2dwn: Difference between revisions

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-{{Seed}}
-[[Image:2dwn.png|left|200px]]
-<!--
+==Crystal structure of the PriA protein complexed with oligonucleotides==
-The line below this paragraph, containing "STRUCTURE_2dwn", creates the "Structure Box" on the page.
+<StructureSection load='2dwn' size='340' side='right'caption='[[2dwn]], [[Resolution|resolution]] 3.35&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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='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>
-{{STRUCTURE_2dwn|  PDB=2dwn  |  SCENE=  }}
+</table>
+== 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>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dw/2dwn_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2dwn ConSurf].
+<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.
-===Crystal structure of the PriA protein complexed with oligonucleotides===
+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 2dwn" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-DWN is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWN OCA].
+*[[Helicase 3D structures|Helicase 3D structures]]
-[[Category: Escherichia coli]]
+== References ==
-[[Category: Kohda, D.]]
+<references/>
-[[Category: Maenaka, K.]]
+__TOC__
-[[Category: Masai, H.]]
+</StructureSection>
-[[Category: Ose, T.]]
+[[Category: Escherichia coli K-12]]
-[[Category: Sasaki, K.]]
+[[Category: Large Structures]]
-[[Category: Tanaka, T.]]
+[[Category: Synthetic construct]]
-[[Category: Hydrolase-dna complex]]
+[[Category: Kohda D]]
-[[Category: Protein-dna complex]]
+[[Category: Maenaka K]]
+[[Category: Masai H]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 21 08:52:00 2010''
+[[Category: Ose T]]
+[[Category: Sasaki K]]
+[[Category: Tanaka T]]