6dcr: Difference between revisions

Latest revision as of 06:02, 11 October 2023

E. coli PriA helicase winged helix domain deletion protein

Structural highlights

6dcr is a 2 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.978Å
Ligands:	SO4, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PRIA_ECOLI Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA. Is also involved in initiation of normal DNA replication in various plasmids and phages. Binds to branched DNA structures that resemble D-loops or to the primosome assembly site (PAS). Binds to DNA in two distinct modes, either dependent on or independent of the 3' terminus recognition.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10]

Publication Abstract from PubMed

DNA replication restart, the essential process that reinitiates prematurely terminated genome replication reactions, relies on exquisitely specific recognition of abandoned DNA replication-fork structures. The PriA DNA helicase mediates this process in bacteria through mechanisms that remain poorly defined. We report the crystal structure of a PriA/replication-fork complex, which resolves leading-strand duplex DNA bound to the protein. Interaction with PriA unpairs one end of the DNA and sequesters the 3'-most nucleotide from the nascent leading strand into a conserved protein pocket. Cross-linking studies reveal a surface on the winged-helix domain of PriA that binds to parental duplex DNA. Deleting the winged-helix domain alters PriA's structure-specific DNA unwinding properties and impairs its activity in vivo. Our observations lead to a model in which coordinated parental-, leading-, and lagging-strand DNA binding provide PriA with the structural specificity needed to act on abandoned DNA replication forks.

Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase.,Windgassen TA, Leroux M, Satyshur KA, Sandler SJ, Keck JL Proc Natl Acad Sci U S A. 2018 Sep 10. pii: 1809842115. doi:, 10.1073/pnas.1809842115. PMID:30201718^[11]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Lee MS, Marians KJ. Escherichia coli replication factor Y, a component of the primosome, can act as a DNA helicase. Proc Natl Acad Sci U S A. 1987 Dec;84(23):8345-9. PMID:2825188
↑ Allen GC Jr, Kornberg A. Assembly of the primosome of DNA replication in Escherichia coli. J Biol Chem. 1993 Sep 15;268(26):19204-9. PMID:8366072
↑ Jones JM, Nakai H. Duplex opening by primosome protein PriA for replisome assembly on a recombination intermediate. J Mol Biol. 1999 Jun 11;289(3):503-16. PMID:10356325 doi:https://dx.doi.org/10.1006/jmbi.1999.2783
↑ Jezewska MJ, Bujalowski W. Interactions of Escherichia coli replicative helicase PriA protein with single-stranded DNA. Biochemistry. 2000 Aug 29;39(34):10454-67. PMID:10956036
↑ Rangarajan S, Woodgate R, Goodman MF. Replication restart in UV-irradiated Escherichia coli involving pols II, III, V, PriA, RecA and RecFOR proteins. Mol Microbiol. 2002 Feb;43(3):617-28. PMID:11929519
↑ Tanaka T, Taniyama C, Arai K, Masai H. ATPase/helicase motif mutants of Escherichia coli PriA protein essential for recombination-dependent DNA replication. Genes Cells. 2003 Mar;8(3):251-61. PMID:12622722
↑ Mizukoshi T, Tanaka T, Arai K, Kohda D, Masai H. A critical role of the 3' terminus of nascent DNA chains in recognition of stalled replication forks. J Biol Chem. 2003 Oct 24;278(43):42234-9. Epub 2003 Aug 13. PMID:12917421 doi:https://dx.doi.org/10.1074/jbc.C300285200
↑ Cadman CJ, McGlynn P. PriA helicase and SSB interact physically and functionally. Nucleic Acids Res. 2004 Dec 2;32(21):6378-87. Print 2004. PMID:15576682 doi:https://dx.doi.org/10.1093/nar/gkh980
↑ Tanaka T, Mizukoshi T, Sasaki K, Kohda D, Masai H. Escherichia coli PriA protein, two modes of DNA binding and activation of ATP hydrolysis. J Biol Chem. 2007 Jul 6;282(27):19917-27. Epub 2007 May 4. PMID:17483094 doi:https://dx.doi.org/10.1074/jbc.M701848200
↑ Manhart CM, McHenry CS. The PriA replication restart protein blocks replicase access prior to helicase assembly and directs template specificity through its ATPase activity. J Biol Chem. 2013 Feb 8;288(6):3989-99. doi: 10.1074/jbc.M112.435966. Epub 2012, Dec 20. PMID:23264623 doi:https://dx.doi.org/10.1074/jbc.M112.435966
↑ Windgassen TA, Leroux M, Satyshur KA, Sandler SJ, Keck JL. Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase. Proc Natl Acad Sci U S A. 2018 Sep 10. pii: 1809842115. doi:, 10.1073/pnas.1809842115. PMID:30201718 doi:https://dx.doi.org/10.1073/pnas.1809842115

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Lee MS, Marians KJ. Escherichia coli replication factor Y, a component of the primosome, can act as a DNA helicase. Proc Natl Acad Sci U S A. 1987 Dec;84(23):8345-9. PMID:2825188

[2] Allen GC Jr, Kornberg A. Assembly of the primosome of DNA replication in Escherichia coli. J Biol Chem. 1993 Sep 15;268(26):19204-9. PMID:8366072

