1x9s: Difference between revisions

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-[[Image:1x9s.png|left|200px]]
-{{STRUCTURE_1x9s|  PDB=1x9s  |  SCENE=  }}
+==T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-CTP as the incoming nucleotide.==
+<StructureSection load='1x9s' size='340' side='right'caption='[[1x9s]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
-===T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-CTP as the incoming nucleotide.===
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1x9s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [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=1X9S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X9S FirstGlance]. <br>
-{{ABSTRACT_PUBMED_15528277}}
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2DT:3-DEOXYTHYMIDINE-5-MONOPHOSPHATE'>2DT</scene>, <scene name='pdbligand=AFG:N-(5-PHOSPHO-2-DEOXYGUANOSIN-8-YL)-2-AMINOFLUORENE'>AFG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-==About this Structure==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1x9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x9s OCA], [https://pdbe.org/1x9s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x9s RCSB], [https://www.ebi.ac.uk/pdbsum/1x9s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x9s ProSAT]</span></td></tr>
-[[1x9s]] is a 4 chain structure of [[DNA polymerase]] and [[Thioredoxin]] with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X9S OCA].
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPOL_BPT7 DPOL_BPT7] Replicates viral genomic DNA. Non-processive DNA polymerase that achieves processivity by binding to host thioredoxin (TrxA). This interaction increases the rate of dNTP incorporation to yield a processivity of approximately 800 nucleotides (nt) per binding event. Interacts with DNA helicase gp4 to coordinate nucleotide polymerization with unwinding of the DNA. The leading strand is synthesized continuously while synthesis of the lagging strand requires the synthesis of oligoribonucleotides by the primase domain of gp4.<ref>PMID:9218486</ref> <ref>PMID:21606333</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/x9/1x9s_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=1x9s ConSurf].
+<div style="clear:both"></div>
 ==See Also==
-*[[DNA polymerase|DNA polymerase]]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-*[[Thioredoxin|Thioredoxin]]
+*[[Thioredoxin 3D structures|Thioredoxin 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:015528277</ref><references group="xtra"/>
+__TOC__
-[[Category: DNA-directed DNA polymerase]]
+</StructureSection>
-[[Category: Enterobacteria phage t7]]
 [[Category: Escherichia coli]]
-[[Category: Dutta, S.]]
+[[Category: Escherichia phage T7]]
-[[Category: Dzantiev, L.]]
+[[Category: Large Structures]]
-[[Category: Ellenberger, T.]]
+[[Category: Dutta S]]
-[[Category: Johnson, D.]]
+[[Category: Dzantiev L]]
-[[Category: Li, Y.]]
+[[Category: Ellenberger T]]
-[[Category: Richardson, C C.]]
+[[Category: Johnson D]]
-[[Category: Romano, L J.]]
+[[Category: Li Y]]
-[[Category: Dna polymerase]]
+[[Category: Richardson CC]]
-[[Category: Mutagenesis]]
+[[Category: Romano LJ]]
-[[Category: N-2-aminofluorene]]
-[[Category: Replication block]]
-[[Category: Transferase-electron transport-dna complex]]