7fiq - Revision history

OCA at 17:16, 29 November 2023

2023-11-29T17:16:32Z

←Older revision		Revision as of 17:16, 29 November 2023
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	<StructureSection load='7fiq' size='340' side='right'caption='[[7fiq]], [[Resolution\|resolution]] 2.22Å' scene=''>		<StructureSection load='7fiq' size='340' side='right'caption='[[7fiq]], [[Resolution\|resolution]] 2.22Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7fiq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FIQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FIQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7fiq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoanaerobacter_sp._X514 Thermoanaerobacter sp. X514]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FIQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FIQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.22Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-1,2-mannobiose_phosphorylase Beta-1,2-mannobiose phosphorylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.339 2.4.1.339] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=7fiq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fiq OCA], [https://pdbe.org/7fiq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fiq RCSB], [https://www.ebi.ac.uk/pdbsum/7fiq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fiq 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=7fiq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fiq OCA], [https://pdbe.org/7fiq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fiq RCSB], [https://www.ebi.ac.uk/pdbsum/7fiq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fiq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/BMBP_THEPX BMBP_THEPX]] Probably involved in a salvage pathway for GDP-D-mannose biosynthesis (PubMed:25500577). Catalyzes the reversible phosphorolysis of 1,2-beta-oligomannan. In phosphorolytic reactions, prefers beta-1,2-mannobiose (beta-1,2-Man2) as substrate. Produces alpha-D-mannose 1-phosphate, which is the precursor of GDP-D-mannose (PubMed:25500577).<ref>PMID:25500577</ref>	+	[https://www.uniprot.org/uniprot/BMBP_THEPX BMBP_THEPX] Probably involved in a salvage pathway for GDP-D-mannose biosynthesis (PubMed:25500577). Catalyzes the reversible phosphorolysis of 1,2-beta-oligomannan. In phosphorolytic reactions, prefers beta-1,2-mannobiose (beta-1,2-Man2) as substrate. Produces alpha-D-mannose 1-phosphate, which is the precursor of GDP-D-mannose (PubMed:25500577).<ref>PMID:25500577</ref>
	<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: Beta-1,2-mannobiose phosphorylase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chang, Z]]	+	[[Category: Thermoanaerobacter sp. X514]]
-	[[Category: Chen, C C]]	+	[[Category: Chang Z]]
-	[[Category: Dai, L]]	+	[[Category: Chen C-C]]
-	[[Category: Guo, R T]]	+	[[Category: Dai L]]
-	[[Category: Huang, J]]	+	[[Category: Guo R-T]]
-	[[Category: Liu, W]]	+	[[Category: Huang J]]
-	[[Category: Sun, Y]]	+	[[Category: Liu W]]
-	[[Category: Yang, J]]	+	[[Category: Sun Y]]
-	[[Category: Yang, Y]]	+	[[Category: Yang J]]
-	[[Category: Zhang, L]]	+	[[Category: Yang Y]]
-	~~[[Category: Complex structure]]~~	+	[[Category: Zhang L]]
-	~~[[Category: Crystallization]]~~	+
-	~~[[Category: Mannobiose]]~~	+
-	~~[[Category: Phosphorylase]]~~	+
-	~~[[Category: Thermoanaerobacter]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:18, 9 March 2022

