5iao - Revision history

OCA at 13:43, 30 August 2023

OCA — Wed, 30 Aug 2023 13:43:45 GMT

←Older revision		Revision as of 13:43, 30 August 2023
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	<StructureSection load='5iao' size='340' side='right'caption='[[5iao]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5iao' size='340' side='right'caption='[[5iao]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5iao]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Mycta Mycta~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IAO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5IAO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5iao]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Ra Mycobacterium tuberculosis H37Ra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IAO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IAO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=URF:5~~-~~FLUOROURACIL'>URF</scene>~~</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]] 2.598Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>pyrR, MRA_1388 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~419947 MYCTA])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URF:5-FLUOROURACIL'>URF</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Uracil_phosphoribosyltransferase Uracil phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.9 2.4.2.9]~~ </~~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=5iao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iao OCA], [https://pdbe.org/5iao PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5iao RCSB], [https://www.ebi.ac.uk/pdbsum/5iao PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5iao ProSAT]</span></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=5iao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iao OCA], [~~http~~://pdbe.org/5iao PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5iao RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5iao PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5iao ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~PYRR_MYCTA PYRR_MYCTA]~~] Regulates the transcription of the pyrimidine nucleotide (pyr) operon in response to exogenous pyrimidines. Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant.	+	[https://www.uniprot.org/uniprot/PYRR_MYCTU PYRR_MYCTU] Regulates the transcription of the pyrimidine nucleotide (pyr) operon in response to exogenous pyrimidines (By similarity). Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant (By similarity).
	<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: ~~Mycta]]~~	+	[[Category: Mycobacterium tuberculosis H37Ra]]
-	~~[[Category: Uracil phosphoribosyltransferase~~]]	+	[[Category: Ghode P]]
-	[[Category: Ghode, P]]	+	[[Category: Ramachandran S]]
-	[[Category: Ramachandran, S]]	+	[[Category: Sivaraman J]]
-	[[Category: Sivaraman, J]]	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:10, 3 June 2020

OCA — Wed, 03 Jun 2020 07:10:26 GMT

←Older revision		Revision as of 07:10, 3 June 2020
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	==Structure and mapping of spontaneous mutational sites of PyrR from Mycobacterium tuberculosis==		==Structure and mapping of spontaneous mutational sites of PyrR from Mycobacterium tuberculosis==
-	<StructureSection load='5iao' size='340' side='right' caption='[[5iao]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5iao' size='340' side='right'caption='[[5iao]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5iao]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IAO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca.weizmann~~.~~ac.il/oca-docs~~/fgij/fg.htm?mol=5IAO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5iao]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycta Mycta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IAO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IAO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=URF:5-FLUOROURACIL'>URF</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=URF:5-FLUOROURACIL'>URF</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrR, MRA_1388 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419947 MYCTA])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil_phosphoribosyltransferase Uracil phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.9 2.4.2.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil_phosphoribosyltransferase Uracil phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.9 2.4.2.9] </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=5iao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iao OCA], [http://pdbe.org/5iao PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iao RCSB], [http://www.ebi.ac.uk/pdbsum/5iao PDBsum]</span></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=5iao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iao OCA], [http://pdbe.org/5iao PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iao RCSB], [http://www.ebi.ac.uk/pdbsum/5iao PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iao ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Mycta]]
	[[Category: Uracil phosphoribosyltransferase]]		[[Category: Uracil phosphoribosyltransferase]]
	[[Category: Ghode, P]]		[[Category: Ghode, P]]

