4ysv - Revision history

OCA at 15:38, 8 November 2023

2023-11-08T15:38:37Z

←Older revision		Revision as of 15:38, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ysv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lentilactobacillus_buchneri Lentilactobacillus buchneri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YSV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YSV FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ysv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lentilactobacillus_buchneri Lentilactobacillus buchneri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YSV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YSV 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=4ysv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysv OCA], [https://pdbe.org/4ysv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ysv RCSB], [https://www.ebi.ac.uk/pdbsum/4ysv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ysv 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]] 2.77Å</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=4ysv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysv OCA], [https://pdbe.org/4ysv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ysv RCSB], [https://www.ebi.ac.uk/pdbsum/4ysv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ysv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 08:30, 3 May 2023

2023-05-03T08:30:40Z

←Older revision		Revision as of 08:30, 3 May 2023
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	<StructureSection load='4ysv' size='340' side='right'caption='[[4ysv]], [[Resolution\|resolution]] 2.77Å' scene=''>		<StructureSection load='4ysv' size='340' side='right'caption='[[4ysv]], [[Resolution\|resolution]] 2.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ysv]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_buchneri"_(sic)_henneberg_1903 "bacillus~~ buchneri~~" (sic) henneberg 1903~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YSV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YSV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ysv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lentilactobacillus_buchneri Lentilactobacillus buchneri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YSV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YSV FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ysn\|4ysn]]</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=4ysv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysv OCA], [https://pdbe.org/4ysv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ysv RCSB], [https://www.ebi.ac.uk/pdbsum/4ysv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ysv 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=4ysv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysv OCA], [~~http~~://pdbe.org/4ysv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ysv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ysv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ysv ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ILE2E_LENBU ILE2E_LENBU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hayashi, J]]	+	[[Category: Lentilactobacillus buchneri]]
-	[[Category: Mutaguchi, Y]]	+	[[Category: Hayashi J]]
-	[[Category: Ohshima, T]]	+	[[Category: Mutaguchi Y]]
-	[[Category: Sakuraba, H]]	+	[[Category: Ohshima T]]
-	~~[[Category: Fold type i of plp-dependent enzyme]]~~	+	[[Category: Sakuraba H]]
-	~~[[Category: Isomerase~~]]	+

OCA at 07:33, 4 March 2020

2020-03-04T07:33:02Z

←Older revision		Revision as of 07:33, 4 March 2020
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	==Structure of aminoacid racemase in apo-form==		==Structure of aminoacid racemase in apo-form==
-	<StructureSection load='4ysv' size='340' side='right' caption='[[4ysv]], [[Resolution\|resolution]] 2.77Å' scene=''>	+	<StructureSection load='4ysv' size='340' side='right'caption='[[4ysv]], [[Resolution\|resolution]] 2.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ysv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_buchneri"_(sic)_henneberg_1903 "bacillus buchneri" (sic) henneberg 1903]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YSV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YSV FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ysv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_buchneri"_(sic)_henneberg_1903 "bacillus buchneri" (sic) henneberg 1903]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YSV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YSV FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Hayashi, J]]		[[Category: Hayashi, J]]
	[[Category: Mutaguchi, Y]]		[[Category: Mutaguchi, Y]]

OCA at 12:24, 16 November 2017

2017-11-16T12:24:54Z

←Older revision		Revision as of 12:24, 16 November 2017
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	<StructureSection load='4ysv' size='340' side='right' caption='[[4ysv]], [[Resolution\|resolution]] 2.77Å' scene=''>		<StructureSection load='4ysv' size='340' side='right' caption='[[4ysv]], [[Resolution\|resolution]] 2.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ysv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YSV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YSV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ysv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_buchneri"_(sic)_henneberg_1903 "bacillus buchneri" (sic) henneberg 1903]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YSV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YSV FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ysn\|4ysn]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ysn\|4ysn]]</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=4ysv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysv OCA], [http://pdbe.org/4ysv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ysv RCSB], [http://www.ebi.ac.uk/pdbsum/4ysv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ysv 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=4ysv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysv OCA], [http://pdbe.org/4ysv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ysv RCSB], [http://www.ebi.ac.uk/pdbsum/4ysv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ysv ProSAT]</span></td></tr>

