3uxl - Revision history

OCA at 14:11, 14 March 2024

OCA — Thu, 14 Mar 2024 14:11:22 GMT

←Older revision		Revision as of 14:11, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3uxl' size='340' side='right'caption='[[3uxl]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='3uxl' size='340' side='right'caption='[[3uxl]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3uxl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UXL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3uxl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UXL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CFI:1~~-~~HYDROXY-2-OXO-1-PHENYLHYDRAZINE'>CFI</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.201Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1mdr\|1mdr]], [[3uxk\|3uxk]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CFI:1-HYDROXY-2-OXO-1-PHENYLHYDRAZINE'>CFI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>mdlA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~303~~ "~~Bacillus fluorescens putidus~~" ~~Flugge 1886])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Mandelate_racemase Mandelate racemase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.2.2 5.1.2.2]~~ </~~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=3uxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uxl OCA], [https://pdbe.org/3uxl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uxl RCSB], [https://www.ebi.ac.uk/pdbsum/3uxl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uxl 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=3uxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uxl OCA], [https://pdbe.org/3uxl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uxl RCSB], [https://www.ebi.ac.uk/pdbsum/3uxl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uxl ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/MANR_PSEPU MANR_PSEPU]
-	Mandelate racemase (MR, EC 5.1.2.2) from Pseudomonas putida catalyzes the Mg(2+)-dependent interconversion of the enantiomers of mandelate, stabilizing the altered substrate in the transition state by 26 kcal/mol relative to the substrate in the ground state. To understand the origins of this binding discrimination, we determined the X-ray crystal structures of wild-type MR complexed with two analogues of the putative aci-carboxylate intermediate, benzohydroxamate and Cupferron, to 2.2-A resolution. Benzohydroxamate is shown to be a reasonable mimic of the transition state and/or intermediate because its binding affinity for 21 MR variants correlates well with changes in the free energy of transition state stabilization afforded by these variants. Both benzohydroxamate and Cupferron chelate the active site divalent metal ion and are bound in a conformation with the phenyl ring coplanar with the hydroxamate and diazeniumdiolate moieties, respectively. Structural overlays of MR complexed with benzohydroxamate, Cupferron, and the ground state analogue (S)-atrolactate reveal that the para carbon of the substrate phenyl ring moves by 0.8-1.2 A between the ground state and intermediate state, consistent with the proposal that the phenyl ring moves during MR catalysis while the polar groups remain relatively fixed. Although the overall protein structure of MR with bound intermediate analogues is very similar to that of MR with bound (S)-atrolactate, the intermediate-Mg(2+) distance becomes shorter, suggesting a tighter complex with the catalytic Mg(2+). In addition, Tyr 54 moves closer to the phenyl ring of the bound intermediate analogues, contributing to an overall constriction of the active site cavity. However, site-directed mutagenesis experiments revealed that the role of Tyr 54 in MR catalysis is relatively minor, suggesting that alterations in enzyme structure that contribute to discrimination between the altered substrate in the transition state and the ground state by this proficient enzyme are extremely subtle.	+
-		+
-	~~Structure of Mandelate Racemase with Bound Intermediate Analogues Benzohydroxamate and Cupferron.,Lietzan AD, Nagar M, Pellmann EA, Bourque JR, Bearne SL, St Maurice M Biochemistry. 2012 Feb 3. PMID~~:~~22264153<ref>PMID:22264153<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3uxl" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[Mandelate racemase\|Mandelate racemase]]		*[[Mandelate racemase\|Mandelate racemase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus fluorescens putidus flugge 1886]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Mandelate racemase~~]]	+	[[Category: Pseudomonas putida]]
-	[[Category: Lietzan~~, A D]]~~	+	[[Category: Lietzan AD]]
-	~~[[Category: Maurice, M St~~]]	+	[[Category: Pellmann E]]
-	[[Category: Pellmann, E]]	+	[[Category: St Maurice M]]
-	[[Category: ~~Enolase superfamily enzyme]]~~	+
-	~~[[Category: Isomerase~~]]	+

OCA at 08:15, 20 July 2022

OCA — Wed, 20 Jul 2022 08:15:13 GMT

←Older revision		Revision as of 08:15, 20 July 2022
Line 1:		Line 1:

	==P. putida mandelate racemase co-crystallized with the intermediate analogue cupferron==		==P. putida mandelate racemase co-crystallized with the intermediate analogue cupferron==
-	<StructureSection load='3uxl' size='340' side='right' caption='[[3uxl]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='3uxl' size='340' side='right'caption='[[3uxl]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3uxl]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UXL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3UXL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3uxl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UXL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CFI:1-HYDROXY-2-OXO-1-PHENYLHYDRAZINE'>CFI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CFI:1-HYDROXY-2-OXO-1-PHENYLHYDRAZINE'>CFI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mdr\|1mdr]], [[3uxk\|3uxk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1mdr\|1mdr]], [[3uxk\|3uxk]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mdlA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mdlA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Mandelate_racemase Mandelate racemase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.2.2 5.1.2.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Mandelate_racemase Mandelate racemase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.2.2 5.1.2.2] </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=3uxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uxl OCA], [~~http~~://pdbe.org/3uxl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3uxl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3uxl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3uxl 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=3uxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uxl OCA], [https://pdbe.org/3uxl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uxl RCSB], [https://www.ebi.ac.uk/pdbsum/3uxl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uxl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus fluorescens putidus flugge 1886]]		[[Category: Bacillus fluorescens putidus flugge 1886]]
		+	[[Category: Large Structures]]
	[[Category: Mandelate racemase]]		[[Category: Mandelate racemase]]
	[[Category: Lietzan, A D]]		[[Category: Lietzan, A D]]

