6q70 - Revision history

OCA at 11:54, 24 January 2024

OCA — Wed, 24 Jan 2024 11:54:26 GMT

←Older revision		Revision as of 11:54, 24 January 2024
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	<StructureSection load='6q70' size='340' side='right'caption='[[6q70]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='6q70' size='340' side='right'caption='[[6q70]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6q70]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q70 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6Q70 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6q70]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q70 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Q70 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 2.05Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5irp\|5irp~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>alr2, yncD, BSU17640 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1423~~ "~~Vibrio subtilis~~" ~~Ehrenberg 1835])~~<~~/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=6q70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q70 OCA], [https://pdbe.org/6q70 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6q70 RCSB], [https://www.ebi.ac.uk/pdbsum/6q70 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6q70 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=6q70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q70 OCA], [~~http~~://pdbe.org/6q70 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6q70 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6q70 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6q70 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ALR2_BACSU ALR2_BACSU]] Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids.	+	[https://www.uniprot.org/uniprot/ALR2_BACSU ALR2_BACSU] Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6q70" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6q70" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Alanine racemase 3D structures\|Alanine racemase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835]]~~	+	[[Category: Bacillus subtilis]]
-	~~[[Category: Alanine racemase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bernardo-Garcia, N]]	+	[[Category: Bernardo-Garcia N]]
-	[[Category: Gago, F]]	+	[[Category: Gago F]]
-	[[Category: Hermoso~~, J A]]~~	+	[[Category: Hermoso JA]]
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Molecular modeling]]~~	+
-	~~[[Category: Racemase~~]]	+

OCA at 09:23, 1 May 2019

OCA — Wed, 01 May 2019 09:23:58 GMT

←Older revision		Revision as of 09:23, 1 May 2019
Line 3:		Line 3:
	<StructureSection load='6q70' size='340' side='right'caption='[[6q70]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='6q70' size='340' side='right'caption='[[6q70]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6q70]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q70 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q70 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6q70]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q70 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q70 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5irp\|5irp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5irp\|5irp]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alr2, yncD, BSU17640 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=6q70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q70 OCA], [http://pdbe.org/6q70 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q70 RCSB], [http://www.ebi.ac.uk/pdbsum/6q70 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q70 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=6q70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q70 OCA], [http://pdbe.org/6q70 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q70 RCSB], [http://www.ebi.ac.uk/pdbsum/6q70 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q70 ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Vibrio subtilis ehrenberg 1835]]
	[[Category: Alanine racemase]]		[[Category: Alanine racemase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 07:08, 24 April 2019

OCA — Wed, 24 Apr 2019 07:08:53 GMT

←Older revision		Revision as of 07:08, 24 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6q70 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the alanine racemase Bsu17640 from Bacillus subtilis in the presence of HEPES==
		+	<StructureSection load='6q70' size='340' side='right'caption='[[6q70]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6q70]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q70 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q70 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5irp\|5irp]]</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=6q70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q70 OCA], [http://pdbe.org/6q70 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q70 RCSB], [http://www.ebi.ac.uk/pdbsum/6q70 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q70 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ALR2_BACSU ALR2_BACSU]] Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pyridoxal 5'-phosphate (PLP) is a versatile cofactor involved in a large variety of enzymatic processes. Most of PLP-catalysed reactions, such as those of alanine racemases (AlaRs), present a common resting state in which the PLP is covalently bound to an active-site lysine to form an internal aldimine. The crystal structure of BsAlaR grown in the presence of Tris lacks this covalent linkage and the PLP cofactor appears deformylated. However, loss of activity in a Tris buffer only occurred after the solution was frozen prior to carrying out the enzymatic assay. This evidence strongly suggests that Tris can access the active site at subzero temperatures and behave as an alternate racemase substrate leading to mechanism-based enzyme inactivation, a hypothesis that is supported by additional X-ray structures and theoretical results from QM/MM calculations. Taken together, our findings highlight a possibly underappreciated role for a common buffer component widely used in biochemical and biophysical experiments.

-	~~Authors:~~ Bernardo-Garcia, N., ~~Gago~~, F., Hermoso, J.A.	+	Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase.,Bernardo-Garcia N, Sanchez-Murcia PA, Espaillat A, Martinez-Caballero S, Cava F, Hermoso JA, Gago F Org Biomol Chem. 2019 Apr 12. doi: 10.1039/c9ob00223e. PMID:30977502<ref>PMID:30977502</ref>

-	~~Description: Crystal structure~~ of the ~~alanine racemase Bsu17640 from Bacillus subtilis in the presence~~ of ~~HEPES~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6q70" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Alanine racemase]]
		+	[[Category: Large Structures]]
	[[Category: Bernardo-Garcia, N]]		[[Category: Bernardo-Garcia, N]]
-	[[Category: Hermoso, J.A]]
	[[Category: Gago, F]]		[[Category: Gago, F]]
		+	[[Category: Hermoso, J A]]
		+	[[Category: Isomerase]]
		+	[[Category: Molecular modeling]]
		+	[[Category: Racemase]]

OCA: Protected "6q70" [edit=sysop:move=sysop]

OCA — Wed, 19 Dec 2018 06:48:28 GMT

Protected "6q70" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:48, 19 December 2018

OCA: New page: '''Unreleased structure''' The entry 6q70 is ON HOLD until Paper Publication Authors: Bernardo-Garcia, N., Gago, F., Hermoso, J.A. Description: Crystal structure of the alanine racemas...

OCA — Wed, 19 Dec 2018 06:48:26 GMT

New page: '''Unreleased structure''' The entry 6q70 is ON HOLD until Paper Publication Authors: Bernardo-Garcia, N., Gago, F., Hermoso, J.A. Description: Crystal structure of the alanine racemas...

New page

'''Unreleased structure'''

The entry 6q70 is ON HOLD until Paper Publication

Authors: Bernardo-Garcia, N., Gago, F., Hermoso, J.A.

Description: Crystal structure of the alanine racemase Bsu17640 from Bacillus subtilis in the presence of HEPES
[[Category: Unreleased Structures]]
[[Category: Bernardo-Garcia, N]]
[[Category: Hermoso, J.A]]
[[Category: Gago, F]]