4cbm - Revision history

OCA at 12:07, 20 December 2023

OCA — Wed, 20 Dec 2023 12:07:12 GMT

←Older revision		Revision as of 12:07, 20 December 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4cbm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Classical_swine_fever_virus Classical swine fever virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CBM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CBM FirstGlance]. <br>		<table><tr><td colspan='2'>[[4cbm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Classical_swine_fever_virus Classical swine fever virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CBM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CBM FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4cbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cbm OCA], [https://pdbe.org/4cbm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cbm RCSB], [https://www.ebi.ac.uk/pdbsum/4cbm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cbm ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.27Å</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4cbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cbm OCA], [https://pdbe.org/4cbm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cbm RCSB], [https://www.ebi.ac.uk/pdbsum/4cbm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cbm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/POLG_CSFVA POLG_CSFVA]] E(rns), E1 and E2 are responsible of cell attachment and subsequent fusion of viral and cellular membrane. P7 forms a leader sequence to properly orient NS2 in the membrane. Uncleaved NS2-3 is required for production of infectious virus. NS2 protease seems to play a vital role in viral RNA replication control and in the pathogenicity of the virus.[PROSITE-ProRule:PRU01029] NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS4A is a cofactor for the NS3 protease activity. RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome.[PROSITE-ProRule:PRU00539]	+	[https://www.uniprot.org/uniprot/POLG_CSFVA POLG_CSFVA] E(rns), E1 and E2 are responsible of cell attachment and subsequent fusion of viral and cellular membrane. P7 forms a leader sequence to properly orient NS2 in the membrane. Uncleaved NS2-3 is required for production of infectious virus. NS2 protease seems to play a vital role in viral RNA replication control and in the pathogenicity of the virus.[PROSITE-ProRule:PRU01029] NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS4A is a cofactor for the NS3 protease activity. RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome.[PROSITE-ProRule:PRU00539]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pestiviruses form a genus in the Flaviviridae family of small enveloped viruses with a positive-sense single-stranded RNA genome. Viral replication in this family requires the activity of a superfamily 2 RNA helicase contained in the C-terminal domain of the non-structural protein 3 (NS3). NS3 features two conserved RecA-like domains (D1 and D2) with ATPase activity, plus a third domain (D3) that is important for unwinding nucleic acid duplexes. We report here the X-ray structure of the pestivirus NS3 helicase domain (pNS3h) at 2.5 A resolution. The structure deviates significantly from that of NS3 of other genera in the Flaviviridae family in D3, which contains two important insertions that result in a narrower nucleic acid binding groove. We also show that mutations in pNS3h that rescue viruses with deleted core protein map to D3, suggesting that this domain may be involved in interactions that facilitate particle assembly. Finally, structural comparisons of the enzyme in different crystalline environments, together with small angle X-ray scattering studies in solution, show that D2 is mobile with respect to the rest of the enzyme, oscillating between closed and open conformations. Binding of a non-hydrolyzable ATP analog locks pNS3h in a conformation that is more compact than the closest apo-form in our crystals. Together, our results provide new insight and bring up new questions about pNS3h function during pestivirus replication. IMPORTANCE: Although pestivirus infections impose an important toll on the livestock industry worldwide, little information is available about the non-structural proteins essential for viral replication, such as the NS3 helicase. We provide here a comparative structural and functional analysis of pNS3h with respect to its orthologs in other viruses of the same family, the flaviviruses and the hepatitis C virus. Our studies reveal differences in the nucleic acid binding groove that could have implications for understanding the unwinding specificity of pNS3h, which is only active on RNA duplexes. We also show that pNS3h has a highly dynamic behavior - a characteristic probably shared with NS3 helicases from all Flaviviridae members - that could be targeted for drug design by using recent algorithms to specifically block molecular motion. Compounds that lock the enzyme in a single conformation, or limit its dynamic range of conformations are indeed likely to block its helicase function.
		+
		+	X-ray structure of the pestivirus NS3 helicase and its conformation in solution.,Tortorici MA, Duquerroy S, Kwok J, Vonrhein C, Perez J, Lamp B, Bricogne G, Rumenapf T, Vachette P, Rey FA J Virol. 2015 Feb 4. pii: JVI.03165-14. PMID:25653438<ref>PMID:25653438</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4cbm" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
		+	*[[Helicase 3D structures\|Helicase 3D structures]]
	*[[Nonstructural protein 3D structures\|Nonstructural protein 3D structures]]		*[[Nonstructural protein 3D structures\|Nonstructural protein 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:37, 7 September 2022

