3kgd

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[[Image:3kgd.png|left|200px]]
 
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==Crystal structure of E. coli RNA 3' cyclase==
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The line below this paragraph, containing "STRUCTURE_3kgd", creates the "Structure Box" on the page.
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<StructureSection load='3kgd' size='340' side='right'caption='[[3kgd]], [[Resolution|resolution]] 1.68&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3kgd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MG1655 Escherichia coli str. K-12 substr. MG1655]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KGD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KGD FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.68&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_3kgd| PDB=3kgd | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3kgd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kgd OCA], [https://pdbe.org/3kgd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kgd RCSB], [https://www.ebi.ac.uk/pdbsum/3kgd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kgd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RTCA_ECOLI RTCA_ECOLI] Catalyzes the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3'P to produce RNA-N3'PP5'A; (C) and attack of the adjacent 2'-hydroxyl on the 3'-phosphorus in the diester linkage to produce the cyclic end product. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing.<ref>PMID:9738023</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kg/3kgd_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3kgd ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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RNA 3'-phosphate cyclase (RtcA) synthesizes RNA 2',3' cyclic phosphate ends via three steps: reaction with ATP to form a covalent RtcA-AMP intermediate; transfer of adenylate to an RNA 3'-phosphate to form RNA(3')pp(5')A; and attack of the vicinal O2' on the 3'-phosphorus to form a 2',3' cyclic phosphate. Here we report the 1.7 A crystal structure of the RtcA-AMP intermediate, which reveals the mechanism of nucleotidyl transfer. Adenylate is linked via a phosphoamide bond to the His309 Nepsilon atom. A network of hydrogen bonds to the ribose O2' and O3' accounts for the stringent ribonucleotide preference. Adenine is sandwiched in a hydrophobic pocket between Tyr284 and Pro131 and the preference for adenine is enforced by Phe135, which packs against the purine C2 edge. Two sulfates bound near the adenylate plausibly mimic the 3'-terminal and penultimate phosphates of RNA. The structure illuminates how the four alpha2/beta4 domains contribute to substrate binding and catalysis.
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===Crystal structure of E. coli RNA 3' cyclase===
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Structure of the RNA 3'-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer.,Tanaka N, Smith P, Shuman S Structure. 2010 Mar 14;18(4):449-57. PMID:20399182<ref>PMID:20399182</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_20399182}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3kgd" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 20399182 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20399182}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Escherichia coli str. K-12 substr. MG1655]]
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[[3kgd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KGD OCA].
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[[Category: Large Structures]]
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[[Category: Shuman S]]
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==Reference==
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[[Category: Smith P]]
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<ref group="xtra">PMID:020399182</ref><references group="xtra"/>
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[[Category: Tanaka N]]
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[[Category: Escherichia coli]]
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[[Category: RNA-3'-phosphate cyclase]]
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[[Category: Shuman, S.]]
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[[Category: Smith, P.]]
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[[Category: Tanaka, N.]]
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[[Category: 3' modifying enzyme]]
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[[Category: Adenylate]]
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[[Category: Cyclase]]
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[[Category: Ligase]]
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[[Category: Phosphoramidate]]
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[[Category: Rna processing]]
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Current revision

Crystal structure of E. coli RNA 3' cyclase

PDB ID 3kgd

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