OCA at 16:45, 10 May 2016

OCA — Tue, 10 May 2016 16:45:10 GMT

←Older revision		Revision as of 16:45, 10 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5iao is ~~ON HOLD~~	+	==Structure and mapping of spontaneous mutational sites of PyrR from Mycobacterium tuberculosis==
		+	<StructureSection load='5iao' size='340' side='right' caption='[[5iao]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5iao]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IAO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IAO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=URF:5-FLUOROURACIL'>URF</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil_phosphoribosyltransferase Uracil phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.9 2.4.2.9] </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=5iao FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iao OCA], [http://pdbe.org/5iao PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iao RCSB], [http://www.ebi.ac.uk/pdbsum/5iao PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PYRR_MYCTA PYRR_MYCTA]] Regulates the transcription of the pyrimidine nucleotide (pyr) operon in response to exogenous pyrimidines. Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The emergence of resistant Mycobacterium tuberculosis (Mtb) infection and the dearth of drugs against tuberculosis have made it imperative to identify and validate novel targets and classes of drugs for treatment. The pyrimidine operon regulatory protein (PyrR), a regulator of de novo pyrimidine synthesis, is an essential enzyme and a probable 5-fluorouracil (5-FU) target in Mtb, with mutations in PyrR attributable to 5-FU resistance. Here we report, for the first time, the co-crystal structure of the PyrR-5-FU complex along with mapping of spontaneous mutational sites of PyrR. A cluster of mutations in the presence of the drug usually indicates a plausible region of drug-target interaction. Notably, we observed that three of the mutated PyrR residues lie in close proximity to the 5-FU binding site, including the amino acid Val178, which is involved in water mediated hydrogen bonding contact with 5-FU. Computational modeling of the PyrR-5'-phosphoribosyl-alpha-1'-pyrophosphate (PRPP) complex revealed the location of several other mutations at the PRPP binding site of PyrR, indicating their probable role in resistance. Indeed, 5-FU-resistant strains harboring these mutations exhibited decreased susceptibility to 5-FU. Considering that pyrimidine analogs are predominantly regarded to inhibit PyrR, the present studies will be beneficial for the screening of appropriate inhibitors of PyrR and help provide insight into future TB drug design and development.

-	~~Authors: Sivaraman, J~~., Ghode, P., Ramachandran, S.	+	Structure and mapping of spontaneous mutational sites of PyrR from Mycobacterium tuberculosis.,Ghode P, Ramachandran S, Bifani P, Sivaraman J Biochem Biophys Res Commun. 2016 Mar 18;471(4):409-15. doi:, 10.1016/j.bbrc.2016.02.071. Epub 2016 Feb 18. PMID:26902118<ref>PMID:26902118</ref>

-	~~Description: Structure and mapping~~ of ~~spontaneous mutational sites~~ of ~~PyrR from Mycobacterium tuberculosis~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5iao" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Uracil phosphoribosyltransferase]]
		+	[[Category: Ghode, P]]
	[[Category: Ramachandran, S]]		[[Category: Ramachandran, S]]
	[[Category: Sivaraman, J]]		[[Category: Sivaraman, J]]
-	[[Category: ~~Ghode, P~~]]	+	[[Category: Transferase]]

OCA: Protected "5iao" [edit=sysop:move=sysop]

OCA — Wed, 02 Mar 2016 13:38:34 GMT

Protected "5iao" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:38, 2 March 2016

OCA: New page: '''Unreleased structure''' The entry 5iao is ON HOLD Authors: Sivaraman, J., Ghode, P., Ramachandran, S. Description: Structure and mapping of spontaneous mutational sites of PyrR from...

OCA — Wed, 02 Mar 2016 13:38:32 GMT

New page: '''Unreleased structure''' The entry 5iao is ON HOLD Authors: Sivaraman, J., Ghode, P., Ramachandran, S. Description: Structure and mapping of spontaneous mutational sites of PyrR from...

New page

'''Unreleased structure'''

The entry 5iao is ON HOLD

Authors: Sivaraman, J., Ghode, P., Ramachandran, S.

Description: Structure and mapping of spontaneous mutational sites of PyrR from Mycobacterium tuberculosis
[[Category: Unreleased Structures]]
[[Category: Ramachandran, S]]
[[Category: Sivaraman, J]]
[[Category: Ghode, P]]