OCA — Wed, 07 Sep 2022 17:37:01 GMT

←Older revision		Revision as of 17:37, 7 September 2022
Line 3:		Line 3:
	<StructureSection load='4cbm' size='340' side='right'caption='[[4cbm]], [[Resolution\|resolution]] 3.27Å' scene=''>		<StructureSection load='4cbm' size='340' side='right'caption='[[4cbm]], [[Resolution\|resolution]] 3.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4cbm]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Classical_swine_fever_virus Classical swine fever virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CBM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4CBM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4cbm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Classical_swine_fever_virus Classical swine fever virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CBM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CBM FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4cbg\|4cbg]], [[4cbh\|4cbh]], [[4cbi\|4cbi]], [[4cbl\|4cbl]]</td></tr>~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4cbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cbm OCA], [https://pdbe.org/4cbm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cbm RCSB], [https://www.ebi.ac.uk/pdbsum/4cbm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cbm ProSAT]</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=4cbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cbm OCA], [~~http~~://pdbe.org/4cbm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4cbm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4cbm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4cbm ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/POLG_CSFVA POLG_CSFVA]] E(rns), E1 and E2 are responsible of cell attachment and subsequent fusion of viral and cellular membrane. P7 forms a leader sequence to properly orient NS2 in the membrane. Uncleaved NS2-3 is required for production of infectious virus. NS2 protease seems to play a vital role in viral RNA replication control and in the pathogenicity of the virus.[PROSITE-ProRule:PRU01029] NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS4A is a cofactor for the NS3 protease activity. RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome.[PROSITE-ProRule:PRU00539]	+	[[https://www.uniprot.org/uniprot/POLG_CSFVA POLG_CSFVA]] E(rns), E1 and E2 are responsible of cell attachment and subsequent fusion of viral and cellular membrane. P7 forms a leader sequence to properly orient NS2 in the membrane. Uncleaved NS2-3 is required for production of infectious virus. NS2 protease seems to play a vital role in viral RNA replication control and in the pathogenicity of the virus.[PROSITE-ProRule:PRU01029] NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS4A is a cofactor for the NS3 protease activity. RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome.[PROSITE-ProRule:PRU00539]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Pestiviruses form a genus in the Flaviviridae family of small enveloped viruses with a positive-sense single-stranded RNA genome. Viral replication in this family requires the activity of a superfamily 2 RNA helicase contained in the C-terminal domain of the non-structural protein 3 (NS3). NS3 features two conserved RecA-like domains (D1 and D2) with ATPase activity, plus a third domain (D3) that is important for unwinding nucleic acid duplexes. We report here the X-ray structure of the pestivirus NS3 helicase domain (pNS3h) at 2.5 A resolution. The structure deviates significantly from that of NS3 of other genera in the Flaviviridae family in D3, which contains two important insertions that result in a narrower nucleic acid binding groove. We also show that mutations in pNS3h that rescue viruses with deleted core protein map to D3, suggesting that this domain may be involved in interactions that facilitate particle assembly. Finally, structural comparisons of the enzyme in different crystalline environments, together with small angle X-ray scattering studies in solution, show that D2 is mobile with respect to the rest of the enzyme, oscillating between closed and open conformations. Binding of a non-hydrolyzable ATP analog locks pNS3h in a conformation that is more compact than the closest apo-form in our crystals. Together, our results provide new insight and bring up new questions about pNS3h function during pestivirus replication. IMPORTANCE: Although pestivirus infections impose an important toll on the livestock industry worldwide, little information is available about the non-structural proteins essential for viral replication, such as the NS3 helicase. We provide here a comparative structural and functional analysis of pNS3h with respect to its orthologs in other viruses of the same family, the flaviviruses and the hepatitis C virus. Our studies reveal differences in the nucleic acid binding groove that could have implications for understanding the unwinding specificity of pNS3h, which is only active on RNA duplexes. We also show that pNS3h has a highly dynamic behavior - a characteristic probably shared with NS3 helicases from all Flaviviridae members - that could be targeted for drug design by using recent algorithms to specifically block molecular motion. Compounds that lock the enzyme in a single conformation, or limit its dynamic range of conformations are indeed likely to block its helicase function.	+

