5ay9 - Revision history

OCA at 09:06, 20 March 2024

2024-03-20T09:06:25Z

←Older revision		Revision as of 09:06, 20 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ay9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ruminococcus_albus_7_=_DSM_20455 Ruminococcus albus 7 = DSM 20455]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AY9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ay9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ruminococcus_albus_7_=_DSM_20455 Ruminococcus albus 7 = DSM 20455]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AY9 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=5ay9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ay9 OCA], [https://pdbe.org/5ay9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ay9 RCSB], [https://www.ebi.ac.uk/pdbsum/5ay9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ay9 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]] 2.5Å</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=5ay9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ay9 OCA], [https://pdbe.org/5ay9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ay9 RCSB], [https://www.ebi.ac.uk/pdbsum/5ay9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ay9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/MGP_RUMA7 MGP_RUMA7] Converts 4-O-beta-D-mannopyranosyl-D-glucopyranose (Man-Glc) to mannose 1-phosphate (Man1P) and glucose. Involved in a mannan catabolic pathway which feeds into glycolysis.[HAMAP-Rule:MF_00928]<ref>PMID:23093406</ref>		[https://www.uniprot.org/uniprot/MGP_RUMA7 MGP_RUMA7] Converts 4-O-beta-D-mannopyranosyl-D-glucopyranose (Man-Glc) to mannose 1-phosphate (Man1P) and glucose. Involved in a mannan catabolic pathway which feeds into glycolysis.[HAMAP-Rule:MF_00928]<ref>PMID:23093406</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	In Ruminococcus albus, 4-O-beta-d-mannosyl-d-glucose phosphorylase (RaMP1) and beta-(1,4)-mannooligosaccharide phosphorylase (RaMP2) belong to two subfamilies of glycoside hydrolase family 130. The two enzymes phosphorolyze beta-mannosidic linkages at the nonreducing ends of their substrates, and have substantially diverse substrate specificity. The differences in their mechanism of substrate binding have not yet been fully clarified. In the present study, we report the crystal structures of RaMP1 with/without 4-O-beta-d-mannosyl-d-glucose and RaMP2 with/without beta-(1-->4)-mannobiose. The structures of the two enzymes differ at the +1 subsite of the substrate-binding pocket. Three loops are proposed to determine the different substrate specificities. One of these loops is contributed from the adjacent molecule of the oligomer structure. In RaMP1, His245 of loop 3 forms a hydrogen-bond network with the substrate through a water molecule, and is indispensible for substrate binding.
-
-	Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies.,Ye Y, Saburi W, Odaka R, Kato K, Sakurai N, Komoda K, Nishimoto M, Kitaoka M, Mori H, Yao M FEBS Lett. 2016 Mar;590(6):828-37. doi: 10.1002/1873-3468.12105. Epub 2016 Mar 4. PMID:26913570<ref>PMID:26913570</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5ay9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:31, 31 May 2023

