1s49

From Proteopedia

(Difference between revisions)

Revision as of 01:28, 10 September 2015

Crystal Structure of RNA-dependent RNA polymerase construct 1 (residues 71-679) from bovine viral diarrhea virus complexed with GTP

Structural highlights

1s49 is a 1 chain structure with sequence from Bvdv. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	1s48, 1s4f
Gene:	NS5B (BVDV)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[POLG_BVDVN] Initial binding to target cell probably involves interaction of E(rns) with glycosaminoglycans. E1 and/or E2 are responsible of cell attachment with CD46 and subsequent fusion after internalization of the virion by endocytosis (Probable).^[1] ^[2] P7 forms a leader sequence to properly orient NS2 in the membrane (By similarity).^[3] ^[4] Uncleaved NS2-3 is required for production of infectious virus.^[5] ^[6] NS2 protease seems to play a vital role in viral RNA replication control and in the pathogenicity of the virus.^[7] ^[8] NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase.^[9] ^[10] NS4A is a cofactor for the NS3 protease activity (By similarity).^[11] ^[12] RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome.^[13] ^[14]

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

The bovine viral diarrhea virus (BVDV) RNA-dependent RNA polymerase can initiate RNA replication by a de novo mechanism without a primer. The structure of BVDV polymerase, determined to 2.9-A resolution, contains a unique N-terminal domain, in addition to the fingers, palm, and thumb domains common to other polymerases. The structure of BVDV polymerase complexed with GTP, which is required for de novo (primer-independent) initiation, shows that GTP binds adjacent to the initiation NTP, suggesting that the GTP mimics a vestigial RNA product. Comparison of five monomers in two different crystal forms showed conformational changes in the fingertip region and in the thumb domain that may help to translocate the RNA template and product strands during elongation. The putative binding sites of previously reported BVDV inhibitors are also discussed.

The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation.,Choi KH, Groarke JM, Young DC, Kuhn RJ, Smith JL, Pevear DC, Rossmann MG Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4425-30. Epub 2004 Mar 19. PMID:15070734^[15]

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

References

↑ Agapov EV, Murray CL, Frolov I, Qu L, Myers TM, Rice CM. Uncleaved NS2-3 is required for production of infectious bovine viral diarrhea virus. J Virol. 2004 Mar;78(5):2414-25. PMID:14963137
↑ Lecot S, Belouzard S, Dubuisson J, Rouille Y. Bovine viral diarrhea virus entry is dependent on clathrin-mediated endocytosis. J Virol. 2005 Aug;79(16):10826-9. PMID:16051874 doi:10.1128/JVI.79.16.10826-10829.2005
↑ Agapov EV, Murray CL, Frolov I, Qu L, Myers TM, Rice CM. Uncleaved NS2-3 is required for production of infectious bovine viral diarrhea virus. J Virol. 2004 Mar;78(5):2414-25. PMID:14963137
↑ Lecot S, Belouzard S, Dubuisson J, Rouille Y. Bovine viral diarrhea virus entry is dependent on clathrin-mediated endocytosis. J Virol. 2005 Aug;79(16):10826-9. PMID:16051874 doi:10.1128/JVI.79.16.10826-10829.2005
↑ Agapov EV, Murray CL, Frolov I, Qu L, Myers TM, Rice CM. Uncleaved NS2-3 is required for production of infectious bovine viral diarrhea virus. J Virol. 2004 Mar;78(5):2414-25. PMID:14963137
↑ Lecot S, Belouzard S, Dubuisson J, Rouille Y. Bovine viral diarrhea virus entry is dependent on clathrin-mediated endocytosis. J Virol. 2005 Aug;79(16):10826-9. PMID:16051874 doi:10.1128/JVI.79.16.10826-10829.2005
↑ Agapov EV, Murray CL, Frolov I, Qu L, Myers TM, Rice CM. Uncleaved NS2-3 is required for production of infectious bovine viral diarrhea virus. J Virol. 2004 Mar;78(5):2414-25. PMID:14963137
↑ Lecot S, Belouzard S, Dubuisson J, Rouille Y. Bovine viral diarrhea virus entry is dependent on clathrin-mediated endocytosis. J Virol. 2005 Aug;79(16):10826-9. PMID:16051874 doi:10.1128/JVI.79.16.10826-10829.2005
↑ Agapov EV, Murray CL, Frolov I, Qu L, Myers TM, Rice CM. Uncleaved NS2-3 is required for production of infectious bovine viral diarrhea virus. J Virol. 2004 Mar;78(5):2414-25. PMID:14963137
↑ Lecot S, Belouzard S, Dubuisson J, Rouille Y. Bovine viral diarrhea virus entry is dependent on clathrin-mediated endocytosis. J Virol. 2005 Aug;79(16):10826-9. PMID:16051874 doi:10.1128/JVI.79.16.10826-10829.2005
↑ Agapov EV, Murray CL, Frolov I, Qu L, Myers TM, Rice CM. Uncleaved NS2-3 is required for production of infectious bovine viral diarrhea virus. J Virol. 2004 Mar;78(5):2414-25. PMID:14963137
↑ Lecot S, Belouzard S, Dubuisson J, Rouille Y. Bovine viral diarrhea virus entry is dependent on clathrin-mediated endocytosis. J Virol. 2005 Aug;79(16):10826-9. PMID:16051874 doi:10.1128/JVI.79.16.10826-10829.2005
↑ Agapov EV, Murray CL, Frolov I, Qu L, Myers TM, Rice CM. Uncleaved NS2-3 is required for production of infectious bovine viral diarrhea virus. J Virol. 2004 Mar;78(5):2414-25. PMID:14963137
↑ Lecot S, Belouzard S, Dubuisson J, Rouille Y. Bovine viral diarrhea virus entry is dependent on clathrin-mediated endocytosis. J Virol. 2005 Aug;79(16):10826-9. PMID:16051874 doi:10.1128/JVI.79.16.10826-10829.2005
↑ Choi KH, Groarke JM, Young DC, Kuhn RJ, Smith JL, Pevear DC, Rossmann MG. The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation. Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4425-30. Epub 2004 Mar 19. PMID:15070734 doi:10.1073/pnas.0400660101

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1s49"

@@ Line 2: / Line 2: @@
 <StructureSection load='1s49' size='340' side='right' caption='[[1s49]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1s49]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovine_viral_diarrhea_virus_1 Bovine viral diarrhea virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S49 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S49 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1s49]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bvdv Bvdv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S49 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S49 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1s48|1s48]], [[1s4f|1s4f]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NS5B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11099 Bovine viral diarrhea virus 1])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NS5B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11099 BVDV])</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=1s49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s49 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s49 RCSB], [http://www.ebi.ac.uk/pdbsum/1s49 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=1s49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s49 OCA], [http://pdbe.org/1s49 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s49 RCSB], [http://www.ebi.ac.uk/pdbsum/1s49 PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 29: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1s49" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 36: / Line 37: @@
 __TOC__
 </StructureSection>
-[[Category: Bovine viral diarrhea virus 1]]
+[[Category: Bvdv]]
 [[Category: Choi, K H]]
 [[Category: Groarke, J M]]
@@ Line 45: / Line 46: @@
 [[Category: Young, D C]]
 [[Category: Bovine viral diarrhea virus]]
-[[Category: Bvdv]]
 [[Category: De novo initiation]]
 [[Category: Gtp binding]]

1s49

From Proteopedia

Revision as of 01:28, 10 September 2015

Crystal Structure of RNA-dependent RNA polymerase construct 1 (residues 71-679) from bovine viral diarrhea virus complexed with GTP

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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