1je5: Difference between revisions

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-[[Image:1je5.jpg|left|200px]]<br /><applet load="1je5" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1je5, resolution 1.90&Aring;" />
-'''Crystal Structure of gp2.5, a Single-Stranded DNA Binding Protein Encoded by Bacteriophage T7'''<br />
-==Overview==
+==Crystal Structure of gp2.5, a Single-Stranded DNA Binding Protein Encoded by Bacteriophage T7==
-The gene 2.5 protein (gp2.5) of bacteriophage T7 is a single-stranded DNA, (ssDNA) binding protein that has essential roles in DNA replication and, recombination. In addition to binding DNA, gp2.5 physically interacts with, T7 DNA polymerase and T7 primase-helicase during replication to coordinate, events at the replication fork. We have determined a 1.9-A crystal, structure of gp2.5 and show that it has a conserved OB-fold, (oligosaccharide/oligonucleotide binding fold) that is well adapted for, interactions with ssDNA. Superposition of the OB-folds of gp2.5 and other, ssDNA binding proteins reveals a conserved patch of aromatic residues that, stack against the bases of ssDNA in the other crystal structures, suggesting that gp2.5 binds to ssDNA in a similar manner. An acidic, C-terminal extension of the gp2.5 protein, which is required for dimer, formation and for interactions with the T7 DNA polymerase and the, primase-helicase, appears to be flexible and may act as a switch that, modulates the DNA binding affinity of gp2.5.
+<StructureSection load='1je5' size='340' side='right'caption='[[1je5]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1je5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JE5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JE5 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]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=1je5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1je5 OCA], [https://pdbe.org/1je5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1je5 RCSB], [https://www.ebi.ac.uk/pdbsum/1je5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1je5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SSB_BPT7 SSB_BPT7] Single-stranded DNA-binding protein that participates in viral DNA replication, formation of concatemers, recombination and repair of double-stranded breaks (PubMed:16807232, PubMed:8617248, PubMed:9079662, PubMed:11222583). Coats the lagging-strand ssDNA as the replication fork advances and stimulates the activities of viral DNA polymerase and primase/helicase (PubMed:8617248). Coordinates simultaneous synthesis of leading- and lagging-strands (PubMed:9651583). Together with DNA primase/helicase, promotes pairing of two homologous DNA molecules containing complementary single-stranded regions and mediates homologous DNA strand exchange (PubMed:8617248). Promotes also the formation of joint molecules (PubMed:8617248, PubMed:9079662). Disrupts loops, hairpins and other secondary structures present on ssDNA to reduce and eliminate pausing of viral DNA polymerase at specific sites during elongation (PubMed:1634538).[HAMAP-Rule:MF_04153]<ref>PMID:11222583</ref> <ref>PMID:1634538</ref> <ref>PMID:16807232</ref> <ref>PMID:8617248</ref> <ref>PMID:9079662</ref> <ref>PMID:9651583</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/je/1je5_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=1je5 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-JE5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t7 Bacteriophage t7] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JE5 OCA].
+*[[Single-stranded DNA-binding protein 3D structures|Single-stranded DNA-binding protein 3D structures]]
+== References ==
-==Reference==
+<references/>
-Structure of the gene 2.5 protein, a single-stranded DNA binding protein encoded by bacteriophage T7., Hollis T, Stattel JM, Walther DS, Richardson CC, Ellenberger T, Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9557-62. Epub 2001 Jul 31. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11481454 11481454]
+__TOC__
-[[Category: Bacteriophage t7]]
+</StructureSection>
-[[Category: Single protein]]
+[[Category: Escherichia phage T7]]
-[[Category: Ellenberger, T.E.]]
+[[Category: Large Structures]]
-[[Category: Hollis, T.]]
+[[Category: Ellenberger TE]]
-[[Category: Richardson, C.C.]]
+[[Category: Hollis T]]
-[[Category: Stattel, J.M.]]
+[[Category: Richardson CC]]
-[[Category: Walther, D.S.]]
+[[Category: Stattel JM]]
-[[Category: CA]]
+[[Category: Walther DS]]
-[[Category: beta barrel]]
-[[Category: ob-fold]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:09:22 2007''