2023-05-31T06:31:09Z

←Older revision		Revision as of 06:31, 31 May 2023
Line 3:		Line 3:
	<StructureSection load='5ay9' size='340' side='right'caption='[[5ay9]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5ay9' size='340' side='right'caption='[[5ay9]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ay9]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ruma7 Ruma7~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AY9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5AY9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ay9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ruminococcus_albus_7_=_DSM_20455 Ruminococcus albus 7 = DSM 20455]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AY9 FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5aye\|5aye]], [[5ayd\|5ayd]], [[5ayc\|5ayc]]</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=5ay9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ay9 OCA], [https://pdbe.org/5ay9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ay9 RCSB], [https://www.ebi.ac.uk/pdbsum/5ay9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ay9 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rumal_0852 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=697329 RUMA7])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-O-beta-D-mannosyl-D-glucose_phosphorylase 4-O-beta-D-mannosyl-D-glucose phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.281 2.4.1.281] </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=5ay9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ay9 OCA], [~~http~~://pdbe.org/5ay9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ay9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ay9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ay9 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MGP_RUMA7 MGP_RUMA7]] Converts 4-O-beta-D-mannopyranosyl-D-glucopyranose (Man-Glc) to mannose 1-phosphate (Man1P) and glucose. Involved in a mannan catabolic pathway which feeds into glycolysis.[HAMAP-Rule:MF_00928]<ref>PMID:23093406</ref>	+	[https://www.uniprot.org/uniprot/MGP_RUMA7 MGP_RUMA7] Converts 4-O-beta-D-mannopyranosyl-D-glucopyranose (Man-Glc) to mannose 1-phosphate (Man1P) and glucose. Involved in a mannan catabolic pathway which feeds into glycolysis.[HAMAP-Rule:MF_00928]<ref>PMID:23093406</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 4-O-beta-D-mannosyl-D-glucose phosphorylase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ruma7~~]]	+	[[Category: Ruminococcus albus 7 = DSM 20455]]
-	[[Category: Kato, K]]	+	[[Category: Kato K]]
-	[[Category: Saburi, W]]	+	[[Category: Saburi W]]
-	[[Category: Yao, M]]	+	[[Category: Yao M]]
-	[[Category: Ye, Y]]	+	[[Category: Ye Y]]
-	~~[[Category: Glycoside hydrolase family 130]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:56, 10 July 2019

2019-07-10T06:56:06Z

←Older revision		Revision as of 06:56, 10 July 2019
Line 1:		Line 1:

	==Crystal structure of Ruminococcus albus 4-O-beta-D-mannosyl-D-glucose phosphorylase (RaMP1)==		==Crystal structure of Ruminococcus albus 4-O-beta-D-mannosyl-D-glucose phosphorylase (RaMP1)==
-	<StructureSection load='5ay9' size='340' side='right' caption='[[5ay9]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5ay9' size='340' side='right'caption='[[5ay9]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ay9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AY9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AY9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ay9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ruma7 Ruma7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AY9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AY9 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5aye\|5aye]], [[5ayd\|5ayd]], [[5ayc\|5ayc]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5aye\|5aye]], [[5ayd\|5ayd]], [[5ayc\|5ayc]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rumal_0852 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=697329 RUMA7])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-O-beta-D-mannosyl-D-glucose_phosphorylase 4-O-beta-D-mannosyl-D-glucose phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.281 2.4.1.281] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-O-beta-D-mannosyl-D-glucose_phosphorylase 4-O-beta-D-mannosyl-D-glucose phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.281 2.4.1.281] </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=5ay9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ay9 OCA], [http://pdbe.org/5ay9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ay9 RCSB], [http://www.ebi.ac.uk/pdbsum/5ay9 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=5ay9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ay9 OCA], [http://pdbe.org/5ay9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ay9 RCSB], [http://www.ebi.ac.uk/pdbsum/5ay9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ay9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 24:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: 4-O-beta-D-mannosyl-D-glucose phosphorylase]]		[[Category: 4-O-beta-D-mannosyl-D-glucose phosphorylase]]
		+	[[Category: Large Structures]]
		+	[[Category: Ruma7]]
	[[Category: Kato, K]]		[[Category: Kato, K]]
	[[Category: Saburi, W]]		[[Category: Saburi, W]]

