1e0k: Difference between revisions

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-[[Image:1e0k.png|left|200px]]
-{{STRUCTURE_1e0k|  PDB=1e0k  |  SCENE=  }}
+==gp4d helicase from phage T7==
+<StructureSection load='1e0k' size='340' side='right'caption='[[1e0k]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1e0k]] is a 6 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=1E0K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E0K 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]] 3.3&#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=1e0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0k OCA], [https://pdbe.org/1e0k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e0k RCSB], [https://www.ebi.ac.uk/pdbsum/1e0k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e0k ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HELIC_BPT7 HELIC_BPT7] ATP-dependent DNA helicase and primase essential for viral DNA replication and recombination (PubMed:21606333, PubMed:22977246, PubMed:32009150). The helicase moves 5' -> 3' on the lagging strand template, unwinding the DNA duplex ahead of the leading strand polymerase at the replication fork and generating ssDNA for both leading and lagging strand synthesis (PubMed:21606333, PubMed:22977246, PubMed:32009150). ATP or dTTP hydrolysis propels each helicase domain to translocate 2 nt per step sequentially along DNA (PubMed:30679383, PubMed:17604719). Mediates strand transfer when a joint molecule is available and participates in recombinational DNA repair through its role in strand exchange (PubMed:9096333, PubMed:8617248). Primase activity synthesizes short RNA primers at the sequence 5'-GTC-3' on the lagging strand that the polymerase elongates using dNTPs and providing the primase is still present (PubMed:6454135, PubMed:9139692).[HAMAP-Rule:MF_04154]<ref>PMID:17604719</ref> <ref>PMID:21606333</ref> <ref>PMID:22977246</ref> <ref>PMID:30679383</ref> <ref>PMID:32009150</ref> <ref>PMID:6454135</ref> <ref>PMID:8617248</ref> <ref>PMID:9096333</ref> <ref>PMID:9139692</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/e0/1e0k_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=1e0k ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We have determined the crystal structure of an active, hexameric fragment of the gene 4 helicase from bacteriophage T7. The structure reveals how subunit contacts stabilize the hexamer. Deviation from expected six-fold symmetry of the hexamer indicates that the structure is of an intermediate on the catalytic pathway. The structural consequences of the asymmetry suggest a "binding change" mechanism to explain how cooperative binding and hydrolysis of nucleotides are coupled to conformational changes in the ring that most likely accompany duplex unwinding. The structure of a complex with a nonhydrolyzable ATP analog provides additional evidence for this hypothesis, with only four of the six possible nucleotide binding sites being occupied in this conformation of the hexamer. This model suggests a mechanism for DNA translocation.
-===GP4D HELICASE FROM PHAGE T7===
+Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides.,Singleton MR, Sawaya MR, Ellenberger T, Wigley DB Cell. 2000 Jun 9;101(6):589-600. PMID:10892646<ref>PMID:10892646</ref>
-{{ABSTRACT_PUBMED_10892646}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1e0k" style="background-color:#fffaf0;"></div>
-[[1e0k]] is a 6 chain structure of [[Helicase]] with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t7 Enterobacteria phage t7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E0K OCA].
 ==See Also==
-*[[Helicase|Helicase]]
+*[[Helicase 3D structures|Helicase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:010892646</ref><ref group="xtra">PMID:015479787</ref><references group="xtra"/>
+__TOC__
-[[Category: Enterobacteria phage t7]]
+</StructureSection>
-[[Category: Ellenberger, T.]]
+[[Category: Escherichia phage T7]]
-[[Category: Sawaya, M R.]]
+[[Category: Large Structures]]
-[[Category: Singleton, M R.]]
+[[Category: Ellenberger T]]
-[[Category: Wigley, D B.]]
+[[Category: Sawaya MR]]
-[[Category: Atpase]]
+[[Category: Singleton MR]]
-[[Category: Dna replication]]
+[[Category: Wigley DB]]
-[[Category: Helicase]]