PXD057294

PXD057294 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	The role and cooperation of AidB dehydrogenase and AlkB dioxygenase in repair of adducts to DNA and RNA bases
Description	The aim of the project is to conduct in vivo, in vitro and in silico studies of the substrate specificity of AidB dehydrogenase against the by-products rising in AlkB dioxygenase repair reaction and AlkB and AidB cooperative interaction in the repair of adducts to DNA and RNA bases. AidB dehydrogenase and AlkB dioxygenase are induced in the E. coli adaptive response to alkylating agents. As a result of direct AlkB removal of base modifications, toxic and mutagenic by-products are formed: formaldehyde, glyoxal or malondialdehyde. Our studies indicate that AlkB is efficiently inhibited in vitro by the side products of the repair reaction. The biological role and substrates of AidB are unknown. It is known that AidB does not repair DNA lesions; its crystallographic structure points to small molecule substrates. This allowed me to formulate the hypothesis that AidB dehydrogenase may be involved in the detoxification of highly reactive by-products generated as a result of AlkB repair and that to prevent their release to the cell, these enzymes can interact directly in the cell homeostasis maintenance.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_04:49:44.448.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ewa Sitkiewicz
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Synapt MS

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-29 07:40:17	ID requested
⏵ 1	2025-05-07 04:49:45	announced

Publication List

10.1021/acs.jproteome.4c00700;
Pucha, ł, a W, Kistowski M, Zhukova L, Burdukiewicz M, Dadlez M, HRaDeX: R Package and Web Server for Computing High-Resolution Deuterium Uptake Rates for HDX-MS Data. J Proteome Res, 24(4):1688-1700(2025) [pubmed]

10.1021/acs.jproteome.4c00700;

Pucha, ł, a W, Kistowski M, Zhukova L, Burdukiewicz M, Dadlez M, HRaDeX: R Package and Web Server for Computing High-Resolution Deuterium Uptake Rates for HDX-MS Data. J Proteome Res, 24(4):1688-1700(2025) [pubmed]

Keyword List

submitter keyword: AidB dehydrogenase, DNA repair, AlkB dioxygenase, E.coli, RNA repair

submitter keyword: AidB dehydrogenase, DNA repair, AlkB dioxygenase, E.coli, RNA repair

Contact List

Michał Dadlez
contact affiliation	Institute of Biochemistry and Biophysics, Pol. Acad. Sci. Mass Sepctrometry Laboratory, Head
contact email	michald@ibb.waw.pl
lab head
Ewa Sitkiewicz
contact affiliation	Mass Spectrometry Laboratory Institute of Biochemistry and Biophysics Polish Academy of Sciences
contact email	ewa@ibb.waw.pl
dataset submitter

Full Dataset Link List

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/2025/05/PXD057294
PRIDE project URI

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/2025/05/PXD057294

PRIDE project URI

Repository Record List

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