6s1w - Revision history

OCA at 12:33, 24 January 2024

OCA — Wed, 24 Jan 2024 12:33:16 GMT

←Older revision		Revision as of 12:33, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6s1w' size='340' side='right'caption='[[6s1w]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='6s1w' size='340' side='right'caption='[[6s1w]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6s1w]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S1W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6S1W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6s1w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mason-Pfizer_monkey_virus Mason-Pfizer monkey virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S1W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S1W FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[3sqf\|3sqf]]~~, [[~~3hvp~~\|~~3hvp]], [[4hvp\|4hvp]], [[1ivp\|1ivp]], [[1az5\|1az5]], [[2rsp\|2rsp]], [[1bai\|1bai]], [[4fiv\|4fiv]], [[2fmb\|2fmb]], [[3liy\|3liy]], [[3slz\|3slz~~]]</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]] 1.98Å</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=6s1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s1w OCA], [~~http~~://pdbe.org/6s1w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6s1w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6s1w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6s1w ProSAT]</span></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=6s1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s1w OCA], [https://pdbe.org/6s1w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s1w RCSB], [https://www.ebi.ac.uk/pdbsum/6s1w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s1w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/POL_MPMV POL_MPMV]] Matrix protein p10: Matrix protein. Nucleocapsid protein p14: Nucleocapsid protein. Capsid protein p27: Capsid protein. Protease 17 kDa: The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell.[PROSITE-ProRule:PRU00275]<ref>PMID:9636364</ref> Protease 13 kDa: The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell.[PROSITE-ProRule:PRU00275]<ref>PMID:9636364</ref> G-patch peptide: Enhances the activity of the reverse transcriptase. May be part of the mature RT.<ref>PMID:22171253</ref> Reverse transcriptase/ribonuclease H: RT is a multifunctional enzyme that converts the viral dimeric RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA binds to the primer-binding site (PBS) situated at the 5' end of the viral RNA. RT uses the 3' end of the tRNA primer to perfom a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perfom the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5' end of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primers. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends.[PROSITE-ProRule:PRU00405] Integrase: Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions.<ref>PMID:28458055</ref>	+	[https://www.uniprot.org/uniprot/POL_MPMV POL_MPMV] Matrix protein p10: Matrix protein. Nucleocapsid protein p14: Nucleocapsid protein. Capsid protein p27: Capsid protein. Protease 17 kDa: The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell.[PROSITE-ProRule:PRU00275]<ref>PMID:9636364</ref> Protease 13 kDa: The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell.[PROSITE-ProRule:PRU00275]<ref>PMID:9636364</ref> G-patch peptide: Enhances the activity of the reverse transcriptase. May be part of the mature RT.<ref>PMID:22171253</ref> Reverse transcriptase/ribonuclease H: RT is a multifunctional enzyme that converts the viral dimeric RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA binds to the primer-binding site (PBS) situated at the 5' end of the viral RNA. RT uses the 3' end of the tRNA primer to perfom a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perfom the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5' end of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primers. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends.[PROSITE-ProRule:PRU00405] Integrase: Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions.<ref>PMID:28458055</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6s1w" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6s1w" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Journal:Acta Cryst D:S2059798319011355\|Journal:Acta Cryst D:S2059798319011355]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gilski, M]]	+	[[Category: Mason-Pfizer monkey virus]]
-	[[Category: Jaskolski, M]]	+	[[Category: Gilski M]]
-	[[Category: Pichova, I]]	+	[[Category: Jaskolski M]]
-	[[Category: Wosicki, S]]	+	[[Category: Pichova I]]
-	[[Category: Zabranska, H]]	+	[[Category: Wosicki S]]
-	~~[[Category: Apo]]~~	+	[[Category: Zabranska H]]
-	~~[[Category: Aspartic protease]]~~	+
-	~~[[Category: Dimerization]]~~	+
-	~~[[Category: Flap structure]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: M-pmv]]~~	+
-	~~[[Category: Mason-pfizer monkey virus]]~~	+
-	~~[[Category: Retropepsin]]~~	+
-	~~[[Category: Retrovirus~~]]	+

