1f5a: Difference between revisions

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-{{Seed}}
-[[Image:1f5a.png|left|200px]]
-<!--
+==CRYSTAL STRUCTURE OF MAMMALIAN POLY(A) POLYMERASE==
-The line below this paragraph, containing "STRUCTURE_1f5a", creates the "Structure Box" on the page.
+<StructureSection load='1f5a' size='340' side='right'caption='[[1f5a]], [[Resolution|resolution]] 2.50&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'>[[1f5a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. The October 2008 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Poly(A) Polymerase''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2008_10 10.2210/rcsb_pdb/mom_2008_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F5A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F5A 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]] 2.5&#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=3PO:TRIPHOSPHATE'>3PO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_1f5a|  PDB=1f5a  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1f5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f5a OCA], [https://pdbe.org/1f5a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f5a RCSB], [https://www.ebi.ac.uk/pdbsum/1f5a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f5a 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/f5/1f5a_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=1f5a ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA. We have solved the crystal structure of bovine poly(A) polymerase bound to an ATP analog at 2.5 A resolution. The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase. The C-terminal domain unexpectedly folds into a compact domain reminiscent of the RNA-recognition motif fold. The three invariant aspartates of the catalytic triad ligate two of the three active site metals. One of these metals also contacts the adenine ring. Furthermore, conserved, catalytically important residues contact the nucleotide. These contacts, taken together with metal coordination of the adenine base, provide a structural basis for ATP selection by poly(A) polymerase.
-===CRYSTAL STRUCTURE OF MAMMALIAN POLY(A) POLYMERASE===
+Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP.,Martin G, Keller W, Doublie S EMBO J. 2000 Aug 15;19(16):4193-203. PMID:10944102<ref>PMID:10944102</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1f5a" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10944102}}, 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 10944102 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10944102}}
+__TOC__
+</StructureSection>
-==About this Structure==
-F5A 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=1F5A OCA].
-==Reference==
-Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP., Martin G, Keller W, Doublie S, EMBO J. 2000 Aug 15;19(16):4193-203. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10944102 10944102]
 [[Category: Bos taurus]]
-[[Category: Polynucleotide adenylyltransferase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Doublie, S.]]
+[[Category: Doublie S]]
-[[Category: Keller, W.]]
+[[Category: Keller W]]
-[[Category: Martin, G.]]
+[[Category: Martin G]]
-[[Category: Alternative splicing helical turn motif]]
-[[Category: Mrna processing]]
-[[Category: Nuclear protein]]
-[[Category: Nucleotidyl transferase catalytic domain]]
-[[Category: Phosphorylation]]
-[[Category: Rna-binding]]
-[[Category: Transcription]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 02:43:10 2008''