6vpt - Revision history

OCA at 08:16, 11 October 2023

2023-10-11T08:16:40Z

←Older revision		Revision as of 08:16, 11 October 2023
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	<StructureSection load='6vpt' size='340' side='right'caption='[[6vpt]], [[Resolution\|resolution]] 2.72Å' scene=''>		<StructureSection load='6vpt' size='340' side='right'caption='[[6vpt]], [[Resolution\|resolution]] 2.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vpt]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VPT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6VPT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vpt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VPT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VPT FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ERS023446_02740~~, ~~EZX46_08560, FDK60_02635, FDK62_05385, SAMEA2682864_03253, SAMEA2683035_03439 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])~~</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]] 2.718Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6vpt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vpt OCA], [~~http~~://pdbe.org/6vpt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vpt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vpt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vpt 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=6vpt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vpt OCA], [https://pdbe.org/6vpt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vpt RCSB], [https://www.ebi.ac.uk/pdbsum/6vpt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vpt ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DITCY_MYCTU DITCY_MYCTU] Catalyzes the formation of tuberculosinyl diphosphate from geranylgeranyl diphosphate (GGPP). It could also react with (14R/S)-14,15-oxidoGGPP to generate 3alpha- and 3beta-hydroxytuberculosinyl diphosphate.<ref>PMID:15719101</ref> <ref>PMID:19618417</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: DiMaio, F]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: Prach, L]]	+	[[Category: DiMaio F]]
-	[[Category: Siegel, J]]	+	[[Category: Prach L]]
-	[[Category: Zhang, T]]	+	[[Category: Siegel J]]
-	~~[[Category: Diterpene cyclase]]~~	+	[[Category: Zhang T]]
-	~~[[Category: Diterpene synthase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 06:48, 9 December 2020

2020-12-09T06:48:48Z

←Older revision		Revision as of 06:48, 9 December 2020
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	==Crystal structure and mechanistic molecular modeling studies of Rv3377c: the Mycobacterium tuberculosis diterpene cyclase==		==Crystal structure and mechanistic molecular modeling studies of Rv3377c: the Mycobacterium tuberculosis diterpene cyclase==
-	<StructureSection load='6vpt' size='340' side='right'caption='[[6vpt]]' scene=''>	+	<StructureSection load='6vpt' size='340' side='right'caption='[[6vpt]], [[Resolution\|resolution]] 2.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VPT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VPT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vpt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VPT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VPT FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vpt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vpt OCA], [http://pdbe.org/6vpt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vpt RCSB], [http://www.ebi.ac.uk/pdbsum/6vpt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vpt ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ERS023446_02740, EZX46_08560, FDK60_02635, FDK62_05385, SAMEA2682864_03253, SAMEA2683035_03439 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vpt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vpt OCA], [http://pdbe.org/6vpt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vpt RCSB], [http://www.ebi.ac.uk/pdbsum/6vpt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vpt ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Terpenes make up the largest class of natural products, with extensive chemical and structural diversity. Diterpenes, mostly isolated from plants and rarely prokaryotes, exhibit a variety of important biological activities and valuable applications, including providing antitumor and antibiotic pharmaceuticals. These natural products are constructed by terpene synthases, a class of enzymes that catalyze one of the most complex chemical reactions in biology: converting simple acyclic oligo-isoprenyl diphosphate substrates to complex polycyclic products via carbocation intermediates. Here we obtained the second ever crystal structure of a class II diterpene synthase from bacteria, tuberculosinol pyrophosphate synthase (i.e., Halimadienyl diphosphate synthase, MtHPS, or Rv3377c) from Mycobacterium tuberculosis (Mtb). This enzyme transforms (E,E,E)-geranylgeranyl diphosphate into tuberculosinol pyrophosphate (Halimadienyl diphosphate). Rv3377c is part of the Mtb diterpene pathway along with Rv3378c, which converts tuberculosinol pyrophosphate to 1-tuberculosinyl adenosine (1-TbAd). This pathway was shown to exist only in virulent Mycobacterium species, but not in closely related avirulent species, and was proposed to be involved in phagolysosome maturation arrest. To gain further insight into the reaction pathway and the mechanistically relevant enzyme substrate binding orientation, electronic structure calculation and docking studies of reaction intermediates were carried out. Results reveal a plausible binding mode of the substrate that can provide the information to guide future drug design and anti-infective therapies of this biosynthetic pathway.
		+
		+	Crystal Structure and Mechanistic Molecular Modeling Studies of Mycobacterium tuberculosis Diterpene Cyclase Rv3377c.,Zhang Y, Prach LM, O'Brien TE, DiMaio F, Prigozhin DM, Corn JE, Alber T, Siegel JB, Tantillo DJ Biochemistry. 2020 Dec 1;59(47):4507-4515. doi: 10.1021/acs.biochem.0c00762. Epub, 2020 Nov 12. PMID:33182997<ref>PMID:33182997</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6vpt" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: DiMaio F]]	+	[[Category: DiMaio, F]]
-	[[Category: Prach L]]	+	[[Category: Prach, L]]
-	[[Category: Siegel J]]	+	[[Category: Siegel, J]]
-	[[Category: Zhang T]]	+	[[Category: Zhang, T]]
		+	[[Category: Diterpene cyclase]]
		+	[[Category: Diterpene synthase]]
		+	[[Category: Lyase]]

