4dyj - Revision history

OCA at 06:47, 3 April 2024

OCA — Wed, 03 Apr 2024 06:47:07 GMT

←Older revision		Revision as of 06:47, 3 April 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dyj]] is a 2 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=4DYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DYJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dyj]] is a 2 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=4DYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DYJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.45Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=4dyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dyj OCA], [https://pdbe.org/4dyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dyj RCSB], [https://www.ebi.ac.uk/pdbsum/4dyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dyj 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=4dyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dyj OCA], [https://pdbe.org/4dyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dyj RCSB], [https://www.ebi.ac.uk/pdbsum/4dyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dyj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/BSR_PSEPU BSR_PSEPU]] Amino-acid racemase that catalyzes the interconversion of L-lysine and D-lysine, and L-arginine and D-arginine (PubMed:23118975). To a lesser extent, is also able to interconvert alanine and isoleucine enantiomers (PubMed:23118975, PubMed:22806802).<ref>PMID:22806802</ref> <ref>PMID:23118975</ref>	+	[https://www.uniprot.org/uniprot/BSR_PSEPU BSR_PSEPU] Amino-acid racemase that catalyzes the interconversion of L-lysine and D-lysine, and L-arginine and D-arginine (PubMed:23118975). To a lesser extent, is also able to interconvert alanine and isoleucine enantiomers (PubMed:23118975, PubMed:22806802).<ref>PMID:22806802</ref> <ref>PMID:23118975</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Lysine racemase, a pyridoxal 5'-phosphate (PLP)-dependent amino acid racemase that catalyzes the interconversion of lysine enantiomers, is valuable to serve as a novel non-antibiotic selectable marker in the generation of transgenic plants. Here, we have determined the first crystal structure of a lysine racemase (Lyr) from Proteus mirabilis BCRC10725, which shows the highest activity toward lysine and weaker activity towards arginine. In addition, we establish the first broad-specificity amino acid racemase (Bar) structure from Pseudomonas putida DSM84, which presents not only the highest activity toward lysine but also remarkably broad substrate specificity. A complex structure of Bar-lysine is also established here. These structures demonstrate the similar fold of alanine racemase, which is a head-to-tail homodimer with each protomer containing an N-terminal (alpha/beta)(8) barrel and a C-terminal beta-stranded domain. The active-site residues are located at the protomer interface that is a funnel-like cavity with two catalytic bases, one from each protomer, and the PLP binding site is at the bottom of this cavity. Structural comparisons, site-directed mutagenesis, kinetic, and modeling studies identify a conserved arginine and an adjacent conserved asparagine that fix the orientation of the PLP O3 atom in both structures and assist in the enzyme activity. Furthermore, side chains of two residues in alpha-helix 10 have been discovered to point toward the cavity and define the substrate specificity. Our results provide a structural foundation for the design of racemases with pre-determined substrate specificity and for the development of the non-antibiotic selection system in transgenic plants.	+
-		+
-	Crystal structures of lysine-preferred racemases, the non-antibiotic selectable markers for transgenic plants.,Wu HM, Kuan YC, Chu CH, Hsu WH, Wang WC PLoS One. 2012;7(10):e48301. doi: 10.1371/journal.pone.0048301. Epub 2012 Oct 31. PMID:23118975<ref>PMID:23118975</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4dyj" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:43, 21 September 2022

OCA — Wed, 21 Sep 2022 08:43:58 GMT

←Older revision		Revision as of 08:43, 21 September 2022
Line 3:		Line 3:
	<StructureSection load='4dyj' size='340' side='right'caption='[[4dyj]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='4dyj' size='340' side='right'caption='[[4dyj]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4dyj]] is a 2 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=4DYJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4DYJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4dyj]] is a 2 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=4DYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DYJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene><~~/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=4dyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dyj OCA], [https://pdbe.org/4dyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dyj RCSB], [https://www.ebi.ac.uk/pdbsum/4dyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dyj ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Amino-acid_racemase Amino-acid racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.10 5.1.1.10]~~ </~~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=4dyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dyj OCA], [~~http~~://pdbe.org/4dyj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4dyj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4dyj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4dyj ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/BSR_PSEPU BSR_PSEPU]] Amino-acid racemase that catalyzes the interconversion of L-lysine and D-lysine, and L-arginine and D-arginine (PubMed:23118975). To a lesser extent, is also able to interconvert alanine and isoleucine enantiomers (PubMed:23118975, PubMed:22806802).<ref>PMID:22806802</ref> <ref>PMID:23118975</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus fluorescens putidus flugge 1886]]
-	[[Category: Amino-acid racemase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Wang, W C~~]]	+	[[Category: Pseudomonas putida]]
-	[[Category: ~~Wu, H M~~]]	+	[[Category: Wang WC]]
-	[[Category: ~~Isomerase]]~~	+	[[Category: Wu HM]]
-	~~[[Category: Plp binding]]~~	+
-	~~[[Category: Racemization~~]]	+

