4cmv - Revision history

OCA at 07:22, 14 September 2022

OCA — Wed, 14 Sep 2022 07:22:27 GMT

←Older revision		Revision as of 07:22, 14 September 2022
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	<StructureSection load='4cmv' size='340' side='right'caption='[[4cmv]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='4cmv' size='340' side='right'caption='[[4cmv]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4cmv]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myctu Myctu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CMV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4CMV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4cmv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CMV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CMV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4cmw\|4cmw]], [[4cmx\|4cmx]]~~</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=4cmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cmv OCA], [https://pdbe.org/4cmv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cmv RCSB], [https://www.ebi.ac.uk/pdbsum/4cmv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cmv 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=4cmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cmv OCA], [~~http~~://pdbe.org/4cmv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4cmv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4cmv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4cmv ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/~~TUBOL_MYCTU TUBOL_MYCTU~~]] ~~Catalyzes~~ the PP-~~removal~~ from ~~tuberculosinyl~~ diphosphate to produce both ~~tubercilosinol~~ and isotuberculosinol. ~~Can~~ also use labdadienyl diphosphates, copalyl diphosphate (CDP), ent-CDP and syn-CDP in vitro.	+	[[https://www.uniprot.org/uniprot/TUBAT_MYCTU TUBAT_MYCTU]] Tuberculosinyl transferase that catalyzes the condensation of adenosine and tuberculosinyl diphosphate (TbPP) to generate 1-tuberculosinyladenosine (1-TbAd), which acts as an antiacid that directly protects M.tuberculosis from acid pH and physically remodels M.tuberculosis phagolysosomes (PubMed:24516143, PubMed:31427817). In addition, acts as a phosphatase that catalyzes the diphosphate-removal from TbPP to produce both tuberculosinol (TOH) and isotuberculosinol (iso-TOH) (PubMed:21228491, PubMed:24475925). Has broad substrate specificity, and can also use the 3 labdadienyl diphosphates, copalyl diphosphate (CDP), ent-CDP and syn-CDP in vitro (PubMed:21290071).<ref>PMID:21228491</ref> <ref>PMID:21290071</ref> <ref>PMID:24475925</ref> <ref>PMID:24516143</ref> <ref>PMID:31427817</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myctu~~]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: Alber, T]]	+	[[Category: Alber T]]
-	[[Category: Annand~~, J W~~]]	+	[[Category: Annand JW]]
-	[[Category: Buter, J]]	+	[[Category: Buter J]]
-	[[Category: Fortune~~, S M~~]]	+	[[Category: Fortune SM]]
-	[[Category: Layre, E]]	+	[[Category: Layre E]]
-	[[Category: Lee~~, H J~~]]	+	[[Category: Lee HJ]]
-	[[Category: Martinot~~, A J~~]]	+	[[Category: Martinot AJ]]
-	[[Category: Matsunaga, I]]	+	[[Category: Matsunaga I]]
-	[[Category: Minnaard~~, A J~~]]	+	[[Category: Minnaard AJ]]
-	[[Category: Moody~~, D B~~]]	+	[[Category: Moody DB]]
-	[[Category: Rubin~~, E J~~]]	+	[[Category: Rubin EJ]]
-	[[Category: Snider~~, B B~~]]	+	[[Category: Snider BB]]
-	[[Category: Young~~, D C]]~~	+	[[Category: Young DC]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nuclear protein~~]]	+

OCA at 16:40, 28 August 2019

OCA — Wed, 28 Aug 2019 16:40:39 GMT

←Older revision		Revision as of 16:40, 28 August 2019
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	==Crystal structure of Rv3378c==		==Crystal structure of Rv3378c==
-	<StructureSection load='4cmv' size='340' side='right' caption='[[4cmv]], [[Resolution\|resolution]] 2.31Å' scene=''>	+	<StructureSection load='4cmv' size='340' side='right'caption='[[4cmv]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4cmv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CMV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CMV FirstGlance]. <br>		<table><tr><td colspan='2'>[[4cmv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CMV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CMV FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Myctu]]		[[Category: Myctu]]
	[[Category: Alber, T]]		[[Category: Alber, T]]

