3nqf - Revision history

OCA at 09:19, 6 September 2023

OCA — Wed, 06 Sep 2023 09:19:30 GMT

←Older revision		Revision as of 09:19, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3nqf' size='340' side='right'caption='[[3nqf]], [[Resolution\|resolution]] 1.31Å' scene=''>		<StructureSection load='3nqf' size='340' side='right'caption='[[3nqf]], [[Resolution\|resolution]] 1.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nqf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NQF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nqf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NQF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BMP:6~~-~~HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.312Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3g18\|3g18]], [[3nq6\|3nq6]], [[3nq7\|3nq7]], [[3nqa\|3nqa]], [[3nqc\|3nqc]], [[3nqd\|3nqd]], [[3nqe\|3nqe]], [[3nqg\|3nqg]], [[3nqm\|3nqm]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>pyrF, MTH_129 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~145262~~ "~~Methanobacterium thermoautotrophicus~~" ~~(sic) Zeikus and Wolfe 1972])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23]~~ </~~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=3nqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nqf OCA], [https://pdbe.org/3nqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nqf RCSB], [https://www.ebi.ac.uk/pdbsum/3nqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nqf 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=3nqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nqf OCA], [https://pdbe.org/3nqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nqf RCSB], [https://www.ebi.ac.uk/pdbsum/3nqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nqf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH]] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]	+	[https://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]
	<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: ~~Orotidine-5'-phosphate decarboxylase~~]]	+	[[Category: Methanothermobacter thermautotrophicus]]
-	[[Category: Almo~~, S C~~]]	+	[[Category: Almo SC]]
-	[[Category: Fedorov~~, A A~~]]	+	[[Category: Fedorov AA]]
-	[[Category: Fedorov~~, E V~~]]	+	[[Category: Fedorov EV]]
-	[[Category: Gerlt~~, J A~~]]	+	[[Category: Gerlt JA]]
-	[[Category: Wood~~, B M]]~~	+	[[Category: Wood BM]]
-	~~[[Category: Inhibitor bmp]]~~	+
-	~~[[Category: Lyase-lyase inhibitor complex]]~~	+
-	~~[[Category: Methanobacterium thermoautotrophicum]]~~	+
-	~~[[Category: Orotidine 5'-monophosphate decarboxylase~~]]	+

OCA at 07:07, 12 May 2022

OCA — Thu, 12 May 2022 07:07:52 GMT

←Older revision		Revision as of 07:07, 12 May 2022
Line 1:		Line 1:

	==Crystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP==		==Crystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP==
-	<StructureSection load='3nqf' size='340' side='right' caption='[[3nqf]], [[Resolution\|resolution]] 1.31Å' scene=''>	+	<StructureSection load='3nqf' size='340' side='right'caption='[[3nqf]], [[Resolution\|resolution]] 1.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nqf]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NQF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3NQF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nqf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NQF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g18\|3g18]], [[3nq6\|3nq6]], [[3nq7\|3nq7]], [[3nqa\|3nqa]], [[3nqc\|3nqc]], [[3nqd\|3nqd]], [[3nqe\|3nqe]], [[3nqg\|3nqg]], [[3nqm\|3nqm]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3g18\|3g18]], [[3nq6\|3nq6]], [[3nq7\|3nq7]], [[3nqa\|3nqa]], [[3nqc\|3nqc]], [[3nqd\|3nqd]], [[3nqe\|3nqe]], [[3nqg\|3nqg]], [[3nqm\|3nqm]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF, MTH_129 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF, MTH_129 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </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=3nqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nqf OCA], [~~http~~://pdbe.org/3nqf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3nqf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3nqf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3nqf 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=3nqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nqf OCA], [https://pdbe.org/3nqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nqf RCSB], [https://www.ebi.ac.uk/pdbsum/3nqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nqf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH]] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]	+	[[https://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH]] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:

	==See Also==		==See Also==
-	*[[Uridine 5'-monophosphate synthase\|Uridine 5'-monophosphate synthase]]	+	*[[Uridine 5'-monophosphate synthase 3D structures\|Uridine 5'-monophosphate synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]

OCA at 10:28, 30 January 2019

OCA — Wed, 30 Jan 2019 10:28:03 GMT

←Older revision		Revision as of 10:28, 30 January 2019
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 3nqf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3nqf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Uridine 5'-monophosphate synthase\|Uridine 5'-monophosphate synthase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:48, 5 August 2016

