General Information

Database Accession: DI1200013

Name: PriA helicase bound to SSB C-terminal peptide motif

PDB ID: 4nl8 PDB

Experimental method: X-ray (4.08 Å)

Source organism: Klebsiella pneumoniae subsp. pneumoniae

Proof of disorder: Confirmed

Primary publication of the structure:

Bhattacharyya B, George NP, Thurmes TM, Zhou R, Jani N, Wessel SR, Sandler SJ, Ha T, Keck JL
Structural mechanisms of PriA-mediated DNA replication restart.
(2014) Proc. Natl. Acad. Sci. U.S.A. 111: 1373-8

PMID: 24379377 PubMed

Abstract:

Collisions between cellular DNA replication machinery (replisomes) and damaged DNA or immovable protein complexes can dissociate replisomes before the completion of replication. This potentially lethal problem is resolved by cellular "replication restart" reactions that recognize the structures of prematurely abandoned replication forks and mediate replisomal reloading. In bacteria, this essential activity is orchestrated by the PriA DNA helicase, which identifies replication forks via structure-specific DNA binding and interactions with fork-associated ssDNA-binding proteins (SSBs). However, the mechanisms by which PriA binds replication fork DNA and coordinates subsequent replication restart reactions have remained unclear due to the dearth of high-resolution structural information available for the protein. Here, we describe the crystal structures of full-length PriA and PriA bound to SSB. The structures reveal a modular arrangement for PriA in which several DNA-binding domains surround its helicase core in a manner that appears to be poised for binding to branched replication fork DNA structures while simultaneously allowing complex formation with SSB. PriA interaction with SSB is shown to modulate SSB/DNA complexes in a manner that exposes a potential replication initiation site. From these observations, a model emerges to explain how PriA links recognition of diverse replication forks to replication restart.

Function and Biology Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.

Molecular function:

DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GeneOntology

Biological process:

DNA replication The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. GeneOntology

Cellular component: not assigned

Structure Summary Structural annotations of the participating protein chains.

Entry contents: 2 distinct polypeptide molecules

Chains: C, A

Notes: Chains B, D, E and F were removed as chains A and C highlight the biologically relevant interaction.

Chain C

Name: Single-stranded DNA-binding protein Disordered Confirmed

Source organism: Klebsiella pneumoniae subsp. pneumoniae

Length: 9 residues

Sequence:Sequence according to PDB SEQRESMDFDDDIPF

UniProtKB AC: A0A0H3GL04 (positions: 166-174) UniProt Coverage: 5.2%

UniRef90 AC: UniRef90_P0A2F7 (positions: 166-174) UniRef90

Chain A

Name: Primosomal protein N' Ordered

Source organism: Klebsiella pneumoniae subsp. pneumoniae

Length: 731 residues

Sequence:Sequence according to PDB SEQRESMSVAHVALPVPLPRTFDYLLPEGMAVKAGCRVRVPFGKQERIGIVAAVSERSELPLDELKPVAEALDDEPVFSTTVWRLLMWAAEYYHHPIGDVLFHALPVMLRQGKPASATPLWYWFATEQGQVVDLNGLKRSRKQQQALAALRQGKIWRHQVGELEFNEAALQALRGKGLAELACEAPALTDWRSAYSVAGERLRLNTEQATAVGAIHSAADRFSAWLLAGITGSGKTEVYLSVLENVLAQGRQALVMVPEIGLTPQTIARFRQRFNAPVEVLHSGLNDSERLSAWLKAKNGEAAIVIGTRSSLFTPFKDLGVIVIDEEHDSSYKQQEGWRYHARDLAVWRAHSEQIPIILGSATPALETLHNVRQGKYRQLTLSKRAGNARPAQQHVLDLKGQPLQAGLSPALISRMRQHLQADNQVILFLNRRGFAPALLCHDCGWIAECPRCDSYYTLHQAQHHLRCHHCDSQRPIPRQCPSCGSTHLVPVGIGTEQLEQALAPLFPEVPISRIDRDTTSRKGALEEHLAAVHRGGARILIGTQMLAKGHHFPDVTLVSLLDVDGALFSADFRSAERFAQLYTQVSGRAGRAGKQGEVILQTHHPEHPLLQTLLYKGYDAFAEQALAERQTMQLPPWTSHVLIRAEDHNNQQAPLFLQQLRNLLQASPLADEKLWVLGPVPALAPKRGGRWRWQILLQHPSRVRLQHIVSGTLALINTLPEARKVKWVLDVDPIEG

UniProtKB AC: A6TGC5 (positions: 1-731) UniProt Coverage: 100%

UniRef90 AC: UniRef90_B5XZ33 (positions: 1-731) UniRef90

Evidence Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding.

Chain C: Disordered Confirmed

The SSB C-terminal tail is intrinsically disordered (PMID: 15169953) and carries a well-known highly conserved linear motif on its very C-terminal end. The 113-178 region described in DisProt entry DP00722 covers 100% of the binding sequence in a homologous protein.

Chain A: Ordered

The dead box helicase and helicase C-terminal domains involved in the interaction are known to adopt a stable structure (see Pfam domain PF00270 and PF00271). A solved structure of this dead box helicase is represented by PDB ID 4nl4.

Related Structure(s) Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap).

No related structure was found in the Protein Data Bank.

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