OCA at 16:14, 10 May 2016

2016-05-10T16:14:18Z

←Older revision		Revision as of 16:14, 10 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ay9 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of Ruminococcus albus 4-O-beta-D-mannosyl-D-glucose phosphorylase (RaMP1)==
		+	<StructureSection load='5ay9' size='340' side='right' caption='[[5ay9]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ay9]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AY9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AY9 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5aye\|5aye]], [[5ayd\|5ayd]], [[5ayc\|5ayc]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-O-beta-D-mannosyl-D-glucose_phosphorylase 4-O-beta-D-mannosyl-D-glucose phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.281 2.4.1.281] </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=5ay9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ay9 OCA], [http://pdbe.org/5ay9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ay9 RCSB], [http://www.ebi.ac.uk/pdbsum/5ay9 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MGP_RUMA7 MGP_RUMA7]] Converts 4-O-beta-D-mannopyranosyl-D-glucopyranose (Man-Glc) to mannose 1-phosphate (Man1P) and glucose. Involved in a mannan catabolic pathway which feeds into glycolysis.[HAMAP-Rule:MF_00928]<ref>PMID:23093406</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In Ruminococcus albus, 4-O-beta-d-mannosyl-d-glucose phosphorylase (RaMP1) and beta-(1,4)-mannooligosaccharide phosphorylase (RaMP2) belong to two subfamilies of glycoside hydrolase family 130. The two enzymes phosphorolyze beta-mannosidic linkages at the nonreducing ends of their substrates, and have substantially diverse substrate specificity. The differences in their mechanism of substrate binding have not yet been fully clarified. In the present study, we report the crystal structures of RaMP1 with/without 4-O-beta-d-mannosyl-d-glucose and RaMP2 with/without beta-(1-->4)-mannobiose. The structures of the two enzymes differ at the +1 subsite of the substrate-binding pocket. Three loops are proposed to determine the different substrate specificities. One of these loops is contributed from the adjacent molecule of the oligomer structure. In RaMP1, His245 of loop 3 forms a hydrogen-bond network with the substrate through a water molecule, and is indispensible for substrate binding.

-	~~Authors: Ye~~, Y., Saburi, W., Kato, K., ~~Yao~~, M.	+	Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies.,Ye Y, Saburi W, Odaka R, Kato K, Sakurai N, Komoda K, Nishimoto M, Kitaoka M, Mori H, Yao M FEBS Lett. 2016 Mar;590(6):828-37. doi: 10.1002/1873-3468.12105. Epub 2016 Mar 4. PMID:26913570<ref>PMID:26913570</ref>

-	~~Description:~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Ye, Y]]~~	+	<div class="pdbe-citations 5ay9" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Yao, M~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 4-O-beta-D-mannosyl-D-glucose phosphorylase]]
	[[Category: Kato, K]]		[[Category: Kato, K]]
	[[Category: Saburi, W]]		[[Category: Saburi, W]]
		+	[[Category: Yao, M]]
		+	[[Category: Ye, Y]]
		+	[[Category: Glycoside hydrolase family 130]]
		+	[[Category: Transferase]]

OCA at 09:59, 16 December 2015

2015-12-16T09:59:59Z

←Older revision		Revision as of 09:59, 16 December 2015
Line 7:		Line 7:
	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Saburi, W]]
	[[Category: Ye, Y]]		[[Category: Ye, Y]]
	[[Category: Yao, M]]		[[Category: Yao, M]]
	[[Category: Kato, K]]		[[Category: Kato, K]]
		+	[[Category: Saburi, W]]

OCA at 10:00, 2 September 2015

2015-09-02T10:00:29Z

←Older revision		Revision as of 10:00, 2 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ay9 is ON HOLD	+	The entry 5ay9 is ON HOLD until Paper Publication

	Authors: Ye, Y., Saburi, W., Kato, K., Yao, M.		Authors: Ye, Y., Saburi, W., Kato, K., Yao, M.

OCA: Protected "5ay9" [edit=sysop:move=sysop]

2015-08-20T10:05:14Z

Protected "5ay9" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:05, 20 August 2015

OCA: New page: '''Unreleased structure''' The entry 5ay9 is ON HOLD Authors: Ye, Y., Saburi, W., Kato, K., Yao, M. Description: Category: Unreleased Structures Category: Saburi, W [[Category...

2015-08-20T10:05:13Z

New page: '''Unreleased structure''' The entry 5ay9 is ON HOLD Authors: Ye, Y., Saburi, W., Kato, K., Yao, M. Description: Category: Unreleased Structures Category: Saburi, W [[Category...

New page

'''Unreleased structure'''

The entry 5ay9 is ON HOLD

Authors: Ye, Y., Saburi, W., Kato, K., Yao, M.

Description:
[[Category: Unreleased Structures]]
[[Category: Saburi, W]]
[[Category: Ye, Y]]
[[Category: Yao, M]]
[[Category: Kato, K]]