OCA — Fri, 05 Aug 2016 16:48:16 GMT

←Older revision		Revision as of 16:48, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP==		==Crystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP==
	<StructureSection load='3nqf' size='340' side='right' caption='[[3nqf]], [[Resolution\|resolution]] 1.31Å' scene=''>		<StructureSection load='3nqf' size='340' side='right' caption='[[3nqf]], [[Resolution\|resolution]] 1.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nqf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NQF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nqf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NQF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g18\|3g18]], [[3nq6\|3nq6]], [[3nq7\|3nq7]], [[3nqa\|3nqa]], [[3nqc\|3nqc]], [[3nqd\|3nqd]], [[3nqe\|3nqe]], [[3nqg\|3nqg]], [[3nqm\|3nqm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g18\|3g18]], [[3nq6\|3nq6]], [[3nq7\|3nq7]], [[3nqa\|3nqa]], [[3nqc\|3nqc]], [[3nqd\|3nqd]], [[3nqe\|3nqe]], [[3nqg\|3nqg]], [[3nqm\|3nqm]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF, MTH_129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 ~~Methanothermobacter thermautotrophicus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF, MTH_129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </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=3nqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nqf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nqf RCSB], [http://www.ebi.ac.uk/pdbsum/3nqf 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=3nqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nqf OCA], [http://pdbe.org/3nqf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nqf RCSB], [http://www.ebi.ac.uk/pdbsum/3nqf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nqf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 3nqf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]

OCA at 20:24, 25 December 2014

OCA — Thu, 25 Dec 2014 20:24:44 GMT

←Older revision		Revision as of 20:24, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3nqf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NQF FirstGlance]. <br>		<table><tr><td colspan='2'>[[3nqf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NQF FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g18\|3g18]], [[3nq6\|3nq6]], [[3nq7\|3nq7]], [[3nqa\|3nqa]], [[3nqc\|3nqc]], [[3nqd\|3nqd]], [[3nqe\|3nqe]], [[3nqg\|3nqg]], [[3nqm\|3nqm]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g18\|3g18]], [[3nq6\|3nq6]], [[3nq7\|3nq7]], [[3nqa\|3nqa]], [[3nqc\|3nqc]], [[3nqd\|3nqd]], [[3nqe\|3nqe]], [[3nqg\|3nqg]], [[3nqm\|3nqm]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF, MTH_129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF, MTH_129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </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=3nqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nqf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nqf RCSB], [http://www.ebi.ac.uk/pdbsum/3nqf 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=3nqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nqf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nqf RCSB], [http://www.ebi.ac.uk/pdbsum/3nqf PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH]] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 17:
	Mechanism of the Orotidine 5'-Monophosphate Decarboxylase-Catalyzed Reaction: Importance of Residues in the Orotate Binding Site.,Iiams V, Desai BJ, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA Biochemistry. 2011 Sep 6. PMID:21870810<ref>PMID:21870810</ref>		Mechanism of the Orotidine 5'-Monophosphate Decarboxylase-Catalyzed Reaction: Importance of Residues in the Orotate Binding Site.,Iiams V, Desai BJ, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA Biochemistry. 2011 Sep 6. PMID:21870810<ref>PMID:21870810</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 23:		Line 25:
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
-	[[Category: Almo, S C.]]	+	[[Category: Almo, S C]]
-	[[Category: Fedorov, A A.]]	+	[[Category: Fedorov, A A]]
-	[[Category: Fedorov, E V.]]	+	[[Category: Fedorov, E V]]
-	[[Category: Gerlt, J A.]]	+	[[Category: Gerlt, J A]]
-	[[Category: Wood, B M.]]	+	[[Category: Wood, B M]]
	[[Category: Inhibitor bmp]]		[[Category: Inhibitor bmp]]
	[[Category: Lyase-lyase inhibitor complex]]		[[Category: Lyase-lyase inhibitor complex]]
	[[Category: Methanobacterium thermoautotrophicum]]		[[Category: Methanobacterium thermoautotrophicum]]
	[[Category: Orotidine 5'-monophosphate decarboxylase]]		[[Category: Orotidine 5'-monophosphate decarboxylase]]

OCA at 10:42, 28 May 2014

OCA — Wed, 28 May 2014 10:42:17 GMT

←Older revision		Revision as of 10:42, 28 May 2014
Line 1:		Line 1:
-	[[~~Image:~~3nqf.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP==
		+	<StructureSection load='3nqf' size='340' side='right' caption='[[3nqf]], [[Resolution\|resolution]] 1.31Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3nqf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NQF FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g18\|3g18]], [[3nq6\|3nq6]], [[3nq7\|3nq7]], [[3nqa\|3nqa]], [[3nqc\|3nqc]], [[3nqd\|3nqd]], [[3nqe\|3nqe]], [[3nqg\|3nqg]], [[3nqm\|3nqm]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF, MTH_129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </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=3nqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nqf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nqf RCSB], [http://www.ebi.ac.uk/pdbsum/3nqf PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The reaction catalyzed by orotidine 5'-monophosphate decarboxylase (OMPDC) is accompanied by exceptional values for rate enhancement (k(cat)/k(non) = 7.1 x 10(16)) and catalytic proficiency [(k(cat)/K(M))/k(non) = 4.8 x 10(22) M(-1)]. Although a stabilized vinyl carbanion/carbene intermediate is located on the reaction coordinate, the structural strategies by which the reduction in the activation energy barrier is realized remain incompletely understood. This laboratory recently reported that "substrate destabilization" by Asp 70 in the OMPDC from Methanothermobacter thermoautotrophicus (MtOMPDC) lowers the activation energy barrier by approximately 5 kcal/mol (contributing approximately 2.7 x 10(3) to the rate enhancement) [Chan, K. K., Wood, B. M., Fedorov, A. A., Fedorov, E. V., Imker, H. J., Amyes, T. L., Richard, J. P., Almo, S. C., and Gerlt, J. A. (2009) Biochemistry 48, 5518-5531]. We now report that substitutions of hydrophobic residues in a pocket proximal to the carboxylate group of the substrate (Ile 96, Leu 123, and Val 155) with neutral hydrophilic residues decrease the value of k(cat) by as much as 400-fold but have a minimal effect on the value of k(ex) for exchange of H6 of the FUMP product analogue with solvent deuterium; we hypothesize that this pocket destabilizes the substrate by preventing hydration of the substrate carboxylate group. We also report that substitutions of Ser 127 that is proximal to O4 of the orotate ring decrease the value of k(cat)/K(M), with the S127P substitution that eliminates hydrogen bonding interactions with O4 producing a 2.5 x 10(6)-fold reduction; this effect is consistent with delocalization of the negative charge of the carbanionic intermediate on O4 that produces an anionic carbene intermediate and thereby provides a structural strategy for stabilization of the intermediate. These observations provide additional information about the identities of the active site residues that contribute to the rate enhancement and, therefore, insights into the structural strategies for catalysis.