-	X-ray structure of the pestivirus NS3 helicase and its conformation in solution.,Tortorici MA, Duquerroy S, Kwok J, Vonrhein C, Perez J, Lamp B, Bricogne G, Rumenapf T, Vachette P, Rey FA J Virol. 2015 Feb 4. pii: JVI.03165-14. PMID:25653438<ref>PMID:25653438</ref>	+	==See Also==
-		+	*[[Nonstructural protein 3D structures\|Nonstructural protein 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4cbm" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Classical swine fever virus]]		[[Category: Classical swine fever virus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bricogne, G]]	+	[[Category: Bricogne G]]
-	[[Category: Duquerroy, S]]	+	[[Category: Duquerroy S]]
-	[[Category: Kwok, J]]	+	[[Category: Kwok J]]
-	[[Category: Lamp, B]]	+	[[Category: Lamp B]]
-	[[Category: Perez, J]]	+	[[Category: Perez J]]
-	[[Category: Rey~~, F A~~]]	+	[[Category: Rey FA]]
-	[[Category: Rumenapf, T]]	+	[[Category: Rumenapf T]]
-	[[Category: Tortorici~~, M A~~]]	+	[[Category: Tortorici MA]]
-	[[Category: Vachette, P]]	+	[[Category: Vachette P]]
-	[[Category: Vonrhein, C]]	+	[[Category: Vonrhein C]]
-	~~[[Category: Flaviviridae ns3]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Sax]]~~	+
-	~~[[Category: Sf2 helicase~~]]	+

OCA at 08:52, 20 March 2019

OCA — Wed, 20 Mar 2019 08:52:34 GMT

←Older revision		Revision as of 08:52, 20 March 2019
Line 1:		Line 1:

	==Pestivirus NS3 helicase==		==Pestivirus NS3 helicase==
-	<StructureSection load='4cbm' size='340' side='right' caption='[[4cbm]], [[Resolution\|resolution]] 3.27Å' scene=''>	+	<StructureSection load='4cbm' size='340' side='right'caption='[[4cbm]], [[Resolution\|resolution]] 3.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4cbm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CBM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4cbm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Classical_swine_fever_virus Classical swine fever virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CBM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4cbg\|4cbg]], [[4cbh\|4cbh]], [[4cbi\|4cbi]], [[4cbl\|4cbl]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4cbg\|4cbg]], [[4cbh\|4cbh]], [[4cbi\|4cbi]], [[4cbl\|4cbl]]</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=4cbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cbm OCA], [http://pdbe.org/4cbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4cbm RCSB], [http://www.ebi.ac.uk/pdbsum/4cbm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4cbm ProSAT]</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=4cbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cbm OCA], [http://pdbe.org/4cbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4cbm RCSB], [http://www.ebi.ac.uk/pdbsum/4cbm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4cbm ProSAT]</span></td></tr>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Classical swine fever virus]]
		+	[[Category: Large Structures]]
	[[Category: Bricogne, G]]		[[Category: Bricogne, G]]
	[[Category: Duquerroy, S]]		[[Category: Duquerroy, S]]

OCA at 17:21, 18 January 2017

OCA — Wed, 18 Jan 2017 17:21:12 GMT

←Older revision		Revision as of 17:21, 18 January 2017
Line 1:		Line 1:
		+
	==Pestivirus NS3 helicase==		==Pestivirus NS3 helicase==
	<StructureSection load='4cbm' size='340' side='right' caption='[[4cbm]], [[Resolution\|resolution]] 3.27Å' scene=''>		<StructureSection load='4cbm' size='340' side='right' caption='[[4cbm]], [[Resolution\|resolution]] 3.27Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4cbm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CBM FirstGlance]. <br>		<table><tr><td colspan='2'>[[4cbm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CBM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4cbg\|4cbg]], [[4cbh\|4cbh]], [[4cbi\|4cbi]], [[4cbl\|4cbl]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4cbg\|4cbg]], [[4cbh\|4cbh]], [[4cbi\|4cbi]], [[4cbl\|4cbl]]</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=4cbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cbm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4cbm RCSB], [http://www.ebi.ac.uk/pdbsum/4cbm 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=4cbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cbm OCA], [http://pdbe.org/4cbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4cbm RCSB], [http://www.ebi.ac.uk/pdbsum/4cbm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4cbm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4cbm" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:25, 18 February 2015

