6a2f - Revision history

OCA at 09:15, 22 November 2023

OCA — Wed, 22 Nov 2023 09:15:08 GMT

←Older revision		Revision as of 09:15, 22 November 2023
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	<StructureSection load='6a2f' size='340' side='right'caption='[[6a2f]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='6a2f' size='340' side='right'caption='[[6a2f]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6a2f]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pseae Pseae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A2F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6A2F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6a2f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A2F FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ACT:ACETATE+ION'~~>~~ACT</scene>, <scene name='pdbligand=DLY:D~~-~~LYSINE'>DLY</scene>~~, ~~<scene name='pdbligand=MLI:MALONATE+ION'>MLI</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]] 2.5Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DLY:D-LYSINE'>DLY</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=MLI:MALONATE+ION'>MLI</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alr~~, ~~PA4930 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])~~<~~/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=6a2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a2f OCA], [https://pdbe.org/6a2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a2f RCSB], [https://www.ebi.ac.uk/pdbsum/6a2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a2f 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/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1]~~ </~~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=6a2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a2f OCA], [~~http~~://pdbe.org/6a2f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6a2f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6a2f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6a2f ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ALR1_PSEAE ALR1_PSEAE]] Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis.<ref>PMID:10977898</ref>	+	[https://www.uniprot.org/uniprot/ALR1_PSEAE ALR1_PSEAE] Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis.<ref>PMID:10977898</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Alanine racemase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pseae~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: Dong, H]]	+	[[Category: Dong H]]
-	[[Category: Li, S]]	+	[[Category: Li S]]
-	~~[[Category: Alr]]~~	+
-	~~[[Category: D-alanine]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: L-alanine]]~~	+
-	~~[[Category: Pseudomonas aeruginosa~~]]	+

OCA at 16:04, 29 January 2020

OCA — Wed, 29 Jan 2020 16:04:26 GMT

←Older revision		Revision as of 16:04, 29 January 2020
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	==Crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa==		==Crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa==
-	<StructureSection load='6a2f' size='340' side='right' caption='[[6a2f]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='6a2f' size='340' side='right'caption='[[6a2f]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6a2f]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A2F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6a2f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A2F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</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='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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alr, PA4930 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </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=6a2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a2f OCA], [http://pdbe.org/6a2f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a2f RCSB], [http://www.ebi.ac.uk/pdbsum/6a2f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a2f ProSAT]</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=6a2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a2f OCA], [http://pdbe.org/6a2f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a2f RCSB], [http://www.ebi.ac.uk/pdbsum/6a2f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a2f ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ALR1_PSEAE ALR1_PSEAE]] Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis.<ref>PMID:10977898</ref>		[[http://www.uniprot.org/uniprot/ALR1_PSEAE ALR1_PSEAE]] Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis.<ref>PMID:10977898</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Alanine racemase is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that reversibly catalyzes the conversion of l-alanine to d-alanine. d-alanine is an essential constituent in many prokaryotic cell structures. Inhibition of alanine racemase is lethal to prokaryotes, creating an attractive target for designing antibacterial drugs. Here we report the crystal structure of biosynthetic alanine racemase (Alr) from a pathogenic bacteria Pseudomonas aeruginosa PAO1. Structural studies showed that P. aeruginosa Alr (PaAlr) adopts a conserved homodimer structure. A guest substrate d-lysine was observed in the active site and refined to dual-conformation. Two buffer ions, malonate and acetate, were bound in the proximity to d-lysine. Biochemical characterization revealed the optimal reaction conditions for PaAlr.
		+
		+	Enzymatic characterization and crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa PAO1.,Dong H, Han Q, Guo Y, Ju J, Wang S, Yuan C, Long W, He X, Xu S, Li S Biochem Biophys Res Commun. 2018 Sep 18;503(4):2319-2325. doi:, 10.1016/j.bbrc.2018.06.155. Epub 2018 Jun 30. PMID:29964014<ref>PMID:29964014</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6a2f" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Alanine racemase 3D structures\|Alanine racemase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 16:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Alanine racemase]]		[[Category: Alanine racemase]]
		+	[[Category: Large Structures]]
		+	[[Category: Pseae]]
	[[Category: Dong, H]]		[[Category: Dong, H]]
	[[Category: Li, S]]		[[Category: Li, S]]

OCA at 21:45, 9 August 2018

OCA — Thu, 09 Aug 2018 21:45:05 GMT

←Older revision		Revision as of 21:45, 9 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6a2f is ~~ON HOLD~~ ~~until Aug 06 2019~~	+	==Crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa==
-		+	<StructureSection load='6a2f' size='340' side='right' caption='[[6a2f]], [[Resolution\|resolution]] 2.50Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6a2f]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A2F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A2F FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </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=6a2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a2f OCA], [http://pdbe.org/6a2f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a2f RCSB], [http://www.ebi.ac.uk/pdbsum/6a2f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a2f ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ALR1_PSEAE ALR1_PSEAE]] Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis.<ref>PMID:10977898</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Alanine racemase]]
		+	[[Category: Dong, H]]
		+	[[Category: Li, S]]
		+	[[Category: Alr]]
		+	[[Category: D-alanine]]
		+	[[Category: Isomerase]]
		+	[[Category: L-alanine]]
		+	[[Category: Pseudomonas aeruginosa]]

OCA at 03:51, 27 June 2018

OCA — Wed, 27 Jun 2018 03:51:06 GMT

←Older revision		Revision as of 03:51, 27 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6a2f is ON HOLD	+	The entry 6a2f is ON HOLD until Aug 06 2019

	Authors:		Authors:

OCA: Protected "6a2f" [edit=sysop:move=sysop]

OCA — Wed, 20 Jun 2018 03:54:49 GMT

Protected "6a2f" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:54, 20 June 2018

OCA: New page: '''Unreleased structure''' The entry 6a2f is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 20 Jun 2018 03:54:47 GMT

New page: '''Unreleased structure''' The entry 6a2f is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6a2f is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]