3erc: Difference between revisions
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<table><tr><td colspan='2'>[[3erc]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Vaccinia_virus_WR Vaccinia virus WR]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ERC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ERC FirstGlance]. <br> | <table><tr><td colspan='2'>[[3erc]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Vaccinia_virus_WR Vaccinia virus WR]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ERC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ERC 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]] 3.21Å</td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.21Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3AT:3-DEOXYADENOSINE-5-TRIPHOSPHATE'>3AT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3AT:3-DEOXYADENOSINE-5-TRIPHOSPHATE'>3AT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</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=3erc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3erc OCA], [https://pdbe.org/3erc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3erc RCSB], [https://www.ebi.ac.uk/pdbsum/3erc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3erc ProSAT]</span></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=3erc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3erc OCA], [https://pdbe.org/3erc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3erc RCSB], [https://www.ebi.ac.uk/pdbsum/3erc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3erc ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/ | [https://www.uniprot.org/uniprot/PAP1_VACCW PAP1_VACCW] Polymerase that creates the 3'-poly(A) tail of mRNA's. | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/er/3erc_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/er/3erc_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
Latest revision as of 08:47, 17 October 2024
Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase with three fragments of RNA and 3'-deoxy ATPCrystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase with three fragments of RNA and 3'-deoxy ATP
Structural highlights
FunctionPAP1_VACCW Polymerase that creates the 3'-poly(A) tail of mRNA's. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedVaccinia virus protein VP55 translocates continuously with respect to single-stranded nucleic acid while extending its 3'end. Here, all key sites of polymerase-primer interaction were identified, demonstrating the wrapping or looping of polyadenylation primer around the polymerase during translocation. Side-chain substitutions at one of the sites indicated its requirement for tail extension beyond approximately 12 nucleotides in length, and conformational changes observed upon oligonucleotide binding suggested allosteric connectivity during translocation. Conformational changes in VP39 upon VP55 binding suggested that, within the VP55-VP39 complex, VP39's mRNA 5' cap binding site closes. The crystallographic structure showed a PAPase catalytic center without side-chain substitutions, possessing two metal ions and with all known reactive and catalytic groups represented, fitting a classical two-metal ion mechanism for phosphoryl transfer. Polymerase translocation with respect to single-stranded nucleic acid: looping or wrapping of primer around a poly(A) polymerase.,Li C, Li H, Zhou S, Sun E, Yoshizawa J, Poulos TL, Gershon PD Structure. 2009 May 13;17(5):680-9. PMID:19446524[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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