5h42 - Revision history

OCA at 07:23, 9 August 2023

2023-08-09T07:23:07Z

←Older revision		Revision as of 07:23, 9 August 2023
Line 3:		Line 3:
	<StructureSection load='5h42' size='340' side='right'caption='[[5h42]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5h42' size='340' side='right'caption='[[5h42]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h42]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Clostridium_phytofermentans Clostridium~~ phytofermentans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H42 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5H42 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h42]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lachnoclostridium_phytofermentans_ISDg Lachnoclostridium phytofermentans ISDg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H42 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=G1P:ALPHA-D-GLUCOSE-1-PHOSPHATE'>G1P</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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]] 2.1Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h3z\|5h3z]]~~, [[~~5h40~~\|~~5h40]], [[5h41\|5h41~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G1P:ALPHA-D-GLUCOSE-1-PHOSPHATE'>G1P</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>Cphy_0694 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~357809 Clostridium phytofermentans])</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=5h42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h42 OCA], [https://pdbe.org/5h42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h42 RCSB], [https://www.ebi.ac.uk/pdbsum/5h42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h42 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/1,2~~-~~beta~~-~~oligoglucan_phosphorylase 1,2-beta-oligoglucan phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.333 2.4.1.333]~~ </~~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=5h42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h42 OCA], [~~http~~://pdbe.org/5h42 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5h42 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5h42 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5h42 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A9KJS6_LACP7 A9KJS6_LACP7]
	<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: ~~1,2-beta-oligoglucan phosphorylase]]~~	+	[[Category: Lachnoclostridium phytofermentans ISDg]]
-	~~[[Category: Clostridium~~ phytofermentans]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Furukawa, N]]	+	[[Category: Furukawa N]]
-	[[Category: Fushinobu, S]]	+	[[Category: Fushinobu S]]
-	[[Category: Kodutsumi, Y]]	+	[[Category: Kodutsumi Y]]
-	[[Category: Miyanaga, A]]	+	[[Category: Miyanaga A]]
-	[[Category: Nakai, H]]	+	[[Category: Nakai H]]
-	[[Category: Nakajima, M]]	+	[[Category: Nakajima M]]
-	[[Category: Nihira, T]]	+	[[Category: Nihira T]]
-	[[Category: Sugimoto, N]]	+	[[Category: Sugimoto N]]
-	[[Category: Taguchi, H]]	+	[[Category: Taguchi H]]
-	[[Category: Takahashi, Y]]	+	[[Category: Takahashi Y]]
-	[[Category: Tanaka, N]]	+	[[Category: Tanaka N]]
-	~~[[Category: 2-glucan]]~~	+
-	~~[[Category: Beta-1]]~~	+
-	~~[[Category: Glycoside phosphorylase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 10:12, 26 February 2020

2020-02-26T10:12:08Z

←Older revision		Revision as of 10:12, 26 February 2020
Line 1:		Line 1:

	==Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with alpha-d-glucose-1-phosphate==		==Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with alpha-d-glucose-1-phosphate==
-	<StructureSection load='5h42' size='340' side='right' caption='[[5h42]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5h42' size='340' side='right'caption='[[5h42]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h42]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H42 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h42]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_phytofermentans Clostridium phytofermentans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H42 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=G1P:ALPHA-D-GLUCOSE-1-PHOSPHATE'>G1P</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=G1P:ALPHA-D-GLUCOSE-1-PHOSPHATE'>G1P</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h3z\|5h3z]], [[5h40\|5h40]], [[5h41\|5h41]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h3z\|5h3z]], [[5h40\|5h40]], [[5h41\|5h41]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cphy_0694 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=357809 Clostridium phytofermentans])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,2-beta-oligoglucan_phosphorylase 1,2-beta-oligoglucan phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.333 2.4.1.333] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,2-beta-oligoglucan_phosphorylase 1,2-beta-oligoglucan phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.333 2.4.1.333] </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=5h42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h42 OCA], [http://pdbe.org/5h42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h42 RCSB], [http://www.ebi.ac.uk/pdbsum/5h42 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h42 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=5h42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h42 OCA], [http://pdbe.org/5h42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h42 RCSB], [http://www.ebi.ac.uk/pdbsum/5h42 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h42 ProSAT]</span></td></tr>
Line 23:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: 1,2-beta-oligoglucan phosphorylase]]		[[Category: 1,2-beta-oligoglucan phosphorylase]]
		+	[[Category: Clostridium phytofermentans]]
		+	[[Category: Large Structures]]
	[[Category: Furukawa, N]]		[[Category: Furukawa, N]]
	[[Category: Fushinobu, S]]		[[Category: Fushinobu, S]]

