1cr4: Difference between revisions

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-[[Image:1cr4.gif|left|200px]]<br /><applet load="1cr4" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1cr4, resolution 2.50&Aring;" />
-'''CRYSTAL STRUCTURE OF THE HELICASE DOMAIN OF THE GENE 4 PROTEIN OF BACTERIOPHAGE T7: COMPLEX WITH DTDP'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF THE HELICASE DOMAIN OF THE GENE 4 PROTEIN OF BACTERIOPHAGE T7: COMPLEX WITH DTDP==
-Helicases that unwind DNA at the replication fork are ring-shaped, oligomeric enzymes that move along one strand of a DNA duplex and catalyze, the displacement of the complementary strand in a reaction that is coupled, to nucleotide hydrolysis. The helicase domain of the replicative, helicase-primase protein from bacteriophage T7 crystallized as a helical, filament that resembles the Escherichia coli RecA protein, an, ATP-dependent DNA strand exchange factor. When viewed in projection along, the helical axis of the crystals, six protomers of the T7 helicase domain, resemble the hexameric rings seen in electron microscopic images of the, intact T7 helicase-primase. Nucleotides bind at the interface between, pairs of adjacent subunits where an arginine is near the gamma-phosphate, of the nucleotide in trans. The bound nucleotide stabilizes the folded, conformation of a DNA-binding motif located near the center of the ring., These and other observations suggest how conformational changes are, coupled to DNA unwinding activity.
+<StructureSection load='1cr4' size='340' side='right'caption='[[1cr4]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1cr4]] is a 1 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=1CR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CR4 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]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</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=1cr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cr4 OCA], [https://pdbe.org/1cr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cr4 RCSB], [https://www.ebi.ac.uk/pdbsum/1cr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cr4 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/cr/1cr4_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=1cr4 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-CR4 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 SO4 and TYD as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1CR4 OCA].
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
+== References ==
-==Reference==
+<references/>
-Crystal structure of the helicase domain from the replicative helicase-primase of bacteriophage T7., Sawaya MR, Guo S, Tabor S, Richardson CC, Ellenberger T, Cell. 1999 Oct 15;99(2):167-77. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10535735 10535735]
+__TOC__
-[[Category: Bacteriophage t7]]
+</StructureSection>
-[[Category: Single protein]]
+[[Category: Escherichia phage T7]]
-[[Category: Ellenberger, T.]]
+[[Category: Large Structures]]
-[[Category: Guo, S.]]
+[[Category: Ellenberger T]]
-[[Category: Richardson, C.C.]]
+[[Category: Guo S]]
-[[Category: Sawaya, M.R.]]
+[[Category: Richardson CC]]
-[[Category: Tabor, S.]]
+[[Category: Sawaya MR]]
-[[Category: SO4]]
+[[Category: Tabor S]]
-[[Category: TYD]]
-[[Category: reca-type protein fold]]
-[[Category: transferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 12:41:35 2007''