OCA — Wed, 18 Feb 2015 07:25:50 GMT

←Older revision		Revision as of 07:25, 18 February 2015
Line 8:		Line 8:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/POLG_CSFVA POLG_CSFVA]] E(rns), E1 and E2 are responsible of cell attachment and subsequent fusion of viral and cellular membrane. P7 forms a leader sequence to properly orient NS2 in the membrane. Uncleaved NS2-3 is required for production of infectious virus. NS2 protease seems to play a vital role in viral RNA replication control and in the pathogenicity of the virus.[PROSITE-ProRule:PRU01029] NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS4A is a cofactor for the NS3 protease activity. RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome.[PROSITE-ProRule:PRU00539]		[[http://www.uniprot.org/uniprot/POLG_CSFVA POLG_CSFVA]] E(rns), E1 and E2 are responsible of cell attachment and subsequent fusion of viral and cellular membrane. P7 forms a leader sequence to properly orient NS2 in the membrane. Uncleaved NS2-3 is required for production of infectious virus. NS2 protease seems to play a vital role in viral RNA replication control and in the pathogenicity of the virus.[PROSITE-ProRule:PRU01029] NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS4A is a cofactor for the NS3 protease activity. RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome.[PROSITE-ProRule:PRU00539]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pestiviruses form a genus in the Flaviviridae family of small enveloped viruses with a positive-sense single-stranded RNA genome. Viral replication in this family requires the activity of a superfamily 2 RNA helicase contained in the C-terminal domain of the non-structural protein 3 (NS3). NS3 features two conserved RecA-like domains (D1 and D2) with ATPase activity, plus a third domain (D3) that is important for unwinding nucleic acid duplexes. We report here the X-ray structure of the pestivirus NS3 helicase domain (pNS3h) at 2.5 A resolution. The structure deviates significantly from that of NS3 of other genera in the Flaviviridae family in D3, which contains two important insertions that result in a narrower nucleic acid binding groove. We also show that mutations in pNS3h that rescue viruses with deleted core protein map to D3, suggesting that this domain may be involved in interactions that facilitate particle assembly. Finally, structural comparisons of the enzyme in different crystalline environments, together with small angle X-ray scattering studies in solution, show that D2 is mobile with respect to the rest of the enzyme, oscillating between closed and open conformations. Binding of a non-hydrolyzable ATP analog locks pNS3h in a conformation that is more compact than the closest apo-form in our crystals. Together, our results provide new insight and bring up new questions about pNS3h function during pestivirus replication. IMPORTANCE: Although pestivirus infections impose an important toll on the livestock industry worldwide, little information is available about the non-structural proteins essential for viral replication, such as the NS3 helicase. We provide here a comparative structural and functional analysis of pNS3h with respect to its orthologs in other viruses of the same family, the flaviviruses and the hepatitis C virus. Our studies reveal differences in the nucleic acid binding groove that could have implications for understanding the unwinding specificity of pNS3h, which is only active on RNA duplexes. We also show that pNS3h has a highly dynamic behavior - a characteristic probably shared with NS3 helicases from all Flaviviridae members - that could be targeted for drug design by using recent algorithms to specifically block molecular motion. Compounds that lock the enzyme in a single conformation, or limit its dynamic range of conformations are indeed likely to block its helicase function.
		+
		+	X-ray structure of the pestivirus NS3 helicase and its conformation in solution.,Tortorici MA, Duquerroy S, Kwok J, Vonrhein C, Perez J, Lamp B, Bricogne G, Rumenapf T, Vachette P, Rey FA J Virol. 2015 Feb 4. pii: JVI.03165-14. PMID:25653438<ref>PMID:25653438</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:55, 21 January 2015