OCA at 11:52, 11 August 2016

OCA — Thu, 11 Aug 2016 11:52:20 GMT

←Older revision		Revision as of 11:52, 11 August 2016
Line 1:		Line 1:
		+
	==P. putida mandelate racemase co-crystallized with the intermediate analogue cupferron==		==P. putida mandelate racemase co-crystallized with the intermediate analogue cupferron==
	<StructureSection load='3uxl' size='340' side='right' caption='[[3uxl]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='3uxl' size='340' side='right' caption='[[3uxl]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3uxl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_putida Pseudomonas putida~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UXL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UXL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3uxl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UXL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UXL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CFI:1-HYDROXY-2-OXO-1-PHENYLHYDRAZINE'>CFI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CFI:1-HYDROXY-2-OXO-1-PHENYLHYDRAZINE'>CFI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mdr\|1mdr]], [[3uxk\|3uxk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mdr\|1mdr]], [[3uxk\|3uxk]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mdlA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 ~~Pseudomonas putida~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mdlA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mandelate_racemase Mandelate racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.2.2 5.1.2.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mandelate_racemase Mandelate racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.2.2 5.1.2.2] </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=3uxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uxl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uxl RCSB], [http://www.ebi.ac.uk/pdbsum/3uxl 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=3uxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uxl OCA], [http://pdbe.org/3uxl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3uxl RCSB], [http://www.ebi.ac.uk/pdbsum/3uxl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3uxl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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 3uxl" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus fluorescens putidus flugge 1886]]
	[[Category: Mandelate racemase]]		[[Category: Mandelate racemase]]
-	[[Category: Pseudomonas putida]]
	[[Category: Lietzan, A D]]		[[Category: Lietzan, A D]]
	[[Category: Maurice, M St]]		[[Category: Maurice, M St]]

OCA at 10:39, 4 January 2015

OCA — Sun, 04 Jan 2015 10:39:48 GMT

←Older revision		Revision as of 10:39, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_3uxl\| PDB=3uxl \| SCENE= }}~~	+	==P. putida mandelate racemase co-crystallized with the intermediate analogue cupferron==
-	===P. putida mandelate racemase co-crystallized with the intermediate analogue cupferron===	+	<StructureSection load='3uxl' size='340' side='right' caption='[[3uxl]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~{{ABSTRACT_PUBMED_22264153}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3uxl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UXL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UXL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CFI:1-HYDROXY-2-OXO-1-PHENYLHYDRAZINE'>CFI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mdr\|1mdr]], [[3uxk\|3uxk]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mdlA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 Pseudomonas putida])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mandelate_racemase Mandelate racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.2.2 5.1.2.2] </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=3uxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uxl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3uxl RCSB], [http://www.ebi.ac.uk/pdbsum/3uxl PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mandelate racemase (MR, EC 5.1.2.2) from Pseudomonas putida catalyzes the Mg(2+)-dependent interconversion of the enantiomers of mandelate, stabilizing the altered substrate in the transition state by 26 kcal/mol relative to the substrate in the ground state. To understand the origins of this binding discrimination, we determined the X-ray crystal structures of wild-type MR complexed with two analogues of the putative aci-carboxylate intermediate, benzohydroxamate and Cupferron, to 2.2-A resolution. Benzohydroxamate is shown to be a reasonable mimic of the transition state and/or intermediate because its binding affinity for 21 MR variants correlates well with changes in the free energy of transition state stabilization afforded by these variants. Both benzohydroxamate and Cupferron chelate the active site divalent metal ion and are bound in a conformation with the phenyl ring coplanar with the hydroxamate and diazeniumdiolate moieties, respectively. Structural overlays of MR complexed with benzohydroxamate, Cupferron, and the ground state analogue (S)-atrolactate reveal that the para carbon of the substrate phenyl ring moves by 0.8-1.2 A between the ground state and intermediate state, consistent with the proposal that the phenyl ring moves during MR catalysis while the polar groups remain relatively fixed. Although the overall protein structure of MR with bound intermediate analogues is very similar to that of MR with bound (S)-atrolactate, the intermediate-Mg(2+) distance becomes shorter, suggesting a tighter complex with the catalytic Mg(2+). In addition, Tyr 54 moves closer to the phenyl ring of the bound intermediate analogues, contributing to an overall constriction of the active site cavity. However, site-directed mutagenesis experiments revealed that the role of Tyr 54 in MR catalysis is relatively minor, suggesting that alterations in enzyme structure that contribute to discrimination between the altered substrate in the transition state and the ground state by this proficient enzyme are extremely subtle.

