5lg5 - Revision history

OCA at 12:17, 10 January 2024

OCA — Wed, 10 Jan 2024 12:17:10 GMT

←Older revision		Revision as of 12:17, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5lg5]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LG5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LG5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5lg5]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LG5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LG5 FirstGlance]. <br>
-	</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=5lg5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lg5 OCA], [https://pdbe.org/5lg5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lg5 RCSB], [https://www.ebi.ac.uk/pdbsum/5lg5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lg5 ProSAT]</span></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]] 2.1Å</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=5lg5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lg5 OCA], [https://pdbe.org/5lg5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lg5 RCSB], [https://www.ebi.ac.uk/pdbsum/5lg5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lg5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/E3SAZ9_PSEFL E3SAZ9_PSEFL]]	+	[https://www.uniprot.org/uniprot/E3SAZ9_PSEFL E3SAZ9_PSEFL]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 06:17, 8 September 2022

OCA — Thu, 08 Sep 2022 06:17:54 GMT

←Older revision		Revision as of 06:17, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='5lg5' size='340' side='right'caption='[[5lg5]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5lg5' size='340' side='right'caption='[[5lg5]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lg5]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus~~ fluorescens ~~liquefaciens" flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LG5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LG5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lg5]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LG5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LG5 FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Allantoin_racemase Allantoin racemase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.3 5.1.99.3] </span></td></tr>	+	</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=5lg5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lg5 OCA], [https://pdbe.org/5lg5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lg5 RCSB], [https://www.ebi.ac.uk/pdbsum/5lg5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lg5 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=5lg5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lg5 OCA], [https://pdbe.org/5lg5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lg5 RCSB], [https://www.ebi.ac.uk/pdbsum/5lg5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lg5 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/E3SAZ9_PSEFL E3SAZ9_PSEFL]]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
-	[[Category: Allantoin racemase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cendron, l]]	+	[[Category: Pseudomonas fluorescens]]
-	[[Category: Liuzzi, A]]	+	[[Category: Cendron l]]
-	[[Category: Maccacaro, E]]	+	[[Category: Liuzzi A]]
-	[[Category: Percudani, R]]	+	[[Category: Maccacaro E]]
-	[[Category: Puggioni, V]]	+	[[Category: Percudani R]]
-	[[Category: Ragazzina, I]]	+	[[Category: Puggioni V]]
-	[[Category: Secchi, A]]	+	[[Category: Ragazzina I]]
-	[[Category: Zanotti, G]]	+	[[Category: Secchi A]]
-	~~[[Category: Evolution of catalytic mechanism]]~~	+	[[Category: Zanotti G]]
-	~~[[Category: Gene identification]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Proton transfer]]~~	+
-	~~[[Category: Racemization intermediate]]~~	+
-	~~[[Category: Rate degradation~~]]	+

OCA at 05:21, 13 July 2022

OCA — Wed, 13 Jul 2022 05:21:13 GMT

←Older revision		Revision as of 05:21, 13 July 2022
Line 3:		Line 3:
	<StructureSection load='5lg5' size='340' side='right'caption='[[5lg5]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5lg5' size='340' side='right'caption='[[5lg5]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lg5]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LG5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5LG5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lg5]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LG5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LG5 FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Allantoin_racemase Allantoin racemase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.3 5.1.99.3] </span></td></tr>	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Allantoin_racemase Allantoin racemase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.3 5.1.99.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5lg5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lg5 OCA], [~~http~~://pdbe.org/5lg5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5lg5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5lg5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5lg5 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=5lg5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lg5 OCA], [https://pdbe.org/5lg5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lg5 RCSB], [https://www.ebi.ac.uk/pdbsum/5lg5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lg5 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 30:
	[[Category: Ragazzina, I]]		[[Category: Ragazzina, I]]
	[[Category: Secchi, A]]		[[Category: Secchi, A]]
-	[[Category: Zanotti, g]]	+	[[Category: Zanotti, G]]
	[[Category: Evolution of catalytic mechanism]]		[[Category: Evolution of catalytic mechanism]]
	[[Category: Gene identification]]		[[Category: Gene identification]]

OCA at 10:35, 12 August 2020

OCA — Wed, 12 Aug 2020 10:35:49 GMT

←Older revision		Revision as of 10:35, 12 August 2020
Line 1:		Line 1:

	==Crystal structure of allantoin racemase from Pseudomonas fluorescens AllR==		==Crystal structure of allantoin racemase from Pseudomonas fluorescens AllR==
-	<StructureSection load='5lg5' size='340' side='right' caption='[[5lg5]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5lg5' size='340' side='right'caption='[[5lg5]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lg5]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LG5 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LG5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lg5]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LG5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5LG5 FirstGlance]. <br>
	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Allantoin_racemase Allantoin racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.3 5.1.99.3] </span></td></tr>		</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Allantoin_racemase Allantoin racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.3 5.1.99.3] </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=5lg5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lg5 OCA], [http://pdbe.org/5lg5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lg5 RCSB], [http://www.ebi.ac.uk/pdbsum/5lg5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lg5 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5lg5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lg5 OCA], [http://pdbe.org/5lg5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lg5 RCSB], [http://www.ebi.ac.uk/pdbsum/5lg5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lg5 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
	[[Category: Allantoin racemase]]		[[Category: Allantoin racemase]]
		+	[[Category: Large Structures]]
	[[Category: Cendron, l]]		[[Category: Cendron, l]]
	[[Category: Liuzzi, A]]		[[Category: Liuzzi, A]]