OCA — Wed, 21 Jan 2015 16:55:02 GMT

←Older revision		Revision as of 16:55, 21 January 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Pestivirus NS3 helicase==
-		+	<StructureSection load='4cbm' size='340' side='right' caption='[[4cbm]], [[Resolution\|resolution]] 3.27Å' scene=''>
-	~~The entry~~ 4cbm is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4cbm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CBM FirstGlance]. <br>
-	~~Authors~~: ~~Tortorici, M~~.A.~~, Duquerroy, S~~.~~, Kwok, J~~.~~, Vonrhein, C~~.~~, Perez, J~~.~~, Lamp, B~~.~~, Bricogne, G~~.~~, Rumenapf, T., Vachette, P., Rey, F.A~~.	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4cbg\|4cbg]], [[4cbh\|4cbh]], [[4cbi\|4cbi]], [[4cbl\|4cbl]]</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=4cbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cbm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4cbm RCSB], [http://www.ebi.ac.uk/pdbsum/4cbm PDBsum]</span></td></tr>
-	~~Description: Pestivirus NS3 helicase~~	+	</table>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	== Function ==
-	[[~~Category: Lamp~~, B]]	+	[[http://www.uniprot.org/uniprot/POLG_CSFVA POLG_CSFVA]] E(rns), E1 and E2 are responsible of cell attachment and subsequent fusion of viral and cellular membrane. P7 forms a leader sequence to properly orient NS2 in the membrane. Uncleaved NS2-3 is required for production of infectious virus. NS2 protease seems to play a vital role in viral RNA replication control and in the pathogenicity of the virus.[PROSITE-ProRule:PRU01029] NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS4A is a cofactor for the NS3 protease activity. RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome.[PROSITE-ProRule:PRU00539]
-	[[~~Category~~: ~~Vachette~~, P]]	+	__TOC__
-	[[~~Category~~: ~~Rumenapf~~, T]]	+	</StructureSection>
	[[Category: Bricogne, G]]		[[Category: Bricogne, G]]
-	[[Category: Perez, J]]
-	[[Category: Vonrhein, C]]
	[[Category: Duquerroy, S]]		[[Category: Duquerroy, S]]
	[[Category: Kwok, J]]		[[Category: Kwok, J]]
-	[[Category: ~~Tortorici~~, ~~M.A~~]]	+	[[Category: Lamp, B]]
-	[[Category: Rey, F.A]]	+	[[Category: Perez, J]]
		+	[[Category: Rey, F A]]
		+	[[Category: Rumenapf, T]]
		+	[[Category: Tortorici, M A]]
		+	[[Category: Vachette, P]]
		+	[[Category: Vonrhein, C]]
		+	[[Category: Flaviviridae ns3]]
		+	[[Category: Hydrolase]]
		+	[[Category: Sax]]
		+	[[Category: Sf2 helicase]]

OCA at 13:18, 24 December 2014

OCA — Wed, 24 Dec 2014 13:18:45 GMT

←Older revision		Revision as of 13:18, 24 December 2014
Line 6:		Line 6:

	Description: Pestivirus NS3 helicase		Description: Pestivirus NS3 helicase
		+	[[Category: Unreleased Structures]]
		+	[[Category: Lamp, B]]
		+	[[Category: Vachette, P]]
		+	[[Category: Rumenapf, T]]
		+	[[Category: Bricogne, G]]
		+	[[Category: Perez, J]]
		+	[[Category: Vonrhein, C]]
		+	[[Category: Duquerroy, S]]
		+	[[Category: Kwok, J]]
		+	[[Category: Tortorici, M.A]]
		+	[[Category: Rey, F.A]]

OCA at 10:46, 17 December 2014

OCA — Wed, 17 Dec 2014 10:46:00 GMT

←Older revision		Revision as of 10:46, 17 December 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4cbm is ON HOLD	+	The entry 4cbm is ON HOLD until Paper Publication

-	Authors: Tortorici, M.A., Duquerroy, S., Vonrhein, C., Perez, J., Lamp, B~~., GirardBlanc, C~~., Bricogne, G., Rumenapf, T., Vachette, P., Rey, F.A.	+	Authors: Tortorici, M.A., Duquerroy, S., Kwok, J., Vonrhein, C., Perez, J., Lamp, B., Bricogne, G., Rumenapf, T., Vachette, P., Rey, F.A.

	Description: Pestivirus NS3 helicase		Description: Pestivirus NS3 helicase

OCA: Protected "4cbm" [edit=sysop:move=sysop]

OCA — Wed, 23 Oct 2013 05:40:24 GMT

Protected "4cbm" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:40, 23 October 2013

OCA: New page: '''Unreleased structure''' The entry 4cbm is ON HOLD Authors: Tortorici, M.A., Duquerroy, S., Vonrhein, C., Perez, J., Lamp, B., GirardBlanc, C., Bricogne, G., Rumenapf, T., Vachette, P...

OCA — Wed, 23 Oct 2013 05:40:22 GMT

New page: '''Unreleased structure''' The entry 4cbm is ON HOLD Authors: Tortorici, M.A., Duquerroy, S., Vonrhein, C., Perez, J., Lamp, B., GirardBlanc, C., Bricogne, G., Rumenapf, T., Vachette, P...

New page

'''Unreleased structure'''

The entry 4cbm is ON HOLD

Authors: Tortorici, M.A., Duquerroy, S., Vonrhein, C., Perez, J., Lamp, B., GirardBlanc, C., Bricogne, G., Rumenapf, T., Vachette, P., Rey, F.A.

Description: Pestivirus NS3 helicase