2dwn

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the PriA protein complexed with oligonucleotides

Structural highlights

2dwn is a 6 chain structure with sequence from Escherichia coli K-12 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.35Å
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.

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^[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:http://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:http://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:http://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:http://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:http://dx.doi.org/10.1074/jbc.M112.435966
↑ Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D. Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA. EMBO J. 2007 May 16;26(10):2584-93. doi: 10.1038/sj.emboj.7601697. Epub 2007 Apr , 26. PMID:17464287 doi:http://dx.doi.org/10.1038/sj.emboj.7601697

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2dwn"

@@ Line 3: / Line 3: @@
 <StructureSection load='2dwn' size='340' side='right'caption='[[2dwn]], [[Resolution|resolution]] 3.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2dwn]] is a 6 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=2DWN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DWN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2dwn]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DWN FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2d7e|2d7e]], [[2d7g|2d7g]], [[2d7h|2d7h]], [[2dwl|2dwl]], [[2dwm|2dwm]]</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]] 3.35&#8491;</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=2dwn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dwn OCA], [https://pdbe.org/2dwn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dwn RCSB], [https://www.ebi.ac.uk/pdbsum/2dwn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dwn 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=2dwn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dwn OCA], [http://pdbe.org/2dwn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dwn RCSB], [http://www.ebi.ac.uk/pdbsum/2dwn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dwn 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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 30: @@
 ==See Also==
-*[[Helicase|Helicase]]
+*[[Helicase 3D structures|Helicase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Kohda, D]]
+[[Category: Synthetic construct]]
-[[Category: Maenaka, K]]
+[[Category: Kohda D]]
-[[Category: Masai, H]]
+[[Category: Maenaka K]]
-[[Category: Ose, T]]
+[[Category: Masai H]]
-[[Category: Sasaki, K]]
+[[Category: Ose T]]
-[[Category: Tanaka, T]]
+[[Category: Sasaki K]]
-[[Category: Hydrolase-dna complex]]
+[[Category: Tanaka T]]
-[[Category: Protein-dna complex]]

2dwn

From Proteopedia

Current revision

Crystal structure of the PriA protein complexed with oligonucleotides

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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