2d7e: Difference between revisions

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<StructureSection load='2d7e' size='340' side='right'caption='[[2d7e]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='2d7e' size='340' side='right'caption='[[2d7e]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2d7e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D7E FirstGlance]. <br>
<table><tr><td colspan='2'>[[2d7e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D7E FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">priA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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]] 2.5&#8491;</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=2d7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7e OCA], [https://pdbe.org/2d7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d7e RCSB], [https://www.ebi.ac.uk/pdbsum/2d7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d7e ProSAT]</span></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=2d7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d7e OCA], [https://pdbe.org/2d7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d7e RCSB], [https://www.ebi.ac.uk/pdbsum/2d7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d7e ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[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>
[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>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2d7e ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2d7e ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In eubacteria, PriA helicase detects the stalled DNA replication forks. This critical role of PriA is ascribed to its ability to bind to the 3' end of a nascent leading DNA strand in the stalled replication forks. The crystal structures in complexes with oligonucleotides and the combination of fluorescence correlation spectroscopy and mutagenesis reveal that the N-terminal domain of PriA possesses a binding pocket for the 3'-terminal nucleotide residue of DNA. The interaction with the deoxyribose 3'-OH is essential for the 3'-terminal recognition. In contrast, the direct interaction with 3'-end nucleobase is unexpected, considering the same affinity for oligonucleotides carrying the four bases at the 3' end. Thus, the N-terminal domain of PriA recognizes the 3'-end base in a base-non-selective manner, in addition to the deoxyribose and 5'-side phosphodiester group, of the 3'-terminal nucleotide to acquire both sufficient affinity and non-selectivity to find all of the stalled replication forks generated during DNA duplication. This unique feature is prerequisite for the proper positioning of the helicase domain of PriA on the unreplicated double-stranded DNA.
Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA.,Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D EMBO J. 2007 May 16;26(10):2584-93. doi: 10.1038/sj.emboj.7601697. Epub 2007 Apr , 26. PMID:17464287<ref>PMID:17464287</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2d7e" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Kohda, D]]
[[Category: Kohda D]]
[[Category: Maenaka, K]]
[[Category: Maenaka K]]
[[Category: Masai, H]]
[[Category: Masai H]]
[[Category: Ose, T]]
[[Category: Ose T]]
[[Category: Sasaki, K]]
[[Category: Sasaki K]]
[[Category: Hydrolase]]
[[Category: Inter-twined]]

Latest revision as of 16:46, 13 March 2024

Crystal structure of N-terminal domain of PriA from E.coliCrystal structure of N-terminal domain of PriA from E.coli

Structural highlights

2d7e is a 4 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  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:http://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:http://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:http://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:http://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:http://dx.doi.org/10.1074/jbc.M112.435966

2d7e, resolution 2.50Å

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