PXD056344

PXD056344 is an original dataset announced via ProteomeXchange.

Title	β-Carotene alleviates substrate inhibition caused by asymmetric cooperativity
Description	Enzymes play a crucial role in biological systems and biotechnological processes as vital and sustainable catalysts that facilitate and regulate biochemical reactions. Inhibition of product formation of an enzyme by its own substrate was originally dismissed as an artifact of biochemical analysis, but is now a proven fact and occurs in about 20% of known enzymes1. Substrate inhibition is attributed to the formation of an unproductive enzyme-substrate complex with no structural evidence of unproductivity provided to date1–6. Here we show in detail the molecular mechanism of substrate inhibition of the tobacco glucosyltransferase NbUGT72AY1, which transfers glucose from its nucleotide donor substrate to phenol acceptors as a plant protection measure. The peculiarity that the effector β-carotene strongly attenuates the substrate inhibition of NbUGT72AY1, although it unexpectedly acts as a competitive acceptor-substrate inhibitor, allowed us to uncover the conformational changes that occur during substrate binding in the active and substrate-inhibited complexes of this protein. X-ray crystallography revealed structurally different ternary enzyme-substrate complexes that do not conform to the classical compulsory ordered or random mechanism of an enzyme-catalyzed sequential bi-substrate reaction. We suggest an alternative pathway in which the two substrates bind randomly to the enzyme, but the reaction is only catalyzed if a specific order of substrate binding is observed (asymmetric cooperativity). The new paradigm explains substrate inhibition in monomeric multi-substrate enzymes and reactivation of activity by competitive inhibitors. This alternative concept opens up new avenues of research in metabolic regulation as well as a wealth of novel industrial applications. The results enable novel approaches, e.g. to minimize the effects of food components on drug metabolism and to study plant defense mechanisms from a new perspective and offer alternative approaches for the design of more efficient production processes.
HostingRepository	PRIDE
AnnounceDate	2025-03-06
AnnouncementXML	Submission_2025-03-06_05:44:23.016.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wieland Steinchen
SpeciesList	scientific name: Nicotiana benthamiana; NCBI TaxID: 4100;
ModificationList	No PTMs are included in the dataset
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-28 05:18:53	ID requested
⏵ 1	2025-03-06 05:44:23	announced

Dataset with its publication pending

ProteomeXchange project tag: Hydrogen Deuterium Exchange (HDX-MS)

submitter keyword: HDXMS, X-ray crystallography,Substrate inhibition, UGT, Nicotiana benthamiana

Wieland Steinchen
contact affiliation	Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, 35043 Marburg, Germany
contact email	wieland.steinchen@synmikro.uni-marburg.de
lab head
Wieland Steinchen
contact affiliation	Philipps-University Marburg, Department of Chemistry & SYNMIKRO, Karl-von-Frisch-Straße 14, 35043 Marburg, GERMANY
contact email	wieland.steinchen@synmikro.uni-marburg.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PXD056344

PRIDE project URI

• PRIDE
  1. PXD056344
     1. Label: PRIDE project
     2. Name: β-Carotene alleviates substrate inhibition caused by asymmetric cooperativity