7RF9 | pdb_00007rf9

O2-, PLP-dependent desaturase Plu4 intermediate-bound enzyme

PDB DOI: https://doi.org/10.2210/pdb7RF9/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Pseudoalteromonas luteoviolacea
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-07-13 Released: 2021-10-06
Deposition Author(s): Hoffarth, E.R., Ryan, K.S.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.194 (Depositor), 0.193 (DCC)
R-Value Work:
0.151 (Depositor), 0.152 (DCC)
R-Value Observed:
0.153 (Depositor)

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

A shared mechanistic pathway for pyridoxal phosphate-dependent arginine oxidases.

Hoffarth, E.R., Caddell Haatveit, K., Kuatsjah, E., MacNeil, G.A., Saroya, S., Walsby, C.J., Eltis, L.D., Houk, K.N., Garcia-Borras, M., Ryan, K.S.

(2021) Proc Natl Acad Sci U S A 118

PubMed: 34580201 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2012591118
Primary Citation Related Structures:
7N79, 7RF9, 7RGB

PubMed Abstract:
The mechanism by which molecular oxygen is activated by the organic cofactor pyridoxal phosphate (PLP) for oxidation reactions remains poorly understood. Recent work has identified arginine oxidases that catalyze desaturation or hydroxylation reactions. Here, we investigate a desaturase from the Pseudoalteromonas luteoviolacea indolmycin pathway. Our work, combining X-ray crystallographic, biochemical, spectroscopic, and computational studies, supports a shared mechanism with arginine hydroxylases, involving two rounds of single-electron transfer to oxygen and superoxide rebound at the 4' carbon of the PLP cofactor. The precise positioning of a water molecule in the active site is proposed to control the final reaction outcome. This proposed mechanism provides a unified framework to understand how oxygen can be activated by PLP-dependent enzymes for oxidation of arginine and elucidates a shared mechanistic pathway and intertwined evolutionary history for arginine desaturases and hydroxylases.

Organizational Affiliation

Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada.

Macromolecule Content

Total Structure Weight: 182.92 kDa
Atom Count: 13,549
Modeled Residue Count: 1,513
Deposited Residue Count: 1,556
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotran_1_2 domain-containing protein	A, B, C, D	389	Pseudoalteromonas luteoviolacea	Mutation(s): 0 Gene Names: JF50_03865
UniProt
Find proteins for A0A0C1MLE8 (Pseudoalteromonas luteoviolacea) Explore A0A0C1MLE8 Go to UniProtKB: A0A0C1MLE8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0C1MLE8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EJ1 (Subject of Investigation/LOI) Query on EJ1 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain S [auth B] SDF format, chain W [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain W [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain W [auth C]	G [auth A], GA [auth D], S [auth B], W [auth C]	(2E)-5-carbamimidamido-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}pentanoic acid C₁₄ H₂₂ N₅ O₇ P RHCMSTSZICWJMS-GXVFZPQQSA-N		Interactions Focus chain G [auth A] Focus chain GA [auth D] Focus chain S [auth B] Focus chain W [auth C] Interactions & Density Focus chain G [auth A] Focus chain GA [auth D] Focus chain S [auth B] Focus chain W [auth C]
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain H [auth A] SDF format, chain Q [auth B] SDF format, chain X [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain X [auth C]	E [auth A], EA [auth D], H [auth A], Q [auth B], X [auth C]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain EA [auth D] Focus chain H [auth A] Focus chain Q [auth B] Focus chain X [auth C] Interactions & Density Focus chain E [auth A] Focus chain EA [auth D] Focus chain H [auth A] Focus chain Q [auth B] Focus chain X [auth C]
AE3 Query on AE3 Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain Y [auth C]	Y [auth C]	2-(2-ETHOXYETHOXY)ETHANOL C₆ H₁₄ O₃ XXJWXESWEXIICW-UHFFFAOYSA-N		Interactions Focus chain Y [auth C] Interactions & Density Focus chain Y [auth C]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] HA [auth D] AA [auth C], BA [auth C], CA [auth C], DA [auth C], HA [auth D], IA [auth D], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], O [auth A], P [auth A], T [auth B], U [auth B], V [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain J [auth A] SDF format, chain R [auth B] SDF format, chain Z [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Z [auth C]	F [auth A], FA [auth D], J [auth A], R [auth B], Z [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain FA [auth D] Focus chain J [auth A] Focus chain R [auth B] Focus chain Z [auth C] Interactions & Density Focus chain F [auth A] Focus chain FA [auth D] Focus chain J [auth A] Focus chain R [auth B] Focus chain Z [auth C]