7NEY | pdb_00007ney

Structure of T. atroviride Fdc wild-type (TaFdc) in complex with prFMN

PDB DOI: https://doi.org/10.2210/pdb7NEY/pdb

Classification: LYASE
Organism(s): Trichoderma atroviride IMI 206040
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-02-05 Released: 2021-08-04
Deposition Author(s): Saaret, A., Leys, D.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.215 (Depositor), 0.219 (DCC)
R-Value Work:
0.182 (Depositor), 0.190 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Directed evolution of prenylated FMN-dependent Fdc supports efficient in vivo isobutene production.

Saaret, A., Villiers, B., Stricher, F., Anissimova, M., Cadillon, M., Spiess, R., Hay, S., Leys, D.

(2021) Nat Commun 12: 5300-5300

PubMed: 34489427 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-25598-0
Primary Citation Related Structures:
7NEY, 7NF0, 7NF1, 7NF2, 7NF3, 7NF4

PubMed Abstract:
Isobutene is a high value gaseous alkene used as fuel additive and a chemical building block. As an alternative to fossil fuel derived isobutene, we here develop a modified mevalonate pathway for the production of isobutene from glucose in vivo. The final step in the pathway consists of the decarboxylation of 3-methylcrotonic acid, catalysed by an evolved ferulic acid decarboxylase (Fdc) enzyme. Fdc belongs to the prFMN-dependent UbiD enzyme family that catalyses reversible decarboxylation of (hetero)aromatic acids or acrylic acids with extended conjugation. Following a screen of an Fdc library for inherent 3-methylcrotonic acid decarboxylase activity, directed evolution yields variants with up to an 80-fold increase in activity. Crystal structures of the evolved variants reveal that changes in the substrate binding pocket are responsible for increased selectivity. Solution and computational studies suggest that isobutene cycloelimination is rate limiting and strictly dependent on presence of the 3-methyl group.

Organizational Affiliation

Department of Chemistry, Manchester Institute for Biotechnology, University of Manchester, Manchester, UK.

Macromolecule Content

Total Structure Weight: 115.22 kDa
Atom Count: 8,124
Modeled Residue Count: 993
Deposited Residue Count: 1,038
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferulic acid decarboxylase 1	A, B	519	Trichoderma atroviride IMI 206040	Mutation(s): 0 Gene Names: FDC1, TRIATDRAFT_53567 EC: 4.1.1.102
UniProt
Find proteins for G9NLP8 (Hypocrea atroviridis (strain ATCC 20476 / IMI 206040)) Explore G9NLP8 Go to UniProtKB: G9NLP8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G9NLP8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4LU (Subject of Investigation/LOI) Query on 4LU Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y l)-D-ribitol C₂₂ H₃₀ N₄ O₉ P KOUJZPGFPGLHCZ-IYOUNJFTSA-O		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	D [auth A], E [auth A], H [auth B], I [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]