8A8I

Xenobiotic reductase A from Pseudomonas putida in complex with ethyl (Z)-2-(hydroxyimino)-3-oxobutanoate

PDB DOI: https://doi.org/10.2210/pdb8A8I/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-06-23 Released: 2023-03-01
Deposition Author(s): Polidori, N., Gruber, K.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.237
R-Value Work: 0.184
R-Value Observed: 0.185

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Mechanistic Insights into the Ene-Reductase-Catalyzed Promiscuous Reduction of Oximes to Amines.

Breukelaar, W.B., Polidori, N., Singh, A., Daniel, B., Glueck, S.M., Gruber, K., Kroutil, W.

(2023) ACS Catal 13: 2610-2618

PubMed: 36846821 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acscatal.2c06137
Primary Citation of Related Structures:
8A8I, 8AU8, 8AU9, 8AUA, 8AUB, 8AUE, 8AUF, 8AUG, 8AUH, 8AUI, 8AUJ, 8AUL, 8AUM, 8AUN, 8AUO, 8AUQ

PubMed Abstract:
The biocatalytic reduction of the oxime moiety to the corresponding amine group has only recently been found to be a promiscuous activity of ene-reductases transforming α-oximo β-keto esters. However, the reaction pathway of this two-step reduction remained elusive. By studying the crystal structures of enzyme oxime complexes, analyzing molecular dynamics simulations, and investigating biocatalytic cascades and possible intermediates, we obtained evidence that the reaction proceeds via an imine intermediate and not via the hydroxylamine intermediate. The imine is reduced further by the ene-reductase to the amine product. Remarkably, a non-canonical tyrosine residue was found to contribute to the catalytic activity of the ene-reductase OPR3, protonating the hydroxyl group of the oxime in the first reduction step.

Organizational Affiliation

Department of Chemistry, NAWI Graz, University of Graz, Heinrichstraße 28, 8010 Graz, Austria.

Macromolecule Content

Total Structure Weight: 83.56 kDa
Atom Count: 6,383
Modelled Residue Count: 718
Deposited Residue Count: 742
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xenobiotic reductase	A [auth B], B [auth D]	371	Pseudomonas putida	Mutation(s): 0 Gene Names: xenA
UniProt
Find proteins for Q9R9V9 (Pseudomonas putida) Explore Q9R9V9 Go to UniProtKB: Q9R9V9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9R9V9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN (Subject of Investigation/LOI) Query on FMN Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain G [auth D] MOL2 format, chain C [auth B] MOL2 format, chain G [auth D] mmCIF format, chain C [auth B] mmCIF format, chain G [auth D]	C [auth B], G [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth B] Focus chain G [auth D] Interactions & Density Focus chain C [auth B] Focus chain G [auth D]
L9I (Subject of Investigation/LOI) Query on L9I Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain H [auth D] MOL2 format, chain D [auth B] MOL2 format, chain H [auth D] mmCIF format, chain D [auth B] mmCIF format, chain H [auth D]	D [auth B], H [auth D]	ethyl (2Z)-2-hydroxyimino-3-oxidanylidene-butanoate C₆ H₉ N O₄ IACSYDRIOYGJNH-ALCCZGGFSA-N		Interactions Focus chain D [auth B] Focus chain H [auth D] Interactions & Density Focus chain D [auth B] Focus chain H [auth D]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain I [auth D] MOL2 format, chain F [auth B] MOL2 format, chain I [auth D] mmCIF format, chain F [auth B] mmCIF format, chain I [auth D]	F [auth B], I [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain F [auth B] Focus chain I [auth D] Interactions & Density Focus chain F [auth B] Focus chain I [auth D]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth D] MOL2 format, chain J [auth D] mmCIF format, chain J [auth D]	J [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth D] Interactions & Density Focus chain J [auth D]