2r7c

From Proteopedia

(Difference between revisions)

Revision as of 11:27, 5 September 2018

Crystallographic and biochemical analysis of rotavirus NSP2 with nucleotides reveals an NDP kinase like activity

Structural highlights

2r7c is a 1 chain structure with sequence from Rotsr. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	1l9v, 2r7j, 2r7p, 2r8f
Gene:	S8, SEGMENT 8 (ROTSR)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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 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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kumar M, Jayaram H, Vasquez-Del Carpio R, Jiang X, Taraporewala ZF, Jacobson RH, Patton JT, Prasad BV. Crystallographic and biochemical analysis of rotavirus NSP2 with nucleotides reveals a nucleoside diphosphate kinase-like activity. J Virol. 2007 Nov;81(22):12272-84. Epub 2007 Sep 5. PMID:17804496 doi:http://dx.doi.org/10.1128/JVI.00984-07

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2r7c"

@@ Line 1: / Line 1: @@
 ==Crystallographic and biochemical analysis of rotavirus NSP2 with nucleotides reveals an NDP kinase like activity==
 <StructureSection load='2r7c' size='340' side='right' caption='[[2r7c]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
@@ Line 7: / Line 8: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1l9v|1l9v]], [[2r7j|2r7j]], [[2r7p|2r7p]], [[2r8f|2r8f]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">S8, SEGMENT 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36435 ROTSR])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r7c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r7c OCA], [http://pdbe.org/2r7c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r7c RCSB], [http://www.ebi.ac.uk/pdbsum/2r7c PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r7c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r7c OCA], [http://pdbe.org/2r7c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r7c RCSB], [http://www.ebi.ac.uk/pdbsum/2r7c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2r7c ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 15: / Line 16: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r7/2r7c_consurf.spt"</scriptWhenChecked>
+    <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/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

2r7c

From Proteopedia

Revision as of 11:27, 5 September 2018

Crystallographic and biochemical analysis of rotavirus NSP2 with nucleotides reveals an NDP kinase like activity

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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