1q79: Difference between revisions

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-{{Seed}}
-[[Image:1q79.png|left|200px]]
-<!--
+==CRYSTAL STRUCTURE OF MAMMALIAN POLY(A) POLYMERASE==
-The line below this paragraph, containing "STRUCTURE_1q79", creates the "Structure Box" on the page.
+<StructureSection load='1q79' size='340' side='right'caption='[[1q79]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1q79]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q79 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q79 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15&#8491;</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=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-{{STRUCTURE_1q79|  PDB=1q79  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1q79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q79 OCA], [https://pdbe.org/1q79 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q79 RCSB], [https://www.ebi.ac.uk/pdbsum/1q79 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q79 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PAPOA_BOVIN PAPOA_BOVIN] Polymerase that creates the 3'-poly(A) tail of mRNA's. Also required for the endoribonucleolytic cleavage reaction at some polyadenylation sites. May acquire specificity through interaction with a cleavage and polyadenylation specificity factor (CPSF) at its C-terminus.<ref>PMID:9463383</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/q7/1q79_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1q79 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Polyadenylation of messenger RNA precursors is an essential process in eukaryotes. Poly(A) polymerase (PAP), a member of the nucleotidyltransferase family that includes DNA polymerase beta, incorporates ATP at the 3' end of mRNAs in a template-independent manner. Although the structures of mammalian and yeast PAPs are known, their mechanism of ATP selection has remained elusive. In a recent bovine PAP structure complexed with an analog of ATP and Mn2+, strictly conserved residues interact selectively with the adenine base, but the nucleotide was found in a "non-productive" conformation. Here we report a second bovine crystal structure, obtained in the presence of Mg2+, where 3'-dATP adopts a "productive" conformation similar to that seen in yeast PAP or DNA polymerase beta. Mutational analysis and activity assays with ATP analogs suggest a role in catalysis for one of the two adenine-binding sites revealed by our structural data. The other site might function to prevent futile hydrolysis of ATP. In order to investigate the role of metals in catalysis we performed steady state kinetics experiments under distributive polymerization conditions. These tests suggest a sequential random mechanism in vitro in the presence of ATP and RNA, without preference for a particular order of binding of the two substrates. In vivo, however, where polyadenylation is processive and the primer does not dissociate from the enzyme, an ordered mechanism with the primer as the leading substrate is more likely.
-===CRYSTAL STRUCTURE OF MAMMALIAN POLY(A) POLYMERASE===
+Biochemical and structural insights into substrate binding and catalytic mechanism of mammalian poly(A) polymerase.,Martin G, Moglich A, Keller W, Doublie S J Mol Biol. 2004 Aug 20;341(4):911-25. PMID:15328606<ref>PMID:15328606</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1q79" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15328606}}, adds the Publication Abstract to the page
+*[[Poly(A) polymerase 3D structures|Poly(A) polymerase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15328606 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15328606}}
+__TOC__
+</StructureSection>
-==About this Structure==
-Q79 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q79 OCA].
-==Reference==
-Biochemical and structural insights into substrate binding and catalytic mechanism of mammalian poly(A) polymerase., Martin G, Moglich A, Keller W, Doublie S, J Mol Biol. 2004 Aug 20;341(4):911-25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15328606 15328606]
 [[Category: Bos taurus]]
-[[Category: Polynucleotide adenylyltransferase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Doublie S]]
-[[Category: Doublie, S.]]
+[[Category: Keller W]]
-[[Category: Keller, W.]]
+[[Category: Martin G]]
-[[Category: Martin, G.]]
+[[Category: Moglich A]]
-[[Category: Moglich, A.]]
-[[Category: Mrna processing]]
-[[Category: Nucleotidyl transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 20:43:08 2008''