1lrt - Revision history

OCA at 08:26, 10 April 2024

OCA — Wed, 10 Apr 2024 08:26:55 GMT

←Older revision		Revision as of 08:26, 10 April 2024
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	<StructureSection load='1lrt' size='340' side='right'caption='[[1lrt]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1lrt' size='340' side='right'caption='[[1lrt]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lrt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LRT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lrt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Tritrichomonas_suis Tritrichomonas suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LRT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TAD:BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINE+DINUCLEOTIDE'>TAD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ak5\|1ak5]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TAD:BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINE+DINUCLEOTIDE'>TAD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/IMP_dehydrogenase IMP dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.205 1.1.1.205] </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=1lrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrt OCA], [https://pdbe.org/1lrt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lrt RCSB], [https://www.ebi.ac.uk/pdbsum/1lrt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lrt 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=1lrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrt OCA], [https://pdbe.org/1lrt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lrt RCSB], [https://www.ebi.ac.uk/pdbsum/1lrt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lrt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/IMDH_TRIFO IMDH_TRIFO]] Catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate-limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth. Could also have a single-stranded nucleic acid-binding activity and could play a role in RNA and/or DNA metabolism.<ref>PMID:10029522</ref>	+	[https://www.uniprot.org/uniprot/IMDH_TRIFO IMDH_TRIFO] Catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate-limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth. Could also have a single-stranded nucleic acid-binding activity and could play a role in RNA and/or DNA metabolism.<ref>PMID:10029522</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1lrt ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1lrt ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the conversion of IMP to XMP with the reduction of NAD(+), which is the rate-limiting step in the biosynthesis of guanine nucleotides. IMPDH is a promising target for chemotherapy. Microbial IMPDHs differ from mammalian enzymes in their lower affinity for inhibitors such as mycophenolic acid (MPA) and thiazole-4-carboxamide adenine dinucleotide (TAD). Part of this resistance is determined by the coupling between nicotinamide and adenosine subsites in the NAD(+) binding site that is postulated to involve an active site flap. To understand the structural basis of the drug selectivity, we solved the X-ray crystal structure of the catalytic core domain of Tritrichomonas foetus IMPDH in complex with IMP and beta-methylene-TAD at 2.2 A resolution. Unlike previous structures of this enzyme, the active site loop is ordered in this complex, and the catalytic Cys319 is 3.6 A from IMP, in the same plane as the hypoxanthine ring. The active site loop forms hydrogen bonds to the carboxamide of beta-Me-TAD which suggests that NAD(+) promotes the nucleophillic attack of Cys319 on IMP. The interactions of the adenosine end of TAD are very different from those in the human enzyme, suggesting the NAD(+) site may be an exploitable target for the design of antimicrobial drugs. In addition, a new K(+) site is observed at the subunit interface. This site is adjacent to beta-Me-TAD, consistent with the link between the K(+) activation and NAD(+). However, contrary to the coupling model, the flap does not cover the adenosine subsite and remains largely disordered.
-
-	Crystal structure of a ternary complex of Tritrichomonas foetus inosine 5'-monophosphate dehydrogenase: NAD+ orients the active site loop for catalysis.,Gan L, Petsko GA, Hedstrom L Biochemistry. 2002 Nov 5;41(44):13309-17. PMID:12403633<ref>PMID:12403633</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1lrt" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: IMP dehydrogenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Gan, L~~]]	+	[[Category: Tritrichomonas suis]]
-	[[Category: ~~Hedstrom,~~ L]]	+	[[Category: Gan L]]
-	[[Category: ~~Petsko, G A~~]]	+	[[Category: Hedstrom L]]
-	[[Category: ~~Alpha-beta barrel]]~~	+	[[Category: Petsko GA]]
-	~~[[Category: Flap]]~~	+
-	~~[[Category: Flexible loop]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Ternary complex~~]]	+

