2p3l

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(New page: 200px<br /><applet load="2p3l" size="450" color="white" frame="true" align="right" spinBox="true" caption="2p3l, resolution 2.20&Aring;" /> '''Crystal Structure of...)
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[[Image:2p3l.jpg|left|200px]]<br /><applet load="2p3l" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2p3l, resolution 2.20&Aring;" />
 
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'''Crystal Structure of Dengue Methyltransferase in Complex with GpppA and S-Adenosyl-L-Homocysteine'''<br />
 
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==Overview==
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==Crystal Structure of Dengue Methyltransferase in Complex with GpppA and S-Adenosyl-L-Homocysteine==
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The N-terminal 33 kDa domain of non-structural protein 5 (NS5) of dengue, virus (DV), named NS5MTase(DV), is involved in two of four steps required, for the formation of the viral mRNA cap (7Me)GpppA(2'OMe), the guanine-N7, and the adenosine-2'O methylation. Its S-adenosyl-l-methionine (AdoMet), dependent 2'O-methyltransferase (MTase) activity has been shown on capped, (7Me+/-)GpppAC(n) RNAs. Here we report structural and binding studies, using cap analogues and capped RNAs. We have solved five crystal, structures at 1.8 A to 2.8 A resolution of NS5MTase(DV) in complex with, cap analogues and the co-product of methylation S-adenosyl-l-homocysteine, (AdoHcy). The cap analogues can adopt several conformations. The guanosine, moiety of all cap analogues occupies a GTP-binding site identified, earlier, indicating that GTP and cap share the same binding site., Accordingly, we show that binding of (7Me)GpppAC(4) and (7Me)GpppAC(5), RNAs is inhibited in the presence of GTP, (7Me)GTP and (7Me)GpppA but not, by ATP. This particular position of the cap is in accordance with the, 2'O-methylation step. A model was generated of a ternary 2'O-methylation, complex of NS5MTase(DV), (7Me)GpppA and AdoMet. RNA-binding increased when, (7Me+/-)GpppAGC(n-1) starting with the consensus sequence GpppAG, was used, instead of (7Me+/-)GpppAC(n). In the NS5MTase(DV)-GpppA complex the cap, analogue adopts a folded, stacked conformation uniquely possible when, adenine is the first transcribed nucleotide at the 5' end of nascent RNA, as it is the case in all flaviviruses. This conformation cannot be a, functional intermediate of methylation, since both the guanine-N7 and, adenosine-2'O positions are too far away from AdoMet. We hypothesize that, this conformation mimics the reaction product of a yet-to-be-demonstrated, guanylyltransferase activity. A putative Flavivirus RNA capping pathway is, proposed combining the different steps where the NS5MTase domain is, involved.
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<StructureSection load='2p3l' size='340' side='right'caption='[[2p3l]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2p3l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dengue_virus_2 Dengue virus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P3L FirstGlance]. <br>
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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]] 2.2&#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=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=G3A:GUANOSINE-P3-ADENOSINE-5,5-TRIPHOSPHATE'>G3A</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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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=2p3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p3l OCA], [https://pdbe.org/2p3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p3l RCSB], [https://www.ebi.ac.uk/pdbsum/2p3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p3l ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q9WLZ5_9FLAV Q9WLZ5_9FLAV] Component of the viral RNA replication complex that functions in virion assembly and antagonizes the host immune response.[ARBA:ARBA00024317] Functions as a signal peptide for NS4B and is required for the interferon antagonism activity of the latter.[ARBA:ARBA00003504] Serine protease subunit NS2B: Required cofactor for the serine protease function of NS3.[PROSITE-ProRule:PRU00859]
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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/p3/2p3l_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2p3l 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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The N-terminal 33 kDa domain of non-structural protein 5 (NS5) of dengue virus (DV), named NS5MTase(DV), is involved in two of four steps required for the formation of the viral mRNA cap (7Me)GpppA(2'OMe), the guanine-N7 and the adenosine-2'O methylation. Its S-adenosyl-l-methionine (AdoMet) dependent 2'O-methyltransferase (MTase) activity has been shown on capped (7Me+/-)GpppAC(n) RNAs. Here we report structural and binding studies using cap analogues and capped RNAs. We have solved five crystal structures at 1.8 A to 2.8 A resolution of NS5MTase(DV) in complex with cap analogues and the co-product of methylation S-adenosyl-l-homocysteine (AdoHcy). The cap analogues can adopt several conformations. The guanosine moiety of all cap analogues occupies a GTP-binding site identified earlier, indicating that GTP and cap share the same binding site. Accordingly, we show that binding of (7Me)GpppAC(4) and (7Me)GpppAC(5) RNAs is inhibited in the presence of GTP, (7Me)GTP and (7Me)GpppA but not by ATP. This particular position of the cap is in accordance with the 2'O-methylation step. A model was generated of a ternary 2'O-methylation complex of NS5MTase(DV), (7Me)GpppA and AdoMet. RNA-binding increased when (7Me+/-)GpppAGC(n-1) starting with the consensus sequence GpppAG, was used instead of (7Me+/-)GpppAC(n). In the NS5MTase(DV)-GpppA complex the cap analogue adopts a folded, stacked conformation uniquely possible when adenine is the first transcribed nucleotide at the 5' end of nascent RNA, as it is the case in all flaviviruses. This conformation cannot be a functional intermediate of methylation, since both the guanine-N7 and adenosine-2'O positions are too far away from AdoMet. We hypothesize that this conformation mimics the reaction product of a yet-to-be-demonstrated guanylyltransferase activity. A putative Flavivirus RNA capping pathway is proposed combining the different steps where the NS5MTase domain is involved.
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==About this Structure==
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Structural and functional analysis of methylation and 5'-RNA sequence requirements of short capped RNAs by the methyltransferase domain of dengue virus NS5.,Egloff MP, Decroly E, Malet H, Selisko B, Benarroch D, Ferron F, Canard B J Mol Biol. 2007 Sep 21;372(3):723-36. Epub 2007 Jul 12. PMID:17686489<ref>PMID:17686489</ref>
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2P3L is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Dengue_virus_type_4 Dengue virus type 4] with SO4, SAH, G3A, CIT and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2P3L OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structural and Functional Analysis of Methylation and 5'-RNA Sequence Requirements of Short Capped RNAs by the Methyltransferase Domain of Dengue Virus NS5., Egloff MP, Decroly E, Malet H, Selisko B, Benarroch D, Ferron F, Canard B, J Mol Biol. 2007 Jul 12;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17686489 17686489]
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</div>
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[[Category: Dengue virus type 4]]
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<div class="pdbe-citations 2p3l" style="background-color:#fffaf0;"></div>
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[[Category: RNA-directed RNA polymerase]]
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== References ==
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[[Category: Single protein]]
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<references/>
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[[Category: Egloff, M.P.]]
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__TOC__
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[[Category: MSGP, Marseilles.Structural.Genomics.Program.@.AFMB.]]
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</StructureSection>
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[[Category: CIT]]
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[[Category: Dengue virus 2]]
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[[Category: G3A]]
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[[Category: Large Structures]]
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[[Category: GOL]]
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[[Category: Egloff MP]]
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[[Category: SAH]]
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[[Category: SO4]]
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[[Category: transferase]]
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[[Category: viral protein]]
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[[Category: vizier; viral enzymes involved in replication; dengue virus methyltransferase; structural genomics; marseilles structural genomics program @ afmb; msgp]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:24:31 2007''
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Current revision

Crystal Structure of Dengue Methyltransferase in Complex with GpppA and S-Adenosyl-L-Homocysteine

PDB ID 2p3l

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