3rlv - Revision history

OCA at 12:28, 14 March 2024

OCA — Thu, 14 Mar 2024 12:28:57 GMT

←Older revision		Revision as of 12:28, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3rlv' size='340' side='right'caption='[[3rlv]], [[Resolution\|resolution]] 1.42Å' scene=''>		<StructureSection load='3rlv' size='340' side='right'caption='[[3rlv]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rlv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Metth Metth~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RLV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RLV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rlv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._Delta_H Methanothermobacter thermautotrophicus str. Delta H]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RLV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RLV 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]] 1.421Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3ltp\|3ltp]], [[3rlu\|3rlu]]</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=~~187420 METTH])</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=3rlv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rlv OCA], [https://pdbe.org/3rlv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rlv RCSB], [https://www.ebi.ac.uk/pdbsum/3rlv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rlv 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=3rlv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rlv OCA], [https://pdbe.org/3rlv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rlv RCSB], [https://www.ebi.ac.uk/pdbsum/3rlv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rlv 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;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The binding of a ligand to orotidine 5'-monophosphate decarboxylase (OMPDC) is accompanied by a conformational change from an open, inactive conformation (E(o)) to a closed, active conformation (E(c)). As the substrate traverses the reaction coordinate to form the stabilized vinyl carbanion/carbene intermediate, interactions that destabilize the carboxylate group of the substrate and stabilize the intermediate (in the E(c).S() complex) are enforced. Focusing on the OMPDC from Methanothermobacter thermautotrophicus, we find the "remote" 5'-phosphate group of the substrate activates the enzyme 2.4 x 10(8)-fold; the activation is equivalently described by an intrinsic binding energy (IBE) of 11.4 kcal/mol. We studied residues in the activation that (1) directly contact the 5'-phosphate group, (2) participate in a hydrophobic cluster near the base of the active site loop that sequesters the bound substrate from the solvent, and (3) form hydrogen bonding interactions across the interface between the "mobile" and "fixed" half-barrel domains of the (beta/alpha)(8)-barrel structure. Our data support a model in which the IBE provided by the 5'-phosphate group is used to allow interactions both near the N-terminus of the active site loop and across the domain interface that stabilize both the E(c).S and E(c).S() complexes relative to the E(o).S complex. The conclusion that the IBE of the 5'-phosphate group provides stabilization to both the E(c).S and E(c).S() complexes, not just the E(c).S() complex, is central to understanding the structural origins of enzymatic catalysis as well as the requirements for the de novo design of enzymes that catalyze novel reactions.	+
-		+
-	Conformational Changes in Orotidine 5'-Monophosphate Decarboxylase: A Structure-Based Explanation for How the 5'-Phosphate Group Activates the Enzyme.,Desai BJ, Wood BM, Fedorov AA, Fedorov EV, Goryanova B, Amyes TL, Richard JP, Almo SC, Gerlt JA Biochemistry. 2012 Oct 17. PMID:23030629<ref>PMID:23030629</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3rlv" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Uridine 5'-monophosphate synthase 3D structures\|Uridine 5'-monophosphate synthase 3D structures]]		*[[Uridine 5'-monophosphate synthase 3D structures\|Uridine 5'-monophosphate synthase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Metth]]~~	+	[[Category: Methanothermobacter thermautotrophicus str. Delta H]]
-	~~[[Category: Orotidine-5'-phosphate decarboxylase~~]]	+	[[Category: Almo SC]]
-	[[Category: Almo~~, S C~~]]	+	[[Category: Desai B]]
-	[[Category: Desai, B]]	+	[[Category: Fedorov AA]]
-	[[Category: Fedorov~~, A A~~]]	+	[[Category: Fedorov EV]]
-	[[Category: Fedorov~~, E V~~]]	+	[[Category: Gerlt JA]]
-	[[Category: Gerlt~~, J A]]~~	+
-	~~[[Category: Lyase-lyase inhibitor complex]]~~	+
-	~~[[Category: Tim barrel fold~~]]	+

OCA at 10:16, 22 June 2022

OCA — Wed, 22 Jun 2022 10:16:23 GMT

←Older revision		Revision as of 10:16, 22 June 2022
Line 1:		Line 1:

