1urj: Difference between revisions

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-[[Image:1urj.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1urj", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1urj|  PDB=1urj  |  SCENE=  }}
-'''SINGLE STRANDED DNA-BINDING PROTEIN(ICP8) FROM HERPES SIMPLEX VIRUS-1'''
+==Single stranded DNA-binding protein(ICP8) from Herpes simplex virus-1==
+<StructureSection load='1urj' size='340' side='right'caption='[[1urj]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1urj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_alphaherpesvirus_1 Human alphaherpesvirus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1URJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1URJ FirstGlance]. <br>
+</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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1urj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1urj OCA], [https://pdbe.org/1urj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1urj RCSB], [https://www.ebi.ac.uk/pdbsum/1urj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1urj ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DNBI_HHV11 DNBI_HHV11] Plays several crucial roles in viral infection. Participates in the opening of the viral DNA origin to initiate replication by interacting with the origin-binding protein UL9. May disrupt loops, hairpins and other secondary structures present on ssDNA to reduce and eliminate pausing of viral DNA polymerase at specific sites during elongation. Promotes viral DNA recombination by performing strand-transfer, characterized by the ability to transfer a DNA strand from a linear duplex to a complementary single-stranded DNA circle. Can also catalyze the renaturation of complementary single strands.<ref>PMID:15078942</ref> <ref>PMID:7961904</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/ur/1urj_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=1urj ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+All organisms including animal viruses use specific proteins to bind single-stranded DNA rapidly in a non-sequence-specific, flexible, and cooperative manner during the DNA replication process. The crystal structure of a 60-residue C-terminal deletion construct of ICP8, the major single-stranded DNA-binding protein from herpes simplex virus-1, was determined at 3.0 A resolution. The structure reveals a novel fold, consisting of a large N-terminal domain (residues 9-1038) and a small C-terminal domain (residues 1049-1129). On the basis of the structure and the nearest neighbor interactions in the crystal, we have presented a model describing the site of single-stranded DNA binding and explaining the basis for cooperative binding. This model agrees with the beaded morphology observed in electron micrographs.
-==Overview==
+The crystal structure of the herpes simplex virus 1 ssDNA-binding protein suggests the structural basis for flexible, cooperative single-stranded DNA binding.,Mapelli M, Panjikar S, Tucker PA J Biol Chem. 2005 Jan 28;280(4):2990-7. Epub 2004 Oct 26. PMID:15507432<ref>PMID:15507432</ref>
-All organisms including animal viruses use specific proteins to bind single-stranded DNA rapidly in a non-sequence-specific, flexible, and cooperative manner during the DNA replication process. The crystal structure of a 60-residue C-terminal deletion construct of ICP8, the major single-stranded DNA-binding protein from herpes simplex virus-1, was determined at 3.0 A resolution. The structure reveals a novel fold, consisting of a large N-terminal domain (residues 9-1038) and a small C-terminal domain (residues 1049-1129). On the basis of the structure and the nearest neighbor interactions in the crystal, we have presented a model describing the site of single-stranded DNA binding and explaining the basis for cooperative binding. This model agrees with the beaded morphology observed in electron micrographs.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-URJ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_1 Human herpesvirus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1URJ OCA].
+</div>
+<div class="pdbe-citations 1urj" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-The crystal structure of the herpes simplex virus 1 ssDNA-binding protein suggests the structural basis for flexible, cooperative single-stranded DNA binding., Mapelli M, Panjikar S, Tucker PA, J Biol Chem. 2005 Jan 28;280(4):2990-7. Epub 2004 Oct 26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15507432 15507432]
+*[[Single-stranded DNA-binding protein 3D structures|Single-stranded DNA-binding protein 3D structures]]
-[[Category: Human herpesvirus 1]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Mapelli, M.]]
+__TOC__
-[[Category: Panjikar, S.]]
+</StructureSection>
-[[Category: Tucker, P A.]]
+[[Category: Human alphaherpesvirus 1]]
-[[Category: Dna replication]]
+[[Category: Large Structures]]
-[[Category: Dna-binding]]
+[[Category: Mapelli M]]
-[[Category: Hsv-1]]
+[[Category: Panjikar S]]
-[[Category: Icp8]]
+[[Category: Tucker PA]]
-[[Category: Nuclear protein.]]
-[[Category: Ssb]]
-[[Category: Zinc-finger]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 11:35:37 2008''