[3] Jones JM, Nakai H. Duplex opening by primosome protein PriA for replisome assembly on a recombination intermediate. J Mol Biol. 1999 Jun 11;289(3):503-16. PMID:10356325 doi:https://dx.doi.org/10.1006/jmbi.1999.2783

[4] Jezewska MJ, Bujalowski W. Interactions of Escherichia coli replicative helicase PriA protein with single-stranded DNA. Biochemistry. 2000 Aug 29;39(34):10454-67. PMID:10956036

[5] Rangarajan S, Woodgate R, Goodman MF. Replication restart in UV-irradiated Escherichia coli involving pols II, III, V, PriA, RecA and RecFOR proteins. Mol Microbiol. 2002 Feb;43(3):617-28. PMID:11929519

[6] Tanaka T, Taniyama C, Arai K, Masai H. ATPase/helicase motif mutants of Escherichia coli PriA protein essential for recombination-dependent DNA replication. Genes Cells. 2003 Mar;8(3):251-61. PMID:12622722

[7] Mizukoshi T, Tanaka T, Arai K, Kohda D, Masai H. A critical role of the 3' terminus of nascent DNA chains in recognition of stalled replication forks. J Biol Chem. 2003 Oct 24;278(43):42234-9. Epub 2003 Aug 13. PMID:12917421 doi:https://dx.doi.org/10.1074/jbc.C300285200

[8] Cadman CJ, McGlynn P. PriA helicase and SSB interact physically and functionally. Nucleic Acids Res. 2004 Dec 2;32(21):6378-87. Print 2004. PMID:15576682 doi:https://dx.doi.org/10.1093/nar/gkh980

[9] Tanaka T, Mizukoshi T, Sasaki K, Kohda D, Masai H. Escherichia coli PriA protein, two modes of DNA binding and activation of ATP hydrolysis. J Biol Chem. 2007 Jul 6;282(27):19917-27. Epub 2007 May 4. PMID:17483094 doi:https://dx.doi.org/10.1074/jbc.M701848200

[10] Manhart CM, McHenry CS. The PriA replication restart protein blocks replicase access prior to helicase assembly and directs template specificity through its ATPase activity. J Biol Chem. 2013 Feb 8;288(6):3989-99. doi: 10.1074/jbc.M112.435966. Epub 2012, Dec 20. PMID:23264623 doi:https://dx.doi.org/10.1074/jbc.M112.435966

[11] Windgassen TA, Leroux M, Satyshur KA, Sandler SJ, Keck JL. Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase. Proc Natl Acad Sci U S A. 2018 Sep 10. pii: 1809842115. doi:, 10.1073/pnas.1809842115. PMID:30201718 doi:https://dx.doi.org/10.1073/pnas.1809842115

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@@ Line 3: / Line 3: @@
 <StructureSection load='6dcr' size='340' side='right'caption='[[6dcr]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6dcr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DCR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DCR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6dcr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DCR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DCR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.978&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4nl4|4nl4]], [[4nl8|4nl8]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">priA, b3935, JW3906 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6dcr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dcr OCA], [https://pdbe.org/6dcr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dcr RCSB], [https://www.ebi.ac.uk/pdbsum/6dcr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dcr ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6dcr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dcr OCA], [http://pdbe.org/6dcr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dcr RCSB], [http://www.ebi.ac.uk/pdbsum/6dcr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dcr ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PRIA_ECOLI PRIA_ECOLI]] Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA. Is also involved in initiation of normal DNA replication in various plasmids and phages. Binds to branched DNA structures that resemble D-loops or to the primosome assembly site (PAS). Binds to DNA in two distinct modes, either dependent on or independent of the 3' terminus recognition.<ref>PMID:2825188</ref> <ref>PMID:8366072</ref> <ref>PMID:10356325</ref> <ref>PMID:10956036</ref> <ref>PMID:11929519</ref> <ref>PMID:12622722</ref> <ref>PMID:12917421</ref> <ref>PMID:15576682</ref> <ref>PMID:17483094</ref> <ref>PMID:23264623</ref>
+[https://www.uniprot.org/uniprot/PRIA_ECOLI PRIA_ECOLI] Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA. Is also involved in initiation of normal DNA replication in various plasmids and phages. Binds to branched DNA structures that resemble D-loops or to the primosome assembly site (PAS). Binds to DNA in two distinct modes, either dependent on or independent of the 3' terminus recognition.<ref>PMID:2825188</ref> <ref>PMID:8366072</ref> <ref>PMID:10356325</ref> <ref>PMID:10956036</ref> <ref>PMID:11929519</ref> <ref>PMID:12622722</ref> <ref>PMID:12917421</ref> <ref>PMID:15576682</ref> <ref>PMID:17483094</ref> <ref>PMID:23264623</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Keck, J L]]
+[[Category: Keck JL]]
-[[Category: Satyshur, K A]]
+[[Category: Satyshur KA]]
-[[Category: Windgassen, T A]]
+[[Category: Windgassen TA]]
-[[Category: Dna binding protein]]
-[[Category: Dna replication restart]]
-[[Category: Helicase]]
-[[Category: Pria]]

6dcr: Difference between revisions

Latest revision as of 06:02, 11 October 2023

E. coli PriA helicase winged helix domain deletion protein

Structural highlights

Function

Publication Abstract from PubMed

References

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