OCA at 09:53, 26 May 2021

OCA — Wed, 26 May 2021 09:53:06 GMT

←Older revision		Revision as of 09:53, 26 May 2021
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	<StructureSection load='1lrt' size='340' side='right'caption='[[1lrt]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1lrt' size='340' side='right'caption='[[1lrt]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lrt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1LRT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lrt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LRT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TAD:BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINE+DINUCLEOTIDE'>TAD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TAD:BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINE+DINUCLEOTIDE'>TAD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ak5\|1ak5]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ak5\|1ak5]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/IMP_dehydrogenase IMP dehydrogenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.205 1.1.1.205] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/IMP_dehydrogenase IMP dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.205 1.1.1.205] </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=1lrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrt OCA], [~~http~~://pdbe.org/1lrt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1lrt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1lrt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1lrt 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=1lrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrt OCA], [https://pdbe.org/1lrt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lrt RCSB], [https://www.ebi.ac.uk/pdbsum/1lrt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lrt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/IMDH_TRIFO IMDH_TRIFO]] Catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate-limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth. Could also have a single-stranded nucleic acid-binding activity and could play a role in RNA and/or DNA metabolism.<ref>PMID:10029522</ref>	+	[[https://www.uniprot.org/uniprot/IMDH_TRIFO IMDH_TRIFO]] Catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate-limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth. Could also have a single-stranded nucleic acid-binding activity and could play a role in RNA and/or DNA metabolism.<ref>PMID:10029522</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
-	*[[Inosine monophosphate dehydrogenase\|Inosine monophosphate dehydrogenase]]	+	*[[Inosine monophosphate dehydrogenase 3D structures\|Inosine monophosphate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:03, 21 August 2019

OCA — Wed, 21 Aug 2019 07:03:00 GMT

←Older revision		Revision as of 07:03, 21 August 2019
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	==CRYSTAL STRUCTURE OF TERNARY COMPLEX OF TRITRICHOMONAS FOETUS INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE: STRUCTURAL CHARACTERIZATION OF NAD+ SITE IN MICROBIAL ENZYME==		==CRYSTAL STRUCTURE OF TERNARY COMPLEX OF TRITRICHOMONAS FOETUS INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE: STRUCTURAL CHARACTERIZATION OF NAD+ SITE IN MICROBIAL ENZYME==
-	<StructureSection load='1lrt' size='340' side='right' caption='[[1lrt]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='1lrt' size='340' side='right'caption='[[1lrt]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lrt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LRT FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lrt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LRT FirstGlance]. <br>
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lr/1lrt_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lr/1lrt_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	</div>		</div>
	<div class="pdbe-citations 1lrt" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1lrt" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Inosine monophosphate dehydrogenase\|Inosine monophosphate dehydrogenase]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: IMP dehydrogenase]]		[[Category: IMP dehydrogenase]]
		+	[[Category: Large Structures]]
	[[Category: Gan, L]]		[[Category: Gan, L]]
	[[Category: Hedstrom, L]]		[[Category: Hedstrom, L]]

OCA at 05:02, 16 November 2017

OCA — Thu, 16 Nov 2017 05:02:24 GMT

←Older revision		Revision as of 05:02, 16 November 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF TERNARY COMPLEX OF TRITRICHOMONAS FOETUS INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE: STRUCTURAL CHARACTERIZATION OF NAD+ SITE IN MICROBIAL ENZYME==		==CRYSTAL STRUCTURE OF TERNARY COMPLEX OF TRITRICHOMONAS FOETUS INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE: STRUCTURAL CHARACTERIZATION OF NAD+ SITE IN MICROBIAL ENZYME==
	<StructureSection load='1lrt' size='340' side='right' caption='[[1lrt]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1lrt' size='340' side='right' caption='[[1lrt]], [[Resolution\|resolution]] 2.20Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ak5\|1ak5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ak5\|1ak5]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/IMP_dehydrogenase IMP dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.205 1.1.1.205] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/IMP_dehydrogenase IMP dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.205 1.1.1.205] </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=1lrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrt OCA], [http://pdbe.org/1lrt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lrt RCSB], [http://www.ebi.ac.uk/pdbsum/1lrt 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=1lrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrt OCA], [http://pdbe.org/1lrt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lrt RCSB], [http://www.ebi.ac.uk/pdbsum/1lrt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lrt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1lrt" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1lrt" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Inosine monophosphate dehydrogenase\|Inosine monophosphate dehydrogenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:01, 7 February 2016

OCA — Sun, 07 Feb 2016 06:01:35 GMT

←Older revision		Revision as of 06:01, 7 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1lrt ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:33, 9 September 2015