OCA at 06:01, 16 October 2019

OCA — Wed, 16 Oct 2019 06:01:13 GMT

←Older revision		Revision as of 06:01, 16 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The entry ~~6s1w~~ is ~~ON HOLD~~	+	==Crystal structure of dimeric M-PMV protease D26N mutant==
		+	<StructureSection load='6s1w' size='340' side='right'caption='[[6s1w]], [[Resolution\|resolution]] 1.98Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6s1w]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S1W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6S1W FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3sqf\|3sqf]], [[3hvp\|3hvp]], [[4hvp\|4hvp]], [[1ivp\|1ivp]], [[1az5\|1az5]], [[2rsp\|2rsp]], [[1bai\|1bai]], [[4fiv\|4fiv]], [[2fmb\|2fmb]], [[3liy\|3liy]], [[3slz\|3slz]]</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=6s1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s1w OCA], [http://pdbe.org/6s1w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6s1w RCSB], [http://www.ebi.ac.uk/pdbsum/6s1w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6s1w ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/POL_MPMV POL_MPMV]] Matrix protein p10: Matrix protein. Nucleocapsid protein p14: Nucleocapsid protein. Capsid protein p27: Capsid protein. Protease 17 kDa: The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell.[PROSITE-ProRule:PRU00275]<ref>PMID:9636364</ref> Protease 13 kDa: The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell.[PROSITE-ProRule:PRU00275]<ref>PMID:9636364</ref> G-patch peptide: Enhances the activity of the reverse transcriptase. May be part of the mature RT.<ref>PMID:22171253</ref> Reverse transcriptase/ribonuclease H: RT is a multifunctional enzyme that converts the viral dimeric RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA binds to the primer-binding site (PBS) situated at the 5' end of the viral RNA. RT uses the 3' end of the tRNA primer to perfom a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perfom the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5' end of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primers. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends.[PROSITE-ProRule:PRU00405] Integrase: Catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions.<ref>PMID:28458055</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Retroviral proteases (RPs) are of high interest owing to their crucial role in the maturation process of retroviral particles. RPs are obligatory homodimers, with a pepsin-like active site built around two aspartates (in DTG triads) that activate a water molecule, as the nucleophile, under two flap loops. Mason-Pfizer monkey virus (M-PMV) is unique among retroviruses as its protease is also stable in the monomeric form, as confirmed by an existing crystal structure of a 13 kDa variant of the protein (M-PMV PR) and its previous biochemical characterization. In the present work, two mutants of M-PMV PR, D26N and C7A/D26N/C106A, were crystallized in complex with a peptidomimetic inhibitor and one mutant (D26N) was crystallized without the inhibitor. The crystal structures were solved at resolutions of 1.6, 1.9 and 2.0 A, respectively. At variance with the previous study, all of the new structures have the canonical dimeric form of retroviral proteases. The protomers within a dimer differ mainly in the flap-loop region, with the most extreme case observed in the apo structure, in which one flap loop is well defined while the other flap loop is not defined by electron density. The presence of the inhibitor molecules in the complex structures was assessed using polder maps, but some details of their conformations remain ambiguous. In all of the presented structures the active site contains a water molecule buried deeply between the Asn26-Thr27-Gly28 triads of the protomers. Such a water molecule is completely unique not only in retropepsins but also in aspartic proteases in general. The C7A and C106A mutations do not influence the conformation of the protein. The Cys106 residue is properly placed at the homodimer interface area for a disulfide cross-link, but the reducing conditions of the crystallization experiment prevented S-S bond formation. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:S2059798319011355.

-	~~Authors: Wosicki~~, S., Gilski, M~~., Jaskolski, M.~~, Zabranska, H., Pichova, I.	+	Comparison of a retroviral protease in monomeric and dimeric states.,Wosicki S, Gilski M, Zabranska H, Pichova I, Jaskolski M Acta Crystallogr D Struct Biol. 2019 Oct 1;75(Pt 10):904-917. doi:, 10.1107/S2059798319011355. Epub 2019 Sep 20. PMID:31588922<ref>PMID:31588922</ref>

-	~~Description: Crystal structure~~ of ~~dimeric M~~-~~PMV protease D26N mutant~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6s1w" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Journal:Acta Cryst D:S2059798319011355\|Journal:Acta Cryst D:S2059798319011355]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Gilski, M]]		[[Category: Gilski, M]]
-	[[Category: ~~Zabranska~~, H]]	+	[[Category: Jaskolski, M]]
	[[Category: Pichova, I]]		[[Category: Pichova, I]]
	[[Category: Wosicki, S]]		[[Category: Wosicki, S]]
-	[[Category: ~~Jaskolski~~, M]]	+	[[Category: Zabranska, H]]
		+	[[Category: Apo]]
		+	[[Category: Aspartic protease]]
		+	[[Category: Dimerization]]
		+	[[Category: Flap structure]]
		+	[[Category: Hydrolase]]
		+	[[Category: M-pmv]]
		+	[[Category: Mason-pfizer monkey virus]]
		+	[[Category: Retropepsin]]
		+	[[Category: Retrovirus]]

OCA: Protected "6s1w" [edit=sysop:move=sysop]

OCA — Wed, 26 Jun 2019 05:30:27 GMT

Protected "6s1w" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:30, 26 June 2019

OCA: New page: '''Unreleased structure''' The entry 6s1w is ON HOLD Authors: Wosicki, S., Gilski, M., Jaskolski, M., Zabranska, H., Pichova, I. Description: Crystal structure of dimeric M-PMV proteas...

OCA — Wed, 26 Jun 2019 05:30:26 GMT

New page: '''Unreleased structure''' The entry 6s1w is ON HOLD Authors: Wosicki, S., Gilski, M., Jaskolski, M., Zabranska, H., Pichova, I. Description: Crystal structure of dimeric M-PMV proteas...

New page

'''Unreleased structure'''

The entry 6s1w is ON HOLD

Authors: Wosicki, S., Gilski, M., Jaskolski, M., Zabranska, H., Pichova, I.

Description: Crystal structure of dimeric M-PMV protease D26N mutant
[[Category: Unreleased Structures]]
[[Category: Gilski, M]]
[[Category: Zabranska, H]]
[[Category: Pichova, I]]
[[Category: Wosicki, S]]
[[Category: Jaskolski, M]]