OCA at 09:00, 17 May 2017

2017-05-17T09:00:19Z

←Older revision		Revision as of 09:00, 17 May 2017
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	<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=4ysv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysv OCA], [http://pdbe.org/4ysv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ysv RCSB], [http://www.ebi.ac.uk/pdbsum/4ysv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ysv 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=4ysv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysv OCA], [http://pdbe.org/4ysv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ysv RCSB], [http://www.ebi.ac.uk/pdbsum/4ysv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ysv ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Crystal structures of Lactobacillus buchneri isoleucine 2-epimerase, a novel branched-chain amino-acid racemase, were determined for the enzyme in the apo form, in complex with pyridoxal 5'-phosphate (PLP), in complex with N-(5'-phosphopyridoxyl)-L-isoleucine (PLP-L-Ile) and in complex with N-(5'-phosphopyridoxyl)-D-allo-isoleucine (PLP-D-allo-Ile) at resolutions of 2.77, 1.94, 2.65 and 2.12 A, respectively. The enzyme assembled as a tetramer, with each subunit being composed of N-terminal, C-terminal and large PLP-binding domains. The active-site cavity in the apo structure was much more solvent-accessible than that in the PLP-bound structure. This indicates that a marked structural change occurs around the active site upon binding of PLP that provides a solvent-inaccessible environment for the enzymatic reaction. The main-chain coordinates of the L. buchneri isoleucine 2-epimerase monomer showed a notable similarity to those of alpha-amino--caprolactam racemase from Achromobactor obae and gamma-aminobutyrate aminotransferase from Escherichia coli. However, the amino-acid residues involved in substrate binding in those two enzymes are only partially conserved in L. buchneri isoleucine 2-epimerase, which may account for the differences in substrate recognition by the three enzymes. The structures bound with reaction-intermediate analogues (PLP-L-Ile and PLP-D-allo-Ile) and site-directed mutagenesis suggest that L-isoleucine epimerization proceeds through abstraction of the alpha-hydrogen of the substrate by Lys280, while Asp222 serves as the catalytic residue adding an alpha-hydrogen to the quinonoid intermediate to form D-allo-isoleucine.
		+
		+	Crystal structure of the novel amino-acid racemase isoleucine 2-epimerase from Lactobacillus buchneri.,Hayashi J, Mutaguchi Y, Minemura Y, Nakagawa N, Yoneda K, Ohmori T, Ohshima T, Sakuraba H Acta Crystallogr D Struct Biol. 2017 May 1;73(Pt 5):428-437. doi:, 10.1107/S2059798317005332. Epub 2017 Apr 19. PMID:28471367<ref>PMID:28471367</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4ysv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:09, 19 April 2017

2017-04-19T06:09:01Z

←Older revision		Revision as of 06:09, 19 April 2017
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[4ysv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YSV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YSV FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ysv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YSV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YSV FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ysn\|4ysn]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ysn\|4ysn]]</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=4ysv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysv OCA], [http://pdbe.org/4ysv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ysv RCSB], [http://www.ebi.ac.uk/pdbsum/4ysv 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=4ysv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysv OCA], [http://pdbe.org/4ysv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ysv RCSB], [http://www.ebi.ac.uk/pdbsum/4ysv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ysv ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 18:38, 12 May 2016

2016-05-12T18:38:26Z

←Older revision		Revision as of 18:38, 12 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 4ysv is ON HOLD until Paper Publication~~	+	==Structure of aminoacid racemase in apo-form==
-		+	<StructureSection load='4ysv' size='340' side='right' caption='[[4ysv]], [[Resolution\|resolution]] 2.77Å' scene=''>
-	~~Authors: Sakuraba, H., Mutaguchi, Y., Hayashi, J., Ohshima, T.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4ysv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YSV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YSV FirstGlance]. <br>
-	~~Description:~~ Structure of aminoacid racemase in apo-form	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ysn\|4ysn]]</td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=4ysv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ysv OCA], [http://pdbe.org/4ysv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ysv RCSB], [http://www.ebi.ac.uk/pdbsum/4ysv PDBsum]</span></td></tr>
-	[[~~Category~~: ~~Sakuraba, H~~]]	+	</table>
-	[[~~Category~~: ~~Ohshima~~, T]]	+	__TOC__
		+	</StructureSection>
	[[Category: Hayashi, J]]		[[Category: Hayashi, J]]
	[[Category: Mutaguchi, Y]]		[[Category: Mutaguchi, Y]]
		+	[[Category: Ohshima, T]]
		+	[[Category: Sakuraba, H]]
		+	[[Category: Fold type i of plp-dependent enzyme]]
		+	[[Category: Isomerase]]

OCA at 23:44, 30 November 2015

2015-11-30T23:44:09Z

←Older revision		Revision as of 23:44, 30 November 2015
Line 7:		Line 7:
	Description: Structure of aminoacid racemase in apo-form		Description: Structure of aminoacid racemase in apo-form
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Mutaguchi, Y]]
	[[Category: Sakuraba, H]]		[[Category: Sakuraba, H]]
	[[Category: Ohshima, T]]		[[Category: Ohshima, T]]
	[[Category: Hayashi, J]]		[[Category: Hayashi, J]]
		+	[[Category: Mutaguchi, Y]]

OCA at 11:51, 1 April 2015

2015-04-01T11:51:24Z

←Older revision		Revision as of 11:51, 1 April 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ysv is ON HOLD	+	The entry 4ysv is ON HOLD until Paper Publication

	Authors: Sakuraba, H., Mutaguchi, Y., Hayashi, J., Ohshima, T.		Authors: Sakuraba, H., Mutaguchi, Y., Hayashi, J., Ohshima, T.

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

2015-03-26T12:47:41Z

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

←Older revision

Revision as of 12:47, 26 March 2015