OCA at 08:02, 27 March 2019

OCA — Wed, 27 Mar 2019 08:02:24 GMT

←Older revision		Revision as of 08:02, 27 March 2019
Line 1:		Line 1:

	==Crystal structure of a broad specificity amino acid racemase (Bar) within internal aldimine linkage==		==Crystal structure of a broad specificity amino acid racemase (Bar) within internal aldimine linkage==
-	<StructureSection load='4dyj' size='340' side='right' caption='[[4dyj]], [[Resolution\|resolution]] 2.45Å' scene=''>	+	<StructureSection load='4dyj' size='340' side='right'caption='[[4dyj]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dyj]] is a 2 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=4DYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DYJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dyj]] is a 2 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=4DYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DYJ FirstGlance]. <br>
Line 24:		Line 24:
	[[Category: Bacillus fluorescens putidus flugge 1886]]		[[Category: Bacillus fluorescens putidus flugge 1886]]
	[[Category: Amino-acid racemase]]		[[Category: Amino-acid racemase]]
		+	[[Category: Large Structures]]
	[[Category: Wang, W C]]		[[Category: Wang, W C]]
	[[Category: Wu, H M]]		[[Category: Wu, H M]]

OCA at 02:43, 11 December 2016

OCA — Sun, 11 Dec 2016 02:43:26 GMT

←Older revision		Revision as of 02:43, 11 December 2016
Line 1:		Line 1:
		+
	==Crystal structure of a broad specificity amino acid racemase (Bar) within internal aldimine linkage==		==Crystal structure of a broad specificity amino acid racemase (Bar) within internal aldimine linkage==
	<StructureSection load='4dyj' size='340' side='right' caption='[[4dyj]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='4dyj' size='340' side='right' caption='[[4dyj]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4dyj]] is a 2 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=4DYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DYJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4dyj]] is a 2 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=4DYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DYJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-~~LYSINE(~~3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-~~YLMETHANE)~~'>LLP</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Amino-acid_racemase Amino-acid racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.10 5.1.1.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Amino-acid_racemase Amino-acid racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.10 5.1.1.10] </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=4dyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dyj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dyj RCSB], [http://www.ebi.ac.uk/pdbsum/4dyj 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=4dyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dyj OCA], [http://pdbe.org/4dyj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dyj RCSB], [http://www.ebi.ac.uk/pdbsum/4dyj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dyj ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4dyj" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus fluorescens putidus flugge 1886]]
	[[Category: Amino-acid racemase]]		[[Category: Amino-acid racemase]]
-	[[Category: Pseudomonas putida]]
	[[Category: Wang, W C]]		[[Category: Wang, W C]]
	[[Category: Wu, H M]]		[[Category: Wu, H M]]

OCA at 15:48, 9 December 2014

OCA — Tue, 09 Dec 2014 15:48:04 GMT

←Older revision		Revision as of 15:48, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4dyj.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of a broad specificity amino acid racemase (Bar) within internal aldimine linkage==
		+	<StructureSection load='4dyj' size='340' side='right' caption='[[4dyj]], [[Resolution\|resolution]] 2.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4dyj]] is a 2 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=4DYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DYJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Amino-acid_racemase Amino-acid racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.10 5.1.1.10] </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=4dyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dyj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dyj RCSB], [http://www.ebi.ac.uk/pdbsum/4dyj PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lysine racemase, a pyridoxal 5'-phosphate (PLP)-dependent amino acid racemase that catalyzes the interconversion of lysine enantiomers, is valuable to serve as a novel non-antibiotic selectable marker in the generation of transgenic plants. Here, we have determined the first crystal structure of a lysine racemase (Lyr) from Proteus mirabilis BCRC10725, which shows the highest activity toward lysine and weaker activity towards arginine. In addition, we establish the first broad-specificity amino acid racemase (Bar) structure from Pseudomonas putida DSM84, which presents not only the highest activity toward lysine but also remarkably broad substrate specificity. A complex structure of Bar-lysine is also established here. These structures demonstrate the similar fold of alanine racemase, which is a head-to-tail homodimer with each protomer containing an N-terminal (alpha/beta)(8) barrel and a C-terminal beta-stranded domain. The active-site residues are located at the protomer interface that is a funnel-like cavity with two catalytic bases, one from each protomer, and the PLP binding site is at the bottom of this cavity. Structural comparisons, site-directed mutagenesis, kinetic, and modeling studies identify a conserved arginine and an adjacent conserved asparagine that fix the orientation of the PLP O3 atom in both structures and assist in the enzyme activity. Furthermore, side chains of two residues in alpha-helix 10 have been discovered to point toward the cavity and define the substrate specificity. Our results provide a structural foundation for the design of racemases with pre-determined substrate specificity and for the development of the non-antibiotic selection system in transgenic plants.

