PubMed Abstract:
Fungal unspecific peroxygenases (UPOs) are gaining momentum in synthetic chemistry. Of special interest is the UPO from Marasmius rotula ( Mro UPO), which shows an exclusive repertoire of oxyfunctionalizations, including the terminal hydroxylation of alkanes, the α-oxidation of fatty acids and the C-C cleavage of corticosteroids. However, the lack of heterologous expression systems to perform directed evolution has impeded its engineering for practical applications. Here, we introduce a close ortholog of Mro UPO, a UPO gene from Marasmius wettsteinii ( Mwe UPO-1), that has a similar reaction profile to Mro UPO and for which we have set up a directed evolution platform based on tandem-yeast expression. Recombinant Mwe UPO-1 was produced at high titers in the bioreactor (0.7 g/L) and characterized at the biochemical and atomic levels. The conjunction of soaking crystallographic experiments at a resolution up to 1.6 Å together with the analysis of reaction patterns sheds light on the substrate preferences of this promiscuous biocatalyst.

Organizational Affiliation

Department of Biocatalysis, Institute of Catalysis, CSIC, 28049 Madrid, Spain.

Macromolecule Content

Total Structure Weight: 55.06 kDa
Atom Count: 4,127
Modelled Residue Count: 480
Deposited Residue Count: 480
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Unspecific peroxygenase	A, B	240	Marasmius wettsteinii	Mutation(s): 0 EC: 1.11.2.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain N [auth B]	C [auth A], N [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain N [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain S [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain S [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain S [auth B]	D [auth A], J [auth A], O [auth B], S [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain S [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain S [auth B]
9IR (Subject of Investigation/LOI) Query on 9IR Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	(4R)-1-methyl-4-(prop-1-en-2-yl)cyclohex-1-ene C₁₀ H₁₆ XMGQYMWWDOXHJM-JTQLQIEISA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Q [auth B] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain G [auth A] mmCIF format, chain Q [auth B]	G [auth A], Q [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain Q [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain U [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain U [auth B]	L [auth A], M [auth A], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain U [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain U [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain R [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain R [auth B]	E [auth A], F [auth A], H [auth A], P [auth B], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain P [auth B] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain P [auth B] Focus chain R [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain T [auth B] MOL2 format, chain K [auth A] MOL2 format, chain T [auth B] mmCIF format, chain K [auth A] mmCIF format, chain T [auth B]	K [auth A], T [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain T [auth B] Interactions & Density Focus chain K [auth A] Focus chain T [auth B]