8ODW | pdb_00008odw

Crystal structure of LbmA Ox-ACP didomain in complex with NADP and ethyl glycinate from the lobatamide PKS (Gynuella sunshinyii)

PDB DOI: https://doi.org/10.2210/pdb8ODW/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Gynuella sunshinyii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-03-09 Released: 2023-05-31
Deposition Author(s): Francois, R.M.M., Fraley, A.E., Piel, J., Weissman, K.J., Gruez, A.
Funding Organization(s): Agence Nationale de la Recherche (ANR), European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.07 Å
R-Value Free:
0.293 (Depositor), 0.294 (DCC)
R-Value Work:
0.237 (Depositor), 0.237 (DCC)
R-Value Observed:
0.240 (Depositor)

Starting Model: in silico
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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

Modular Oxime Formation by a trans-AT Polyketide Synthase.

Minas, H.A., Francois, R.M.M., Hemmerling, F., Fraley, A.E., Dieterich, C.L., Rudisser, S.H., Meoded, R.A., Collin, S., Weissman, K.J., Gruez, A., Piel, J.

(2023) Angew Chem Int Ed Engl 62: e202304481-e202304481

PubMed: 37216334 Search on PubMed
DOI: https://doi.org/10.1002/anie.202304481
Primary Citation Related Structures:
8ODW

PubMed Abstract:
Modular trans-acyltransferase polyketide synthases (trans-AT PKSs) are enzymatic assembly lines that biosynthesize complex polyketide natural products. Relative to their better studied cis-AT counterparts, the trans-AT PKSs introduce remarkable chemical diversity into their polyketide products. A notable example is the lobatamide A PKS, which incorporates a methylated oxime. Here we demonstrate biochemically that this functionality is installed on-line by an unusual oxygenase-containing bimodule. Furthermore, analysis of the oxygenase crystal structure coupled with site-directed mutagenesis allows us to propose a model for catalysis, as well as identifying key protein-protein interactions that support this chemistry. Overall, our work adds oxime-forming machinery to the biomolecular toolbox available for trans-AT PKS engineering, opening the way to introducing such masked aldehyde functionalities into diverse polyketides.

Organizational Affiliation

Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland.

Macromolecule Content

Total Structure Weight: 147.61 kDa
Atom Count: 9,771
Modeled Residue Count: 1,181
Deposited Residue Count: 1,278
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyketide synthase modules-related protein	A, B	639	Gynuella sunshinyii	Mutation(s): 0 Gene Names: YC6258_03642 EC: 2.3.1.39
UniProt
Find proteins for A0A0C5VQJ2 (Gynuella sunshinyii YC6258) Explore A0A0C5VQJ2 Go to UniProtKB: A0A0C5VQJ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0C5VQJ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain C [auth A]	C [auth A], L [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
NAP (Subject of Investigation/LOI) Query on NAP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain M [auth B]	D [auth A], M [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain M [auth B]
GEE (Subject of Investigation/LOI) Query on GEE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ethyl glycinate C₄ H₉ N O₂ NTNZTEQNFHNYBC-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A], J [auth A], K [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
OXY (Subject of Investigation/LOI) Query on OXY Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]