OCA at 09:32, 11 March 2017

2017-03-11T09:32:28Z

←Older revision		Revision as of 09:32, 11 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5h42 is ~~ON HOLD until Oct 28 2018~~	+	==Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with alpha-d-glucose-1-phosphate==
		+	<StructureSection load='5h42' size='340' side='right' caption='[[5h42]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5h42]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H42 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=G1P:ALPHA-D-GLUCOSE-1-PHOSPHATE'>G1P</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h3z\|5h3z]], [[5h40\|5h40]], [[5h41\|5h41]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,2-beta-oligoglucan_phosphorylase 1,2-beta-oligoglucan phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.333 2.4.1.333] </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=5h42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h42 OCA], [http://pdbe.org/5h42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h42 RCSB], [http://www.ebi.ac.uk/pdbsum/5h42 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h42 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glycoside phosphorylases catalyze the phosphorolysis of oligosaccharides into sugar phosphates. Recently, we found a novel phosphorylase acting on beta-1,2-glucooligosaccharides with degrees of polymerization of 3 or more (1,2-beta-oligoglucan phosphorylase, SOGP) in glycoside hydrolase family (GH) 94. Here, we characterized SOGP from Lachnoclostridium phytofermentans (LpSOGP) and determined its crystal structure. LpSOGP is a monomeric enzyme that contains a unique beta-sandwich domain (Ndom1) at its N-terminus. Unlike the dimeric GH94 enzymes possessing catalytic pockets at their dimer interface, LpSOGP has a catalytic pocket between Ndom1 and the catalytic domain. In the complex structure of LpSOGP with sophorose, sophorose binds at subsites +1 to +2. Notably, the Glc moiety at subsite +1 is flipped compared with the corresponding ligands in other GH94 enzymes. This inversion suggests the great distortion of the glycosidic bond between subsites -1 and +1, which is likely unfavorable for substrate binding. Compensation for this disadvantage at subsite +2 can be accounted for by the small distortion of the glycosidic bond in the sophorose molecule. Therefore, the binding mode at subsites +1 and +2 defines the substrate specificity of LpSOGP, which provides mechanistic insights into the substrate specificity of a phosphorylase acting on beta-1,2-glucooligosaccharides.

-	~~Authors: Nakajima~~, M., Tanaka, N., Furukawa, N., Nihira, T., Kodutsumi, Y., Takahashi, Y., Sugimoto, N., Miyanaga, A., Fushinobu, S., Taguchi, H., Nakai, H.	+	Mechanistic insight into the substrate specificity of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans.,Nakajima M, Tanaka N, Furukawa N, Nihira T, Kodutsumi Y, Takahashi Y, Sugimoto N, Miyanaga A, Fushinobu S, Taguchi H, Nakai H Sci Rep. 2017 Feb 15;7:42671. doi: 10.1038/srep42671. PMID:28198470<ref>PMID:28198470</ref>

-	~~Description: Crystal Structure~~ of 1,2-beta-oligoglucan phosphorylase ~~from Lachnoclostridium phytofermentans in complex with alpha-d-glucose-1-phosphate~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5h42" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 1,2-beta-oligoglucan phosphorylase]]
		+	[[Category: Furukawa, N]]
	[[Category: Fushinobu, S]]		[[Category: Fushinobu, S]]
		+	[[Category: Kodutsumi, Y]]
		+	[[Category: Miyanaga, A]]
	[[Category: Nakai, H]]		[[Category: Nakai, H]]
	[[Category: Nakajima, M]]		[[Category: Nakajima, M]]
-	[[Category: ~~Taguchi~~, H]]	+	[[Category: Nihira, T]]
	[[Category: Sugimoto, N]]		[[Category: Sugimoto, N]]
-	[[Category: ~~Furukawa~~, ~~N]]~~	+	[[Category: Taguchi, H]]
-	~~[[Category: Kodutsumi, Y~~]]	+
	[[Category: Takahashi, Y]]		[[Category: Takahashi, Y]]
-	[[Category: Nihira, T]]
	[[Category: Tanaka, N]]		[[Category: Tanaka, N]]
-	[[Category: ~~Miyanaga, A~~]]	+	[[Category: 2-glucan]]
		+	[[Category: Beta-1]]
		+	[[Category: Glycoside phosphorylase]]
		+	[[Category: Transferase]]

OCA at 13:42, 9 December 2016

2016-12-09T13:42:43Z

←Older revision		Revision as of 13:42, 9 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5h42 is ON HOLD	+	The entry 5h42 is ON HOLD until Oct 28 2018

	Authors: Nakajima, M., Tanaka, N., Furukawa, N., Nihira, T., Kodutsumi, Y., Takahashi, Y., Sugimoto, N., Miyanaga, A., Fushinobu, S., Taguchi, H., Nakai, H.		Authors: Nakajima, M., Tanaka, N., Furukawa, N., Nihira, T., Kodutsumi, Y., Takahashi, Y., Sugimoto, N., Miyanaga, A., Fushinobu, S., Taguchi, H., Nakai, H.

-	Description: Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with alpha-d-glucose-1-phosphate.	+	Description: Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with alpha-d-glucose-1-phosphate
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Fushinobu, S]]		[[Category: Fushinobu, S]]

OCA: Protected "5h42" [edit=sysop:move=sysop]

2016-11-02T12:58:31Z

Protected "5h42" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:58, 2 November 2016

OCA: New page: '''Unreleased structure''' The entry 5h42 is ON HOLD Authors: Nakajima, M., Tanaka, N., Furukawa, N., Nihira, T., Kodutsumi, Y., Takahashi, Y., Sugimoto, N., Miyanaga, A., Fushinobu, S....

2016-11-02T12:58:29Z

New page: '''Unreleased structure''' The entry 5h42 is ON HOLD Authors: Nakajima, M., Tanaka, N., Furukawa, N., Nihira, T., Kodutsumi, Y., Takahashi, Y., Sugimoto, N., Miyanaga, A., Fushinobu, S....

New page

'''Unreleased structure'''

The entry 5h42 is ON HOLD

Authors: Nakajima, M., Tanaka, N., Furukawa, N., Nihira, T., Kodutsumi, Y., Takahashi, Y., Sugimoto, N., Miyanaga, A., Fushinobu, S., Taguchi, H., Nakai, H.

Description: Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans in complex with alpha-d-glucose-1-phosphate.
[[Category: Unreleased Structures]]
[[Category: Fushinobu, S]]
[[Category: Nakai, H]]
[[Category: Nakajima, M]]
[[Category: Taguchi, H]]
[[Category: Sugimoto, N]]
[[Category: Furukawa, N]]
[[Category: Kodutsumi, Y]]
[[Category: Takahashi, Y]]
[[Category: Nihira, T]]
[[Category: Tanaka, N]]
[[Category: Miyanaga, A]]