-	<!--	+	Mechanism of the Orotidine 5'-Monophosphate Decarboxylase-Catalyzed Reaction: Importance of Residues in the Orotate Binding Site.,Iiams V, Desai BJ, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA Biochemistry. 2011 Sep 6. PMID:21870810<ref>PMID:21870810</ref>
-	~~The line below this paragraph, containing "STRUCTURE_3nqf", 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~~.	+
-	-->	+
-	~~{{STRUCTURE_3nqf\| PDB=3nqf \| SCENE= }}~~	+

-	~~===Crystal structure~~ of the ~~mutant L123S of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21870810}}, adds the Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21870810 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21870810}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3nqf]] is a 2 chain structure with sequence from [http:~~//en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NQF OCA].	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021870810<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]

OCA at 05:12, 21 September 2011

OCA — Wed, 21 Sep 2011 05:12:32 GMT

←Older revision		Revision as of 05:12, 21 September 2011
Line 1:		Line 1:
-	[[Image:3nqf.~~jpg~~\|left\|200px]]	+	[[Image:3nqf.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Crystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP===		===Crystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21870810}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21870810 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21870810}}

	==About this Structure==		==About this Structure==
	[[3nqf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NQF OCA].		[[3nqf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NQF OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021870810</ref><references group="xtra"/>
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
Line 21:		Line 30:
	[[Category: Gerlt, J A.]]		[[Category: Gerlt, J A.]]
	[[Category: Wood, B M.]]		[[Category: Wood, B M.]]
		+	[[Category: Inhibitor bmp]]
		+	[[Category: Lyase-lyase inhibitor complex]]
		+	[[Category: Methanobacterium thermoautotrophicum]]
		+	[[Category: Orotidine 5'-monophosphate decarboxylase]]

OCA: Protected "3nqf" [edit=sysop:move=sysop]

OCA — Thu, 12 May 2011 04:50:18 GMT

Protected "3nqf" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:50, 12 May 2011

OCA at 04:50, 12 May 2011

OCA — Thu, 12 May 2011 04:50:12 GMT

←Older revision		Revision as of 04:50, 12 May 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3nqf.jpg\|left\|200px]]

-	The ~~entry 3nqf~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3nqf", 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.
		+	-->
		+	{{STRUCTURE_3nqf\| PDB=3nqf \| SCENE= }}

-	~~Authors: Fedorov, A.A., Fedorov, E.V., Wood, B.M., Gerlt, J.A., Almo, S.C.~~	+	===Crystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP===

-	Description: Crystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP

-	~~''Page seeded by~~ [http://oca.weizmann.ac.il/oca OCA ] ~~on Wed Jul 21 10~~:05:~~17 2010'~~'	+	==About this Structure==
		+	[[3nqf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NQF OCA].
		+	[[Category: Methanothermobacter thermautotrophicus]]
		+	[[Category: Orotidine-5'-phosphate decarboxylase]]
		+	[[Category: Almo, S C.]]
		+	[[Category: Fedorov, A A.]]
		+	[[Category: Fedorov, E V.]]
		+	[[Category: Gerlt, J A.]]
		+	[[Category: Wood, B M.]]

OCA at 05:58, 21 July 2010

OCA — Wed, 21 Jul 2010 05:58:51 GMT

←Older revision		Revision as of 05:58, 21 July 2010
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3nqf is ON HOLD	+	The entry 3nqf is ON HOLD until Paper Publication

	Authors: Fedorov, A.A., Fedorov, E.V., Wood, B.M., Gerlt, J.A., Almo, S.C.		Authors: Fedorov, A.A., Fedorov, E.V., Wood, B.M., Gerlt, J.A., Almo, S.C.
Line 7:		Line 7:
	Description: Crystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP		Description: Crystal structure of the mutant L123S of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul ~~14 16~~:08:25 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 21 10:05:17 2010''