-	~~{{STRUCTURE_4dyj\| PDB=4dyj \| SCENE= }}~~	+	Crystal structures of lysine-preferred racemases, the non-antibiotic selectable markers for transgenic plants.,Wu HM, Kuan YC, Chu CH, Hsu WH, Wang WC PLoS One. 2012;7(10):e48301. doi: 10.1371/journal.pone.0048301. Epub 2012 Oct 31. PMID:23118975<ref>PMID:23118975</ref>

-	~~===Crystal structure~~ of ~~a broad specificity amino acid racemase (Bar) within internal aldimine linkage===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_23118975}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[4dyj]] is a 2 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=4DYJ OCA].~~	+	</StructureSection>
	[[Category: Amino-acid racemase]]		[[Category: Amino-acid racemase]]
	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]
-	[[Category: Wang, W C.]]	+	[[Category: Wang, W C]]
-	[[Category: Wu, H M.]]	+	[[Category: Wu, H M]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Plp binding]]		[[Category: Plp binding]]
	[[Category: Racemization]]		[[Category: Racemization]]

OCA at 14:15, 6 March 2013

OCA — Wed, 06 Mar 2013 14:15:11 GMT

←Older revision		Revision as of 14:15, 6 March 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4dyj.jpg\|left\|200px]]

-	~~The entry~~ 4dyj ~~is ON HOLD~~ ~~until Mar 01 2014~~	+	{{STRUCTURE_4dyj\| PDB=4dyj \| SCENE= }}

-	~~Authors: Wang, W.C., Wu, H.M.~~	+	===Crystal structure of a broad specificity amino acid racemase (Bar) within internal aldimine linkage===

-	~~Description: Crystal structure of~~ a ~~broad specificity amino~~ acid racemase ~~(Bar) within internal aldimine linkage~~	+	{{ABSTRACT_PUBMED_23118975}}
		+
		+	==About this Structure==
		+	[[4dyj]] is a 2 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=4DYJ OCA].
		+	[[Category: Amino-acid racemase]]
		+	[[Category: Pseudomonas putida]]
		+	[[Category: Wang, W C.]]
		+	[[Category: Wu, H M.]]
		+	[[Category: Isomerase]]
		+	[[Category: Plp binding]]
		+	[[Category: Racemization]]

OCA at 07:13, 21 March 2012

OCA — Wed, 21 Mar 2012 07:13:53 GMT

←Older revision		Revision as of 07:13, 21 March 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4dyj is ON HOLD	+	The entry 4dyj is ON HOLD until Mar 01 2014

	Authors: Wang, W.C., Wu, H.M.		Authors: Wang, W.C., Wu, H.M.

	Description: Crystal structure of a broad specificity amino acid racemase (Bar) within internal aldimine linkage		Description: Crystal structure of a broad specificity amino acid racemase (Bar) within internal aldimine linkage

OCA: Protected "4dyj" [edit=sysop:move=sysop]

OCA — Thu, 08 Mar 2012 05:29:51 GMT

Protected "4dyj" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:29, 8 March 2012

OCA: New page: '''Unreleased structure''' The entry 4dyj is ON HOLD Authors: Wang, W.C., Wu, H.M. Description: Crystal structure of a broad specificity amino acid racemase (Bar) within internal aldim...

OCA — Thu, 08 Mar 2012 05:29:50 GMT

New page: '''Unreleased structure''' The entry 4dyj is ON HOLD Authors: Wang, W.C., Wu, H.M. Description: Crystal structure of a broad specificity amino acid racemase (Bar) within internal aldim...

New page

'''Unreleased structure'''

The entry 4dyj is ON HOLD

Authors: Wang, W.C., Wu, H.M.

Description: Crystal structure of a broad specificity amino acid racemase (Bar) within internal aldimine linkage