	==Crystal structure of the mutant Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP==		==Crystal structure of the mutant Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP==
-	<StructureSection load='3rlv' size='340' side='right' caption='[[3rlv]], [[Resolution\|resolution]] 1.42Å' scene=''>	+	<StructureSection load='3rlv' size='340' side='right'caption='[[3rlv]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rlv]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RLV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3RLV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rlv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RLV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RLV 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">[[3ltp\|3ltp]], [[3rlu\|3rlu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ltp\|3ltp]], [[3rlu\|3rlu]]</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=187420 METTH])</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=187420 METTH])</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=3rlv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rlv OCA], [~~http~~://pdbe.org/3rlv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3rlv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3rlv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3rlv 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=3rlv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rlv OCA], [https://pdbe.org/3rlv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rlv RCSB], [https://www.ebi.ac.uk/pdbsum/3rlv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rlv 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 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 3rlv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3rlv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Uridine 5'-monophosphate synthase 3D structures\|Uridine 5'-monophosphate synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Metth]]		[[Category: Metth]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]

OCA at 02:33, 5 August 2016

OCA — Fri, 05 Aug 2016 02:33:18 GMT

←Older revision		Revision as of 02:33, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the mutant Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP==		==Crystal structure of the mutant Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP==
	<StructureSection load='3rlv' size='340' side='right' caption='[[3rlv]], [[Resolution\|resolution]] 1.42Å' scene=''>		<StructureSection load='3rlv' size='340' side='right' caption='[[3rlv]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rlv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Methanothermobacter_thermautotrophicus_str._delta_h Methanothermobacter thermautotrophicus str. delta h~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RLV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RLV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rlv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RLV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RLV 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">[[3ltp\|3ltp]], [[3rlu\|3rlu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ltp\|3ltp]], [[3rlu\|3rlu]]</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=187420 ~~Methanothermobacter thermautotrophicus str. Delta H~~])</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=187420 METTH])</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=3rlv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rlv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rlv RCSB], [http://www.ebi.ac.uk/pdbsum/3rlv 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=3rlv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rlv OCA], [http://pdbe.org/3rlv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rlv RCSB], [http://www.ebi.ac.uk/pdbsum/3rlv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rlv 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 3rlv" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Methanothermobacter thermautotrophicus str. delta h~~]]	+	[[Category: Metth]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]

OCA at 22:03, 24 December 2014

OCA — Wed, 24 Dec 2014 22:03:23 GMT

←Older revision		Revision as of 22:03, 24 December 2014
Line 9:		Line 9:
	<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=3rlv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rlv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rlv RCSB], [http://www.ebi.ac.uk/pdbsum/3rlv 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=3rlv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rlv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rlv RCSB], [http://www.ebi.ac.uk/pdbsum/3rlv 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 ==

OCA at 10:07, 19 December 2014

OCA — Fri, 19 Dec 2014 10:07:56 GMT

←Older revision		Revision as of 10:07, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3rlv\| PDB=3rlv \| SCENE= }}~~	+	==Crystal structure of the mutant Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP==
-	===Crystal structure of the mutant Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP===	+	<StructureSection load='3rlv' size='340' side='right' caption='[[3rlv]], [[Resolution\|resolution]] 1.42Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23030629}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3rlv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._delta_h Methanothermobacter thermautotrophicus str. delta h]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RLV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RLV 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>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ltp\|3ltp]], [[3rlu\|3rlu]]</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=187420 Methanothermobacter thermautotrophicus str. Delta H])</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=3rlv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rlv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rlv RCSB], [http://www.ebi.ac.uk/pdbsum/3rlv PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The binding of a ligand to orotidine 5'-monophosphate decarboxylase (OMPDC) is accompanied by a conformational change from an open, inactive conformation (E(o)) to a closed, active conformation (E(c)). As the substrate traverses the reaction coordinate to form the stabilized vinyl carbanion/carbene intermediate, interactions that destabilize the carboxylate group of the substrate and stabilize the intermediate (in the E(c).S() complex) are enforced. Focusing on the OMPDC from Methanothermobacter thermautotrophicus, we find the "remote" 5'-phosphate group of the substrate activates the enzyme 2.4 x 10(8)-fold; the activation is equivalently described by an intrinsic binding energy (IBE) of 11.4 kcal/mol. We studied residues in the activation that (1) directly contact the 5'-phosphate group, (2) participate in a hydrophobic cluster near the base of the active site loop that sequesters the bound substrate from the solvent, and (3) form hydrogen bonding interactions across the interface between the "mobile" and "fixed" half-barrel domains of the (beta/alpha)(8)-barrel structure. Our data support a model in which the IBE provided by the 5'-phosphate group is used to allow interactions both near the N-terminus of the active site loop and across the domain interface that stabilize both the E(c).S and E(c).S() complexes relative to the E(o).S complex. The conclusion that the IBE of the 5'-phosphate group provides stabilization to both the E(c).S and E(c).S() complexes, not just the E(c).S() complex, is central to understanding the structural origins of enzymatic catalysis as well as the requirements for the de novo design of enzymes that catalyze novel reactions.