OCA at 14:01, 4 August 2016

OCA — Thu, 04 Aug 2016 14:01:25 GMT

←Older revision		Revision as of 14:01, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Rv3378c==		==Crystal structure of Rv3378c==
	<StructureSection load='4cmv' size='340' side='right' caption='[[4cmv]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='4cmv' size='340' side='right' caption='[[4cmv]], [[Resolution\|resolution]] 2.31Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4cmw\|4cmw]], [[4cmx\|4cmx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4cmw\|4cmw]], [[4cmx\|4cmx]]</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=4cmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cmv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4cmv RCSB], [http://www.ebi.ac.uk/pdbsum/4cmv 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=4cmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cmv OCA], [http://pdbe.org/4cmv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4cmv RCSB], [http://www.ebi.ac.uk/pdbsum/4cmv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4cmv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 4cmv" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:23, 24 December 2014

OCA — Wed, 24 Dec 2014 15:23:19 GMT

←Older revision		Revision as of 15:23, 24 December 2014
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-	~~{{STRUCTURE_4cmv\| PDB~~=4cmv \| ~~SCENE~~= }}	+	==Crystal structure of Rv3378c==
-	===~~Crystal~~ structure ~~of Rv3378c~~===	+	<StructureSection load='4cmv' size='340' side='right' caption='[[4cmv]], [[Resolution\|resolution]] 2.31Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24516143}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4cmv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CMV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CMV FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4cmw\|4cmw]], [[4cmx\|4cmx]]</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=4cmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cmv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4cmv RCSB], [http://www.ebi.ac.uk/pdbsum/4cmv PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/TUBOL_MYCTU TUBOL_MYCTU]] Catalyzes the PP-removal from tuberculosinyl diphosphate to produce both tubercilosinol and isotuberculosinol. Can also use labdadienyl diphosphates, copalyl diphosphate (CDP), ent-CDP and syn-CDP in vitro.		[[http://www.uniprot.org/uniprot/TUBOL_MYCTU TUBOL_MYCTU]] Catalyzes the PP-removal from tuberculosinyl diphosphate to produce both tubercilosinol and isotuberculosinol. Can also use labdadienyl diphosphates, copalyl diphosphate (CDP), ent-CDP and syn-CDP in vitro.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	To identify lipids with roles in tuberculosis disease, we systematically compared the lipid content of virulent Mycobacterium tuberculosis with the attenuated vaccine strain Mycobacterium bovis bacillus Calmette-Guerin. Comparative lipidomics analysis identified more than 1,000 molecular differences, including a previously unknown, Mycobacterium tuberculosis-specific lipid that is composed of a diterpene unit linked to adenosine. We established the complete structure of the natural product as 1-tuberculosinyladenosine (1-TbAd) using mass spectrometry and NMR spectroscopy. A screen for 1-TbAd mutants, complementation studies, and gene transfer identified Rv3378c as necessary for 1-TbAd biosynthesis. Whereas Rv3378c was previously thought to function as a phosphatase, these studies establish its role as a tuberculosinyl transferase and suggest a revised biosynthetic pathway for the sequential action of Rv3377c-Rv3378c. In agreement with this model, recombinant Rv3378c protein produced 1-TbAd, and its crystal structure revealed a cis-prenyl transferase fold with hydrophobic residues for isoprenoid binding and a second binding pocket suitable for the nucleoside substrate. The dual-substrate pocket distinguishes Rv3378c from classical cis-prenyl transferases, providing a unique model for the prenylation of diverse metabolites. Terpene nucleosides are rare in nature, and 1-TbAd is known only in Mycobacterium tuberculosis. Thus, this intersection of nucleoside and terpene pathways likely arose late in the evolution of the Mycobacterium tuberculosis complex; 1-TbAd serves as an abundant chemical marker of Mycobacterium tuberculosis, and the extracellular export of this amphipathic molecule likely accounts for the known virulence-promoting effects of the Rv3378c enzyme.