2022-03-09T07:18:07Z

←Older revision		Revision as of 07:18, 9 March 2022
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	==The crystal structure of mannose-bound beta-1,2-mannobiose phosphorylase from Thermoanaerobacter sp.==		==The crystal structure of mannose-bound beta-1,2-mannobiose phosphorylase from Thermoanaerobacter sp.==
-	<StructureSection load='7fiq' size='340' side='right'caption='[[7fiq]]' scene=''>	+	<StructureSection load='7fiq' size='340' side='right'caption='[[7fiq]], [[Resolution\|resolution]] 2.22Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FIQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FIQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7fiq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FIQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FIQ 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=7fiq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fiq OCA], [https://pdbe.org/7fiq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fiq RCSB], [https://www.ebi.ac.uk/pdbsum/7fiq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fiq ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-1,2-mannobiose_phosphorylase Beta-1,2-mannobiose phosphorylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.339 2.4.1.339] </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=7fiq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fiq OCA], [https://pdbe.org/7fiq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fiq RCSB], [https://www.ebi.ac.uk/pdbsum/7fiq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fiq ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/BMBP_THEPX BMBP_THEPX]] Probably involved in a salvage pathway for GDP-D-mannose biosynthesis (PubMed:25500577). Catalyzes the reversible phosphorolysis of 1,2-beta-oligomannan. In phosphorolytic reactions, prefers beta-1,2-mannobiose (beta-1,2-Man2) as substrate. Produces alpha-D-mannose 1-phosphate, which is the precursor of GDP-D-mannose (PubMed:25500577).<ref>PMID:25500577</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	1,2-beta-Mannobiose phosphorylases (1,2-beta-MBPs) from glycoside hydrolase 130 (GH130) family are important bio-catalysts in glycochemistry applications owing to their ability in synthesizing oligomannans. Here, we report the crystal structure of a thermostable 1,2-beta-MBP from Thermoanaerobacter sp. X-514 termed Teth514_1789 to reveal the molecular basis of its higher thermostability and mechanism of action. We also solved the enzyme complexes of mannose, mannose-1-phosphate (M1P) and 1,4-beta-mannobiose to manifest the enzyme-substrate interaction networks of three main subsites. Notably, a Zn ion that should be derived from crystallization buffer was found in the active site and coordinates the phosphate moiety of M1P. Nonetheless, this Zn-coordination should reflect an inhibitory status as supplementing Zn severely impairs the enzyme activity. These results indicate that the effects of metal ions should be taken into consideration when applying Teth514_1789 and other related enzymes. Based on the structure, a reliable model of Teth514_1788 that shares 61.7% sequence identity to Teth514_1789 but displays a different substrate preference was built. Analyzing the structural features of these two closely related enzymes, we hypothesized that the length of a loop fragment that covers the entrance of the catalytic center might regulate the substrate selectivity. In conclusion, these information provide in-depth understanding of GH130 1,2-beta-MBPs and should serve as an important guidance for enzyme engineering for further applications.
		+
		+	Structural investigation of a thermostable 1,2-beta-mannobiose phosphorylase from Thermoanaerobacter sp. X-514.,Dai L, Chang Z, Yang J, Liu W, Yang Y, Chen CC, Zhang L, Huang JW, Sun Y, Guo RT Biochem Biophys Res Commun. 2021 Nov 19;579:54-61. doi:, 10.1016/j.bbrc.2021.09.046. Epub 2021 Sep 21. PMID:34587555<ref>PMID:34587555</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7fiq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Beta-1,2-mannobiose phosphorylase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chang Z]]	+	[[Category: Chang, Z]]
-	[[Category: Chen C-C]]	+	[[Category: Chen, C C]]
-	[[Category: Dai L]]	+	[[Category: Dai, L]]
-	[[Category: Guo R-T]]	+	[[Category: Guo, R T]]
-	[[Category: Huang J]]	+	[[Category: Huang, J]]
-	[[Category: Liu W]]	+	[[Category: Liu, W]]
-	[[Category: Sun Y]]	+	[[Category: Sun, Y]]
-	[[Category: Yang J]]	+	[[Category: Yang, J]]
-	[[Category: Yang Y]]	+	[[Category: Yang, Y]]
-	[[Category: Zhang L]]	+	[[Category: Zhang, L]]
		+	[[Category: Complex structure]]
		+	[[Category: Crystallization]]
		+	[[Category: Mannobiose]]
		+	[[Category: Phosphorylase]]
		+	[[Category: Thermoanaerobacter]]
		+	[[Category: Transferase]]

OCA at 10:39, 5 January 2022

2022-01-05T10:39:58Z

←Older revision		Revision as of 10:39, 5 January 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 7fiq is ~~ON HOLD until Paper Publication~~	+	==The crystal structure of mannose-bound beta-1,2-mannobiose phosphorylase from Thermoanaerobacter sp.==
-		+	<StructureSection load='7fiq' size='340' side='right'caption='[[7fiq]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7FIQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7FIQ FirstGlance]. <br>
-	~~Description~~:	+	</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=7fiq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7fiq OCA], [https://pdbe.org/7fiq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7fiq RCSB], [https://www.ebi.ac.uk/pdbsum/7fiq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7fiq ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chang Z]]
		+	[[Category: Chen C-C]]
		+	[[Category: Dai L]]
		+	[[Category: Guo R-T]]
		+	[[Category: Huang J]]
		+	[[Category: Liu W]]
		+	[[Category: Sun Y]]
		+	[[Category: Yang J]]
		+	[[Category: Yang Y]]
		+	[[Category: Zhang L]]

OCA at 11:44, 29 December 2021

2021-12-29T11:44:41Z

←Older revision		Revision as of 11:44, 29 December 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7fiq is ON HOLD	+	The entry 7fiq is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7fiq" [edit=sysop:move=sysop]

2021-08-11T04:58:24Z

Protected "7fiq" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:58, 11 August 2021

OCA: New page: '''Unreleased structure''' The entry 7fiq is ON HOLD Authors: Description: Category: Unreleased Structures

2021-08-11T04:58:23Z

New page: '''Unreleased structure''' The entry 7fiq is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7fiq is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]