-	~~==Function==~~	+	Conformational Changes in Orotidine 5'-Monophosphate Decarboxylase: A Structure-Based Explanation for How the 5'-Phosphate Group Activates the Enzyme.,Desai BJ, Wood BM, Fedorov AA, Fedorov EV, Goryanova B, Amyes TL, Richard JP, Almo SC, Gerlt JA Biochemistry. 2012 Oct 17. PMID:23030629<ref>PMID:23030629</ref>
-	~~[[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]~~	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3rlv]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Methanothermobacter_thermautotrophicus_str~~.~~_delta_h Methanothermobacter thermautotrophicus str. delta h]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3RLV OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:023030629</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Methanothermobacter thermautotrophicus str. delta h]]		[[Category: Methanothermobacter thermautotrophicus str. delta h]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
-	[[Category: Almo, S C.]]	+	[[Category: Almo, S C]]
-	[[Category: Desai, B.]]	+	[[Category: Desai, B]]
-	[[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: Lyase-lyase inhibitor complex]]		[[Category: Lyase-lyase inhibitor complex]]
	[[Category: Tim barrel fold]]		[[Category: Tim barrel fold]]

OCA at 13:21, 19 June 2013

OCA — Wed, 19 Jun 2013 13:21:39 GMT

←Older revision		Revision as of 13:21, 19 June 2013
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-	[[Image:3rlv.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3rlv", 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_3rlv\| PDB=3rlv \| SCENE= }}		{{STRUCTURE_3rlv\| PDB=3rlv \| SCENE= }}
-
	===Crystal structure of the mutant Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP===		===Crystal structure of the mutant Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP===
		+	{{ABSTRACT_PUBMED_23030629}}

		+	==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]

	==About this Structure==		==About this Structure==
-	[[3rlv]] 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=3RLV OCA].	+	[[3rlv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._delta_h Methanothermobacter thermautotrophicus str. delta h]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RLV OCA].
-	[[Category: Methanothermobacter thermautotrophicus]]	+
		+	==Reference==
		+	<ref group="xtra">PMID:023030629</ref><references group="xtra"/><references/>
		+	[[Category: Methanothermobacter thermautotrophicus str. delta h]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]

OCA at 09:20, 25 April 2012

OCA — Wed, 25 Apr 2012 09:20:32 GMT

←Older revision		Revision as of 09:20, 25 April 2012
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-	~~'''Unreleased structure'''~~	+	[[Image:3rlv.jpg\|left\|200px]]

-	The ~~entry 3rlv~~ is ~~ON HOLD~~ ~~until Apr 25 2013~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3rlv", 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_3rlv\| PDB=3rlv \| SCENE= }}

-	~~Authors: Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.~~	+	===Crystal structure of the mutant Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP===

-	~~Description: Crystal~~ structure ~~of the mutant Y206F of orotidine~~ 5'-~~monophosphate~~ decarboxylase ~~from Methanobacterium thermoautotrophicum complexed with the~~ inhibitor ~~BMP~~	+
		+	==About this Structure==
		+	[[3rlv]] 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=3RLV OCA].
		+	[[Category: Methanothermobacter thermautotrophicus]]
		+	[[Category: Orotidine-5'-phosphate decarboxylase]]
		+	[[Category: Almo, S C.]]
		+	[[Category: Desai, B.]]
		+	[[Category: Fedorov, A A.]]
		+	[[Category: Fedorov, E V.]]
		+	[[Category: Gerlt, J A.]]
		+	[[Category: Lyase-lyase inhibitor complex]]
		+	[[Category: Tim barrel fold]]

OCA at 05:13, 8 March 2012

OCA — Thu, 08 Mar 2012 05:13:13 GMT

←Older revision		Revision as of 05:13, 8 March 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3rlv is ON HOLD until ~~Paper Publication~~	+	The entry 3rlv is ON HOLD until Apr 25 2013

	Authors: Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.		Authors: Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.

	Description: Crystal structure of the mutant Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP		Description: Crystal structure of the mutant Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP

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

OCA — Wed, 27 Apr 2011 06:59:14 GMT

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

←Older revision

Revision as of 06:59, 27 April 2011

OCA: New page: '''Unreleased structure''' The entry 3rlv is ON HOLD until Paper Publication Authors: Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C. Description: Crystal structure of...

OCA — Wed, 27 Apr 2011 06:59:13 GMT

New page: '''Unreleased structure''' The entry 3rlv is ON HOLD until Paper Publication Authors: Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C. Description: Crystal structure of...

New page

'''Unreleased structure'''

The entry 3rlv is ON HOLD until Paper Publication

Authors: Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.

Description: Crystal structure of the mutant Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP