PXD013286

PXD013286 is an original dataset announced via ProteomeXchange.

Title	A novel domain essential for interdomain cooperativity in binding of a Rep protein to DNA.
Description	A very important feature of replication initiation proteins is the ability to bind to DNA via a characteristic domain. Usually, one or two DNA-binding domains can be distinguished within each initiator. In this work, we specified a new family of replication initiation proteins (the TrfA-like protein family) with unique domain compositions that are important for interactions with DNA. Using phylogenetic analysis and structure prediction methods simultaneously with biochemical assays, we demonstrate that in the replication initiator of the broad-host-range plasmid RK2, in addition to two winged helix domains, a third domain that interacts with DNA can be described. Mass spectrometric analysis followed by site-directed mutagenesis and in vitro and in vivo analysis of TrfA variants showed that DNA binding by all three domains of TrfA is important for stable nucleoprotein complex formation and the replication activity of the initiator.
HostingRepository	PRIDE
AnnounceDate	2021-09-08
AnnouncementXML	Submission_2021-09-08_10:55:54.476.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Paulina Czaplewska
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	5800 TOF/TOF

Revision	Datetime	Status	ChangeLog Entry
0	2019-03-28 06:48:32	ID requested
⏵ 1	2021-09-08 10:55:55	announced

Wegrzyn K, Zabrocka E, Bury K, Tomiczek B, Wieczor M, Czub J, Uciechowska U, Moreno-Del Alamo M, Walkow U, Grochowina I, Dutkiewicz R, Bujnicki JM, Giraldo R, Konieczny I, Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA. Nucleic Acids Res, 49(6):3394-3408(2021) [pubmed]

submitter keyword: Rep proteins, plasmid RK2, TrfA, Winged Helix Domain, DNA binding domain, DNA replication initiation, mass spectrometry

Paulina Czaplewska
contact affiliation	Laboratory of Mass Spectrometry Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk
contact email	pczaplewska@gmail.com
lab head
Paulina Czaplewska
contact affiliation	University of Gdansk
contact email	pczaplewska@gmail.com
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/2021/09/PXD013286

PRIDE project URI

• PRIDE
  1. PXD013286
     1. Label: PRIDE project
     2. Name: A novel domain essential for interdomain cooperativity in binding of a Rep protein to DNA.