OCA at 12:52, 10 May 2017

OCA — Wed, 10 May 2017 12:52:16 GMT

←Older revision		Revision as of 12:52, 10 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5lg5 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of allantoin racemase from Pseudomonas fluorescens AllR==
		+	<StructureSection load='5lg5' size='340' side='right' caption='[[5lg5]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5lg5]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LG5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LG5 FirstGlance]. <br>
		+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Allantoin_racemase Allantoin racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.3 5.1.99.3] </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=5lg5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lg5 OCA], [http://pdbe.org/5lg5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lg5 RCSB], [http://www.ebi.ac.uk/pdbsum/5lg5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lg5 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The S enantiomer of allantoin is an intermediate of purine degradation in several organisms and the final product of uricolysis in nonhominoid mammals. Bioinformatics indicated that proteins of the Asp/Glu racemase superfamily could be responsible for the allantoin racemase (AllR) activity originally described in Pseudomonas species. In these proteins, a cysteine of the catalytic dyad is substituted with glycine, yet the recombinant enzyme displayed racemization activity with a similar efficiency (kcat/KM approximately 5 x 104 M-1 s-1) for the R and S enantiomers of allantoin. The protein crystal structure identified a glutamate residue located three residues downstream (E78) that can functionally replace the missing cysteine; the catalytic role of E78 was confirmed by site-directed mutagenesis. Allantoin can undergo racemization through formation of a bicyclic intermediate (faster) or proton exchange at the chiral center (slower). By monitoring the two alternative mechanisms by 13C and 1H nuclear magnetic resonance, we found that the velocity of the faster reaction is unaffected by the enzyme, whereas the velocity of the slower reaction is increased by 7 orders of magnitude. Protein phylogenies trace the origin of the racemization mechanism in enzymes acting on glutamate, a substrate for which proton exchange is the only viable reaction mechanism. This mechanism was inherited by allantoin racemase through divergent evolution and conserved in spite of the substitution of catalytic residues.

-	~~Authors: cendron, l~~., ~~zanotti, g., percudani, R., ragazzina~~, I~~., puggioni~~, V~~., maccacaro~~, E., ~~liuzzi~~, A., ~~secchi~~, A.	+	The Structure and Function of a Microbial Allantoin Racemase Reveal the Origin and Conservation of a Catalytic Mechanism.,Cendron L, Ramazzina I, Puggioni V, Maccacaro E, Liuzzi A, Secchi A, Zanotti G, Percudani R Biochemistry. 2016 Nov 22;55(46):6421-6432. Epub 2016 Nov 7. PMID:27797489<ref>PMID:27797489</ref>

-	~~Description: Crystal structure~~ of ~~allantoin~~ racemase ~~from Pseudomonas fluorescens AllR~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5lg5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Allantoin racemase]]
		+	[[Category: Cendron, l]]
	[[Category: Liuzzi, A]]		[[Category: Liuzzi, A]]
-	[[Category: Puggioni, V]]
	[[Category: Maccacaro, E]]		[[Category: Maccacaro, E]]
-	[[Category: Zanotti, G]]
-	[[Category: Ragazzina, I]]
-	[[Category: Cendron, L]]
	[[Category: Percudani, R]]		[[Category: Percudani, R]]
		+	[[Category: Puggioni, V]]
		+	[[Category: Ragazzina, I]]
	[[Category: Secchi, A]]		[[Category: Secchi, A]]
		+	[[Category: Zanotti, g]]
		+	[[Category: Evolution of catalytic mechanism]]
		+	[[Category: Gene identification]]
		+	[[Category: Isomerase]]
		+	[[Category: Proton transfer]]
		+	[[Category: Racemization intermediate]]
		+	[[Category: Rate degradation]]

OCA at 10:39, 9 March 2017

OCA — Thu, 09 Mar 2017 10:39:23 GMT

←Older revision		Revision as of 10:39, 9 March 2017
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Liuzzi, A]]		[[Category: Liuzzi, A]]
-	[[Category: Maccacaro, E]]
-	[[Category: Cendron, L]]
-	[[Category: Secchi, A]]
	[[Category: Puggioni, V]]		[[Category: Puggioni, V]]
		+	[[Category: Maccacaro, E]]
	[[Category: Zanotti, G]]		[[Category: Zanotti, G]]
	[[Category: Ragazzina, I]]		[[Category: Ragazzina, I]]
		+	[[Category: Cendron, L]]
	[[Category: Percudani, R]]		[[Category: Percudani, R]]
		+	[[Category: Secchi, A]]

OCA: Protected "5lg5" [edit=sysop:move=sysop]

OCA — Thu, 14 Jul 2016 10:05:52 GMT

Protected "5lg5" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:05, 14 July 2016

OCA: New page: '''Unreleased structure''' The entry 5lg5 is ON HOLD until Paper Publication Authors: cendron, l., zanotti, g., percudani, R., ragazzina, I., puggioni, V., maccacaro, E., liuzzi, A., se...

OCA — Thu, 14 Jul 2016 10:05:50 GMT

New page: '''Unreleased structure''' The entry 5lg5 is ON HOLD until Paper Publication Authors: cendron, l., zanotti, g., percudani, R., ragazzina, I., puggioni, V., maccacaro, E., liuzzi, A., se...

New page

'''Unreleased structure'''

The entry 5lg5 is ON HOLD until Paper Publication

Authors: cendron, l., zanotti, g., percudani, R., ragazzina, I., puggioni, V., maccacaro, E., liuzzi, A., secchi, A.

Description: Crystal structure of allantoin racemase from Pseudomonas fluorescens AllR
[[Category: Unreleased Structures]]
[[Category: Liuzzi, A]]
[[Category: Maccacaro, E]]
[[Category: Cendron, L]]
[[Category: Secchi, A]]
[[Category: Puggioni, V]]
[[Category: Zanotti, G]]
[[Category: Ragazzina, I]]
[[Category: Percudani, R]]