-	~~==About this~~ Structure==	+	Structure of Mandelate Racemase with Bound Intermediate Analogues Benzohydroxamate and Cupferron.,Lietzan AD, Nagar M, Pellmann EA, Bourque JR, Bearne SL, St Maurice M Biochemistry. 2012 Feb 3. PMID:22264153<ref>PMID:22264153</ref>
-	~~[[3uxl]] is a 4 chain structure~~ with ~~sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_putida Pseudomonas putida]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3UXL OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Mandelate racemase\|Mandelate racemase]]		*[[Mandelate racemase\|Mandelate racemase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:022264153<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Mandelate racemase]]		[[Category: Mandelate racemase]]
	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]
-	[[Category: Lietzan, A D.]]	+	[[Category: Lietzan, A D]]
-	[[Category: Maurice, M St.]]	+	[[Category: Maurice, M St]]
-	[[Category: Pellmann, E.]]	+	[[Category: Pellmann, E]]
	[[Category: Enolase superfamily enzyme]]		[[Category: Enolase superfamily enzyme]]
	[[Category: Isomerase]]		[[Category: Isomerase]]

OCA at 09:54, 11 March 2013

OCA — Mon, 11 Mar 2013 09:54:45 GMT

←Older revision		Revision as of 09:54, 11 March 2013
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-	[[Image:3uxl.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3uxl", 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_3uxl\| PDB=3uxl \| SCENE= }}		{{STRUCTURE_3uxl\| PDB=3uxl \| SCENE= }}
-
	===P. putida mandelate racemase co-crystallized with the intermediate analogue cupferron===		===P. putida mandelate racemase co-crystallized with the intermediate analogue cupferron===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_22264153}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 22264153 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_22264153}}		{{ABSTRACT_PUBMED_22264153}}

	==About this Structure==		==About this Structure==
	[[3uxl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UXL OCA].		[[3uxl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UXL OCA].
		+
		+	==See Also==
		+	*[[Mandelate racemase\|Mandelate racemase]]

	==Reference==		==Reference==

OCA at 08:02, 29 February 2012

OCA — Wed, 29 Feb 2012 08:02:19 GMT

←Older revision		Revision as of 08:02, 29 February 2012
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-	[[Image:3uxl.~~jpg~~\|left\|200px]]	+	[[Image:3uxl.png\|left\|200px]]

	<!--		<!--

OCA at 06:32, 8 February 2012

OCA — Wed, 08 Feb 2012 06:32:36 GMT

←Older revision		Revision as of 06:32, 8 February 2012
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-	~~'''Unreleased structure'''~~	+	[[Image:3uxl.jpg\|left\|200px]]

-	The ~~entry 3uxl~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3uxl", 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_3uxl\| PDB=3uxl \| SCENE= }}

-	~~Authors: Lietzan, A.D., Pellmann, E., St. Maurice, M~~.	+	===P. putida mandelate racemase co-crystallized with the intermediate analogue cupferron===

-	~~Description~~: P. ~~putida mandelate racemase co~~-~~crystallized~~ with ~~the intermediate analogue cupferron~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22264153}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22264153 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22264153}}
		+
		+	==About this Structure==
		+	[[3uxl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UXL OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022264153</ref><references group="xtra"/>
		+	[[Category: Mandelate racemase]]
		+	[[Category: Pseudomonas putida]]
		+	[[Category: Lietzan, A D.]]
		+	[[Category: Maurice, M St.]]
		+	[[Category: Pellmann, E.]]
		+	[[Category: Enolase superfamily enzyme]]
		+	[[Category: Isomerase]]

OCA at 06:44, 28 December 2011

OCA — Wed, 28 Dec 2011 06:44:42 GMT

←Older revision		Revision as of 06:44, 28 December 2011
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Lietzan, A.D., Pellmann, E., St. Maurice, M.		Authors: Lietzan, A.D., Pellmann, E., St. Maurice, M.

	Description: P. putida mandelate racemase co-crystallized with the intermediate analogue cupferron		Description: P. putida mandelate racemase co-crystallized with the intermediate analogue cupferron

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

OCA — Wed, 14 Dec 2011 11:14:25 GMT

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

←Older revision

Revision as of 11:14, 14 December 2011

OCA: New page: '''Unreleased structure''' The entry 3uxl is ON HOLD Authors: Lietzan, A.D., Pellmann, E., St. Maurice, M. Description: P. putida mandelate racemase co-crystallized with the intermedia...

OCA — Wed, 14 Dec 2011 11:14:24 GMT

New page: '''Unreleased structure''' The entry 3uxl is ON HOLD Authors: Lietzan, A.D., Pellmann, E., St. Maurice, M. Description: P. putida mandelate racemase co-crystallized with the intermedia...

New page

'''Unreleased structure'''

The entry 3uxl is ON HOLD

Authors: Lietzan, A.D., Pellmann, E., St. Maurice, M.

Description: P. putida mandelate racemase co-crystallized with the intermediate analogue cupferron