8S4P | pdb_00008s4p

Crystal structure of an Ene-reductase from Penicillium steckii

PDB DOI: https://doi.org/10.2210/pdb8S4P/pdb

Classification: OXIDOREDUCTASE
Organism(s): Penicillium steckii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-22 Released: 2025-03-05
Deposition Author(s): Rozeboom, H.J., Fraaije, M.W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.275 (Depositor), 0.267 (DCC)
R-Value Work:
0.201 (Depositor), 0.199 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Recombinant Production and Characterization of Six Ene-reductases from Penicillium steckii.

Damada, P.H., Rozeboom, H.J., Fraaije, M.W.

(2025) Chembiochem 26: e202401007-e202401007

PubMed: 40072226 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/cbic.202401007
Primary Citation Related Structures:
8S4P

PubMed Abstract:
Fungi, known for their adaptability, are valuable sources of enzymes, making them promising for biocatalyst discovery. This study explored Penicillium steckii, primarily recognized for secondary metabolite production, as a source of ene-reductases (ERs), which reduce α,β-unsaturated compounds. Eleven ER-encoding genes were identified, and plasmids for Escherichia coli expression were generated. Six ERs (PsOYE1-6) were successfully produced and purified as soluble FMN-containing proteins. Sequence analysis classified them into Class II (PsOYE1, PsOYE4, PsOYE6), Class III (PsOYE2, PsOYE3), and Class V (PsOYE5) OYEs. All were active on p-benzoquinone and maleimide, with varying activity on other substrates. Their pH optima ranged from 6 to 7, and they exhibited moderate thermostability (35-50 °C). PsOYE2 was crystallized, and its 2.3 Å structure revealed a stable dimer with a unique active site. PsOYE3, PsOYE4, and PsOYE5 were tested for R-carvone conversion and stereoselectivity, all favouring one diastereomer. These fungal ERs expand the enzymatic toolbox for biocatalysis, emphasizing the need for tailored strategies based on specific applications.

Organizational Affiliation

Molecular Enzymology Group, Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 3, 9747 AG, Groningen, the, Netherlands.

Macromolecule Content

Total Structure Weight: 366.55 kDa
Atom Count: 26,030
Modeled Residue Count: 3,276
Deposited Residue Count: 3,376
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH:flavin oxidoreductase/NADH oxidase N-terminal domain-containing protein	A, B, C, D, E A, B, C, D, E, F, G, H	422	Penicillium steckii	Mutation(s): 0 Gene Names: PENSTE_c029G02105
UniProt
Find proteins for A0A1V6SMJ6 (Penicillium steckii) Explore A0A1V6SMJ6 Go to UniProtKB: A0A1V6SMJ6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1V6SMJ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain S [auth E] SDF format, chain U [auth F] SDF format, chain Y [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F] MOL2 format, chain Y [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain S [auth E] mmCIF format, chain U [auth F] mmCIF format, chain Y [auth G]	BA [auth H] I [auth A] L [auth B] N [auth C] P [auth D] BA [auth H], I [auth A], L [auth B], N [auth C], P [auth D], S [auth E], U [auth F], Y [auth G]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain BA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain Y [auth G] Interactions & Density Focus chain BA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain Y [auth G]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain CA [auth H] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain V [auth F] SDF format, chain W [auth F] SDF format, chain Z [auth G] MOL2 format, chain CA [auth H] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain V [auth F] MOL2 format, chain W [auth F] MOL2 format, chain Z [auth G] mmCIF format, chain CA [auth H] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain V [auth F] mmCIF format, chain W [auth F] mmCIF format, chain Z [auth G]	CA [auth H] O [auth C] Q [auth D] V [auth F] W [auth F] CA [auth H], O [auth C], Q [auth D], V [auth F], W [auth F], Z [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth H] Focus chain O [auth C] Focus chain Q [auth D] Focus chain V [auth F] Focus chain W [auth F] Focus chain Z [auth G] Interactions & Density Focus chain CA [auth H] Focus chain O [auth C] Focus chain Q [auth D] Focus chain V [auth F] Focus chain W [auth F] Focus chain Z [auth G]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain DA [auth H] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain X [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain X [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain X [auth F]	AA [auth G] DA [auth H] K [auth A] M [auth B] R [auth D] AA [auth G], DA [auth H], K [auth A], M [auth B], R [auth D], T [auth E], X [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth G] Focus chain DA [auth H] Focus chain K [auth A] Focus chain M [auth B] Focus chain R [auth D] Focus chain T [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth H] Focus chain K [auth A] Focus chain M [auth B] Focus chain R [auth D] Focus chain T [auth E] Focus chain X [auth F]