-	~~==About this Structure==~~	+	Molecular profiling of Mycobacterium tuberculosis identifies tuberculosinyl nucleoside products of the virulence-associated enzyme Rv3378c.,Layre E, Lee HJ, Young DC, Jezek Martinot A, Buter J, Minnaard AJ, Annand JW, Fortune SM, Snider BB, Matsunaga I, Rubin EJ, Alber T, Moody DB Proc Natl Acad Sci U S A. 2014 Feb 10. PMID:24516143<ref>PMID:24516143</ref>
-	~~[[4cmv]] is a 2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4CMV OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024516143</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Alber, T.]]	+	== References ==
-	[[Category: Annand, J W.]]	+	<references/>
-	[[Category: Buter, J.]]	+	__TOC__
-	[[Category: Fortune, S M.]]	+	</StructureSection>
-	[[Category: Layre, E.]]	+	[[Category: Myctu]]
-	[[Category: Lee, H J.]]	+	[[Category: Alber, T]]
-	[[Category: Martinot, A J.]]	+	[[Category: Annand, J W]]
-	[[Category: Matsunaga, I.]]	+	[[Category: Buter, J]]
-	[[Category: Minnaard, A J.]]	+	[[Category: Fortune, S M]]
-	[[Category: Moody, D B.]]	+	[[Category: Layre, E]]
-	[[Category: Rubin, E J.]]	+	[[Category: Lee, H J]]
-	[[Category: Snider, B B.]]	+	[[Category: Martinot, A J]]
-	[[Category: Young, D C.]]	+	[[Category: Matsunaga, I]]
		+	[[Category: Minnaard, A J]]
		+	[[Category: Moody, D B]]
		+	[[Category: Rubin, E J]]
		+	[[Category: Snider, B B]]
		+	[[Category: Young, D C]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Nuclear protein]]		[[Category: Nuclear protein]]

OCA at 17:21, 19 February 2014

OCA — Wed, 19 Feb 2014 17:21:37 GMT

←Older revision		Revision as of 17:21, 19 February 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4cmv\| PDB=4cmv \| SCENE= }}
		+	===Crystal structure of Rv3378c===
		+	{{ABSTRACT_PUBMED_24516143}}

-	~~The entry 4cmv is ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/TUBOL_MYCTU TUBOL_MYCTU]] Catalyzes the PP-removal from tuberculosinyl diphosphate to produce both tubercilosinol and isotuberculosinol. Can also use labdadienyl diphosphates, copalyl diphosphate (CDP), ent-CDP and syn-CDP in vitro.

-	~~Authors~~: ~~Layre, E., Lee, H.J., Young, D.C., Martinot, A.J., Buter, J., Minnaard, A.J., Annand, J.W., Fortune, S.M., Snider, B.B., Matsunaga, I., Rubin, E.J~~.~~, Alber, T~~.~~, Moody, D~~.B.	+	==About this Structure==
		+	[[4cmv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CMV OCA].

-	~~Description~~: ~~Crystal structure of Rv3378c~~	+	==Reference==
		+	<ref group="xtra">PMID:024516143</ref><references group="xtra"/><references/>
		+	[[Category: Alber, T.]]
		+	[[Category: Annand, J W.]]
		+	[[Category: Buter, J.]]
		+	[[Category: Fortune, S M.]]
		+	[[Category: Layre, E.]]
		+	[[Category: Lee, H J.]]
		+	[[Category: Martinot, A J.]]
		+	[[Category: Matsunaga, I.]]
		+	[[Category: Minnaard, A J.]]
		+	[[Category: Moody, D B.]]
		+	[[Category: Rubin, E J.]]
		+	[[Category: Snider, B B.]]
		+	[[Category: Young, D C.]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nuclear protein]]

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

OCA — Wed, 29 Jan 2014 06:45:56 GMT

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

←Older revision

Revision as of 06:45, 29 January 2014

OCA: New page: '''Unreleased structure''' The entry 4cmv is ON HOLD until Paper Publication Authors: Layre, E., Lee, H.J., Young, D.C., Martinot, A.J., Buter, J., Minnaard, A.J., Annand, J.W., Fortune...

OCA — Wed, 29 Jan 2014 06:45:55 GMT

New page: '''Unreleased structure''' The entry 4cmv is ON HOLD until Paper Publication Authors: Layre, E., Lee, H.J., Young, D.C., Martinot, A.J., Buter, J., Minnaard, A.J., Annand, J.W., Fortune...

New page

'''Unreleased structure'''

The entry 4cmv is ON HOLD until Paper Publication

Authors: Layre, E., Lee, H.J., Young, D.C., Martinot, A.J., Buter, J., Minnaard, A.J., Annand, J.W., Fortune, S.M., Snider, B.B., Matsunaga, I., Rubin, E.J., Alber, T., Moody, D.B.

Description: Crystal structure of Rv3378c