2r7c: Difference between revisions

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-[[Image:2r7c.png|left|200px]]
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+==Crystallographic and biochemical analysis of rotavirus NSP2 with nucleotides reveals an NDP kinase like activity==
-The line below this paragraph, containing "STRUCTURE_2r7c", creates the "Structure Box" on the page.
+<StructureSection load='2r7c' size='340' side='right'caption='[[2r7c]], [[Resolution|resolution]] 2.70&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'>[[2r7c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Simian_11_rotavirus_(serotype_3_/_strain_SA11-Ramig) Simian 11 rotavirus (serotype 3 / strain SA11-Ramig)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R7C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R7C 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]] 2.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PSH:1-THIOPHOSPHONO-L-HISTIDINE'>PSH</scene></td></tr>
-{{STRUCTURE_2r7c|  PDB=2r7c  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2r7c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r7c OCA], [https://pdbe.org/2r7c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r7c RCSB], [https://www.ebi.ac.uk/pdbsum/2r7c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r7c ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NSP2_ROTSR NSP2_ROTSR] Involved in genome replication and packaging. Plays a crucial role, together with NSP5, in the formation of virus factories (viroplasms) which are large inclusions in the cytoplasm where replication intermediates are assembled and RNA replication takes place. Displays ssRNA binding, NTPase, RNA triphosphatase (RTPase) and ATP-independent helix-unwinding activity activities. The unwiding activity may prepare and organize plus-strand RNAs for packaging and replication by removing interfering secondary structures. Unlike typical helicases, NSP2 requires neither a divalent cation nor a nucleotide energy source for helix destabilization. The RTPase activity may account for the absence of the 5'-terminal gamma-phosphate on the minus-strands of dsRNA genome segments (By similarity).
+== 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/r7/2r7c_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=2r7c ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Rotavirus, the major pathogen of infantile gastroenteritis, carries a nonstructural protein, NSP2, essential for viroplasm formation and genome replication/packaging. In addition to RNA-binding and helix-destabilizing properties, NSP2 exhibits nucleoside triphosphatase activity. A conserved histidine (H225) functions as the catalytic residue for this enzymatic activity, and mutation of this residue abrogates genomic double-stranded RNA synthesis without affecting viroplasm formation. To understand the structural basis of the phosphatase activity of NSP2, we performed crystallographic analyses of native NSP2 and a functionally defective H225A mutant in the presence of nucleotides. These studies showed that nucleotides bind inside a cleft between the two domains of NSP2 in a region that exhibits structural similarity to ubiquitous cellular HIT (histidine triad) proteins. Only minor conformational alterations were observed in the cleft upon nucleotide binding and hydrolysis. This hydrolysis involved the formation of a stable phosphohistidine intermediate. These observations, reminiscent of cellular nucleoside diphosphate (NDP) kinases, prompted us to investigate whether NSP2 exhibits phosphoryl-transfer activity. Bioluminometric assay showed that NSP2 exhibits an NDP kinase-like activity that transfers the bound phosphate to NDPs. However, NSP2 is distinct from the highly conserved cellular NDP kinases in both its structure and catalytic mechanism, thus making NSP2 a potential target for antiviral drug design. With structural similarities to HIT proteins, which are not known to exhibit NDP kinase activity, NSP2 represents a unique example among structure-activity relationships. The newly observed phosphoryl-transfer activity of NSP2 may be utilized for homeostasis of nucleotide pools in viroplasms during genome replication.
-===Crystallographic and biochemical analysis of rotavirus NSP2 with nucleotides reveals an NDP kinase like activity===
+Crystallographic and biochemical analysis of rotavirus NSP2 with nucleotides reveals a nucleoside diphosphate kinase-like activity.,Kumar M, Jayaram H, Vasquez-Del Carpio R, Jiang X, Taraporewala ZF, Jacobson RH, Patton JT, Prasad BV J Virol. 2007 Nov;81(22):12272-84. Epub 2007 Sep 5. PMID:17804496<ref>PMID:17804496</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17804496}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2r7c" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17804496 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17804496}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[2r7c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R7C OCA].
+[[Category: Kumar M]]
+[[Category: Prasad BVV]]
-==Reference==
-<ref group="xtra">PMID:17804496</ref><ref group="xtra">PMID:12015608</ref><references group="xtra"/>
-[[Category: Viruses]]
-[[Category: Kumar, M.]]
-[[Category: Prasad, B V.V.]]
-[[Category: Ndp kinase]]
-[[Category: Non structural protein]]
-[[Category: Ntpase]]
-[[Category: Rna binding protein]]
-[[Category: Rna-binding]]
-[[Category: Rotavirus]]