OCA — Wed, 09 Sep 2015 22:33:04 GMT

←Older revision		Revision as of 22:33, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='1lrt' size='340' side='right' caption='[[1lrt]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1lrt' size='340' side='right' caption='[[1lrt]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lrt]] is a 4 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Tritrichomonas_suis Tritrichomonas suis]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LRT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lrt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LRT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TAD:BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINE+DINUCLEOTIDE'>TAD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TAD:BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINE+DINUCLEOTIDE'>TAD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ak5\|1ak5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ak5\|1ak5]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IMPDH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56690 Tritrichomonas suis])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/IMP_dehydrogenase IMP dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.205 1.1.1.205] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/IMP_dehydrogenase IMP dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.205 1.1.1.205] </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=1lrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lrt RCSB], [http://www.ebi.ac.uk/pdbsum/1lrt 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=1lrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrt OCA], [http://pdbe.org/1lrt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lrt RCSB], [http://www.ebi.ac.uk/pdbsum/1lrt PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 28:
	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 1lrt" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: IMP dehydrogenase]]		[[Category: IMP dehydrogenase]]
-	[[Category: Tritrichomonas suis]]
	[[Category: Gan, L]]		[[Category: Gan, L]]
	[[Category: Hedstrom, L]]		[[Category: Hedstrom, L]]

OCA at 08:27, 24 December 2014

OCA — Wed, 24 Dec 2014 08:27:52 GMT

←Older revision		Revision as of 08:27, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lrt]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Tritrichomonas_suis Tritrichomonas suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LRT FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lrt]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Tritrichomonas_suis Tritrichomonas suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LRT FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TAD:BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINE+DINUCLEOTIDE'>TAD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TAD:BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINE+DINUCLEOTIDE'>TAD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ak5\|1ak5]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ak5\|1ak5]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IMPDH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56690 Tritrichomonas suis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IMPDH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56690 Tritrichomonas suis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/IMP_dehydrogenase IMP dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.205 1.1.1.205] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/IMP_dehydrogenase IMP dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.205 1.1.1.205] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1lrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lrt RCSB], [http://www.ebi.ac.uk/pdbsum/1lrt 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=1lrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lrt RCSB], [http://www.ebi.ac.uk/pdbsum/1lrt PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/IMDH_TRIFO IMDH_TRIFO]] Catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate-limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth. Could also have a single-stranded nucleic acid-binding activity and could play a role in RNA and/or DNA metabolism.<ref>PMID:10029522</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: IMP dehydrogenase]]		[[Category: IMP dehydrogenase]]
	[[Category: Tritrichomonas suis]]		[[Category: Tritrichomonas suis]]
-	[[Category: Gan, L.]]	+	[[Category: Gan, L]]
-	[[Category: Hedstrom, L.]]	+	[[Category: Hedstrom, L]]
-	[[Category: Petsko, G A.]]	+	[[Category: Petsko, G A]]
	[[Category: Alpha-beta barrel]]		[[Category: Alpha-beta barrel]]
	[[Category: Flap]]		[[Category: Flap]]

OCA at 14:10, 28 September 2014

OCA — Sun, 28 Sep 2014 14:10:41 GMT

←Older revision		Revision as of 14:10, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1lrt.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF TERNARY COMPLEX OF TRITRICHOMONAS FOETUS INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE: STRUCTURAL CHARACTERIZATION OF NAD+ SITE IN MICROBIAL ENZYME==
		+	<StructureSection load='1lrt' size='340' side='right' caption='[[1lrt]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1lrt]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Tritrichomonas_suis Tritrichomonas suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LRT FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TAD:BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINE+DINUCLEOTIDE'>TAD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ak5\|1ak5]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IMPDH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56690 Tritrichomonas suis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/IMP_dehydrogenase IMP dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.205 1.1.1.205] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1lrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lrt RCSB], [http://www.ebi.ac.uk/pdbsum/1lrt PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lr/1lrt_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the conversion of IMP to XMP with the reduction of NAD(+), which is the rate-limiting step in the biosynthesis of guanine nucleotides. IMPDH is a promising target for chemotherapy. Microbial IMPDHs differ from mammalian enzymes in their lower affinity for inhibitors such as mycophenolic acid (MPA) and thiazole-4-carboxamide adenine dinucleotide (TAD). Part of this resistance is determined by the coupling between nicotinamide and adenosine subsites in the NAD(+) binding site that is postulated to involve an active site flap. To understand the structural basis of the drug selectivity, we solved the X-ray crystal structure of the catalytic core domain of Tritrichomonas foetus IMPDH in complex with IMP and beta-methylene-TAD at 2.2 A resolution. Unlike previous structures of this enzyme, the active site loop is ordered in this complex, and the catalytic Cys319 is 3.6 A from IMP, in the same plane as the hypoxanthine ring. The active site loop forms hydrogen bonds to the carboxamide of beta-Me-TAD which suggests that NAD(+) promotes the nucleophillic attack of Cys319 on IMP. The interactions of the adenosine end of TAD are very different from those in the human enzyme, suggesting the NAD(+) site may be an exploitable target for the design of antimicrobial drugs. In addition, a new K(+) site is observed at the subunit interface. This site is adjacent to beta-Me-TAD, consistent with the link between the K(+) activation and NAD(+). However, contrary to the coupling model, the flap does not cover the adenosine subsite and remains largely disordered.

