5ybw - Revision history

OCA at 08:26, 22 November 2023

2023-11-22T08:26:16Z

←Older revision		Revision as of 08:26, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5ybw' size='340' side='right'caption='[[5ybw]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5ybw' size='340' side='right'caption='[[5ybw]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ybw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YBW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YBW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ybw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Anadara_broughtonii Anadara broughtonii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YBW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YBW FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.9Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Aspartate_racemase Aspartate racemase], with EC number~~ [~~http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=~~5~~.1.1.13 5.1.1.13~~] </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5ybw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ybw OCA], [~~http~~://pdbe.org/5ybw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ybw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ybw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ybw 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=5ybw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ybw OCA], [https://pdbe.org/5ybw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ybw RCSB], [https://www.ebi.ac.uk/pdbsum/5ybw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ybw ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q2L695_ANABR Q2L695_ANABR]
	<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: ~~Aspartate racemase~~]]	+	[[Category: Anadara broughtonii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Abe, K]]	+	[[Category: Abe K]]
-	[[Category: Goto, M]]	+	[[Category: Goto M]]
-	[[Category: Kera, Y]]	+	[[Category: Kera Y]]
-	[[Category: Mizobuchi, T]]	+	[[Category: Mizobuchi T]]
-	[[Category: Nonaka, R]]	+	[[Category: Nonaka R]]
-	[[Category: Takahashi, S]]	+	[[Category: Takahashi S]]
-	[[Category: Yoshimura, M]]	+	[[Category: Yoshimura M]]
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Pyridoxal 5'-phosphate]]~~	+
-	~~[[Category: Scapharca broughtonii]]~~	+
-	~~[[Category: Serine racemase~~]]	+

OCA at 09:15, 21 October 2020

2020-10-21T09:15:32Z

←Older revision		Revision as of 09:15, 21 October 2020
Line 1:		Line 1:

	==Crystal structure of pyridoxal 5'-phosphate-dependent aspartate racemase==		==Crystal structure of pyridoxal 5'-phosphate-dependent aspartate racemase==
-	<StructureSection load='5ybw' size='340' side='right' caption='[[5ybw]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5ybw' size='340' side='right'caption='[[5ybw]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ybw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YBW OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YBW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ybw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YBW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YBW FirstGlance]. <br>
	</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>		</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/Aspartate_racemase Aspartate racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.13 5.1.1.13] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_racemase Aspartate racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.13 5.1.1.13] </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=5ybw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ybw OCA], [http://pdbe.org/5ybw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ybw RCSB], [http://www.ebi.ac.uk/pdbsum/5ybw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ybw 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=5ybw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ybw OCA], [http://pdbe.org/5ybw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ybw RCSB], [http://www.ebi.ac.uk/pdbsum/5ybw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ybw ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Aspartate racemase]]		[[Category: Aspartate racemase]]
		+	[[Category: Large Structures]]
	[[Category: Abe, K]]		[[Category: Abe, K]]
	[[Category: Goto, M]]		[[Category: Goto, M]]

OCA at 06:22, 20 December 2017

2017-12-20T06:22:31Z

←Older revision		Revision as of 06:22, 20 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ybw is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of pyridoxal 5'-phosphate-dependent aspartate racemase==
		+	<StructureSection load='5ybw' size='340' side='right' caption='[[5ybw]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ybw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YBW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YBW FirstGlance]. <br>
		+	</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/Aspartate_racemase Aspartate racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.13 5.1.1.13] </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=5ybw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ybw OCA], [http://pdbe.org/5ybw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ybw RCSB], [http://www.ebi.ac.uk/pdbsum/5ybw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ybw ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aspartate racemase (AspR) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that is responsible for D-aspartate biosynthesis in vivo. To the best of our knowledge, this is the first study to report an X-ray crystal structure of a PLP-dependent AspR, which was resolved at 1.90 A resolution. The AspR derived from the bivalve mollusc Scapharca broughtonii (SbAspR) is a type II PLP-dependent enzyme that is similar to serine racemase (SR) in that SbAspR catalyzes both racemization and dehydration. Structural comparison of SbAspR and SR shows a similar arrangement of the active-site residues and nucleotide-binding site, but a different orientation of the metal-binding site. Superposition of the structures of SbAspR and of rat SR bound to the inhibitor malonate reveals that Arg140 recognizes the beta-carboxyl group of the substrate aspartate in SbAspR. It is hypothesized that the aromatic proline interaction between the domains, which favours the closed form of SbAspR, influences the arrangement of Arg140 at the active site.

-	~~Authors: Mizobuchi~~, T., Nonaka, R., Yoshimura, M., Abe, K., Takahashi, S., Kera, Y., Goto, M.	+	Crystal structure of a pyridoxal 5'-phosphate-dependent aspartate racemase derived from the bivalve mollusc Scapharca broughtonii.,Mizobuchi T, Nonaka R, Yoshimura M, Abe K, Takahashi S, Kera Y, Goto M Acta Crystallogr F Struct Biol Commun. 2017 Dec 1;73(Pt 12):651-656. doi:, 10.1107/S2053230X17015813. Epub 2017 Nov 6. PMID:29199985<ref>PMID:29199985</ref>

-	~~Description: Crystal structure~~ of ~~pyridoxal 5'~~-~~phosphate~~-~~dependent aspartate~~ racemase	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Yoshimura~~, M]]	+	<div class="pdbe-citations 5ybw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Aspartate racemase]]
		+	[[Category: Abe, K]]
		+	[[Category: Goto, M]]
	[[Category: Kera, Y]]		[[Category: Kera, Y]]
	[[Category: Mizobuchi, T]]		[[Category: Mizobuchi, T]]
	[[Category: Nonaka, R]]		[[Category: Nonaka, R]]
-	[[Category: Goto, M]]
	[[Category: Takahashi, S]]		[[Category: Takahashi, S]]
-	[[Category: ~~Abe~~, K]]	+	[[Category: Yoshimura, M]]
		+	[[Category: Isomerase]]
		+	[[Category: Pyridoxal 5'-phosphate]]
		+	[[Category: Scapharca broughtonii]]
		+	[[Category: Serine racemase]]

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

2017-09-27T16:23:07Z

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

←Older revision

Revision as of 16:23, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ybw is ON HOLD until Paper Publication Authors: Mizobuchi, T., Nonaka, R., Yoshimura, M., Abe, K., Takahashi, S., Kera, Y., Goto, M. Description: ...

2017-09-27T16:23:05Z

New page: '''Unreleased structure''' The entry 5ybw is ON HOLD until Paper Publication Authors: Mizobuchi, T., Nonaka, R., Yoshimura, M., Abe, K., Takahashi, S., Kera, Y., Goto, M. Description: ...

New page

'''Unreleased structure'''

The entry 5ybw is ON HOLD until Paper Publication

Authors: Mizobuchi, T., Nonaka, R., Yoshimura, M., Abe, K., Takahashi, S., Kera, Y., Goto, M.

Description: Crystal structure of pyridoxal 5'-phosphate-dependent aspartate racemase
[[Category: Unreleased Structures]]
[[Category: Yoshimura, M]]
[[Category: Kera, Y]]
[[Category: Mizobuchi, T]]
[[Category: Nonaka, R]]
[[Category: Goto, M]]
[[Category: Takahashi, S]]
[[Category: Abe, K]]