OCA at 07:46, 2 December 2020

2020-12-02T07:46:03Z

←Older revision		Revision as of 07:46, 2 December 2020
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-	'''Unreleased structure'''

-	~~The entry 6vpt is ON HOLD until Paper Publication~~	+	==Crystal structure and mechanistic molecular modeling studies of Rv3377c: the Mycobacterium tuberculosis diterpene cyclase==
-		+	<StructureSection load='6vpt' size='340' side='right'caption='[[6vpt]]' scene=''>
-	~~Authors: Zhang, T., Prach, L., DiMaio, F., Siegel, J.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VPT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VPT FirstGlance]. <br>
-	~~Description:~~ Crystal structure and mechanistic molecular modeling studies of Rv3377c: the Mycobacterium tuberculosis diterpene cyclase	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vpt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vpt OCA], [http://pdbe.org/6vpt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vpt RCSB], [http://www.ebi.ac.uk/pdbsum/6vpt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vpt ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Prach, L~~]]	+	__TOC__
-	[[Category: ~~Siegel, J~~]]	+	</StructureSection>
-	[[Category: ~~Zhang, T~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Dimaio, F~~]]	+	[[Category: DiMaio F]]
		+	[[Category: Prach L]]
		+	[[Category: Siegel J]]
		+	[[Category: Zhang T]]

OCA at 03:53, 13 May 2020

2020-05-13T03:53:24Z

←Older revision		Revision as of 03:53, 13 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6vpt is ON HOLD	+	The entry 6vpt is ON HOLD until Paper Publication

	Authors: Zhang, T., Prach, L., DiMaio, F., Siegel, J.		Authors: Zhang, T., Prach, L., DiMaio, F., Siegel, J.

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

2020-02-13T02:46:02Z

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

←Older revision

Revision as of 02:46, 13 February 2020

OCA: New page: '''Unreleased structure''' The entry 6vpt is ON HOLD Authors: Zhang, T., Prach, L., DiMaio, F., Siegel, J. Description: Crystal structure and mechanistic molecular modeling studies of ...

2020-02-13T02:46:01Z

New page: '''Unreleased structure''' The entry 6vpt is ON HOLD Authors: Zhang, T., Prach, L., DiMaio, F., Siegel, J. Description: Crystal structure and mechanistic molecular modeling studies of ...

New page

'''Unreleased structure'''

The entry 6vpt is ON HOLD

Authors: Zhang, T., Prach, L., DiMaio, F., Siegel, J.

Description: Crystal structure and mechanistic molecular modeling studies of Rv3377c: the Mycobacterium tuberculosis diterpene cyclase
[[Category: Unreleased Structures]]
[[Category: Prach, L]]
[[Category: Siegel, J]]
[[Category: Zhang, T]]
[[Category: Dimaio, F]]