-	~~{{STRUCTURE_1lrt\| PDB=1lrt \| SCENE= }}~~	+	Crystal structure of a ternary complex of Tritrichomonas foetus inosine 5'-monophosphate dehydrogenase: NAD+ orients the active site loop for catalysis.,Gan L, Petsko GA, Hedstrom L Biochemistry. 2002 Nov 5;41(44):13309-17. PMID:12403633<ref>PMID:12403633</ref>

-	~~===CRYSTAL STRUCTURE OF TERNARY COMPLEX OF TRITRICHOMONAS FOETUS INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE: STRUCTURAL CHARACTERIZATION OF NAD+ SITE IN MICROBIAL ENZYME===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_12403633}}~~	+	==See Also==
-		+	*[[Inosine monophosphate dehydrogenase\|Inosine monophosphate dehydrogenase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1lrt~~]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Tritrichomonas_foetus Tritrichomonas foetus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRT OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:012403633<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: IMP dehydrogenase]]		[[Category: IMP dehydrogenase]]
-	[[Category: Tritrichomonas ~~foetus~~]]	+	[[Category: Tritrichomonas suis]]
	[[Category: Gan, L.]]		[[Category: Gan, L.]]
	[[Category: Hedstrom, L.]]		[[Category: Hedstrom, L.]]

OCA: Protected "1lrt" [edit=sysop:move=sysop]

OCA — Wed, 12 Dec 2012 21:39:51 GMT

Protected "1lrt" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:39, 12 December 2012

OCA at 21:39, 12 December 2012

OCA — Wed, 12 Dec 2012 21:39:48 GMT

←Older revision		Revision as of 21:39, 12 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1lrt.png\|left\|200px]]		[[Image:1lrt.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1lrt", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
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	{{STRUCTURE_1lrt\| PDB=1lrt \| SCENE= }}		{{STRUCTURE_1lrt\| PDB=1lrt \| SCENE= }}

	===CRYSTAL STRUCTURE OF TERNARY COMPLEX OF TRITRICHOMONAS FOETUS INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE: STRUCTURAL CHARACTERIZATION OF NAD+ SITE IN MICROBIAL ENZYME===		===CRYSTAL STRUCTURE OF TERNARY COMPLEX OF TRITRICHOMONAS FOETUS INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE: STRUCTURAL CHARACTERIZATION OF NAD+ SITE IN MICROBIAL ENZYME===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12403633}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12403633 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12403633}}		{{ABSTRACT_PUBMED_12403633}}

	==About this Structure==		==About this Structure==
-	~~1LRT~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Tritrichomonas_foetus Tritrichomonas foetus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRT OCA].	+	[[1lrt]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Tritrichomonas_foetus Tritrichomonas foetus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRT OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12403633~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012403633</ref><references group="xtra"/>
	[[Category: IMP dehydrogenase]]		[[Category: IMP dehydrogenase]]
	[[Category: Tritrichomonas foetus]]		[[Category: Tritrichomonas foetus]]
Line 32:		Line 20:
	[[Category: Flap]]		[[Category: Flap]]
	[[Category: Flexible loop]]		[[Category: Flexible loop]]
		+	[[Category: Oxidoreductase]]
	[[Category: Ternary complex]]		[[Category: Ternary complex]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 11:49:09 2009''