6s9v - Revision history

OCA at 12:37, 24 January 2024

2024-01-24T12:37:49Z

←Older revision		Revision as of 12:37, 24 January 2024
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	<StructureSection load='6s9v' size='340' side='right'caption='[[6s9v]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='6s9v' size='340' side='right'caption='[[6s9v]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6s9v]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Clostridium_thermosaccharolyticum Clostridium~~ thermosaccharolyticum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S9V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6S9V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6s9v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoanaerobacterium_thermosaccharolyticum_DSM_571 Thermoanaerobacterium thermosaccharolyticum DSM 571]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S9V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.83Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">spp, Tthe_1921 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=580327 Clostridium thermosaccharolyticum])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sucrose_6(F)-phosphate_phosphorylase Sucrose 6(F)-phosphate phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.329 2.4.1.329] </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=6s9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s9v OCA], [https://pdbe.org/6s9v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s9v RCSB], [https://www.ebi.ac.uk/pdbsum/6s9v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s9v 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=6s9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s9v OCA], [~~http~~://pdbe.org/6s9v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6s9v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6s9v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6s9v ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SUCPP_THETC SUCPP_THETC]] Catalyzes the reversible phosphorolysis of sucrose 6(F)-phosphate into alpha-D-glucose 1-phosphate (Glc1P) and D-fructose 6-phosphate. May be involved in a new pathway for the degradation of sucrose, which could become phosphorylated on its fructose moiety during uptake via a PTS system. To a lesser extent, can also reversibly act on sucrose in vitro (PubMed:24599311). Is also able to catalyze transglycosylation reactions in vitro (PubMed:26074151).<ref>PMID:24599311</ref> <ref>PMID:26074151</ref>	+	[https://www.uniprot.org/uniprot/SUCPP_THETC SUCPP_THETC] Catalyzes the reversible phosphorolysis of sucrose 6(F)-phosphate into alpha-D-glucose 1-phosphate (Glc1P) and D-fructose 6-phosphate. May be involved in a new pathway for the degradation of sucrose, which could become phosphorylated on its fructose moiety during uptake via a PTS system. To a lesser extent, can also reversibly act on sucrose in vitro (PubMed:24599311). Is also able to catalyze transglycosylation reactions in vitro (PubMed:26074151).<ref>PMID:24599311</ref> <ref>PMID:26074151</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: Clostridium thermosaccharolyticum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Capra, N]]	+	[[Category: Thermoanaerobacterium thermosaccharolyticum DSM 571]]
-	[[Category: Desmet, T]]	+	[[Category: Capra N]]
-	[[Category: Franceus, J]]	+	[[Category: Desmet T]]
-	[[Category: Thunnissen~~, A M.W H]]~~	+	[[Category: Franceus J]]
-	~~[[Category: Glycoside hydrolase family gh13-18]]~~	+	[[Category: Thunnissen AMWH]]
-	~~[[Category: Glycoside phosphorylase]]~~	+
-	~~[[Category: Sucrose 6-phosphate]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:34, 30 September 2020

2020-09-30T07:34:21Z

←Older revision		Revision as of 07:34, 30 September 2020
Line 3:		Line 3:
	<StructureSection load='6s9v' size='340' side='right'caption='[[6s9v]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='6s9v' size='340' side='right'caption='[[6s9v]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6s9v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S9V OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6S9V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6s9v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermosaccharolyticum Clostridium thermosaccharolyticum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S9V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6S9V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">spp, Tthe_1921 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=580327 Clostridium thermosaccharolyticum])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sucrose_6(F)-phosphate_phosphorylase Sucrose 6(F)-phosphate phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.329 2.4.1.329] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sucrose_6(F)-phosphate_phosphorylase Sucrose 6(F)-phosphate phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.329 2.4.1.329] </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=6s9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s9v OCA], [http://pdbe.org/6s9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6s9v RCSB], [http://www.ebi.ac.uk/pdbsum/6s9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6s9v 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=6s9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s9v OCA], [http://pdbe.org/6s9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6s9v RCSB], [http://www.ebi.ac.uk/pdbsum/6s9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6s9v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Clostridium thermosaccharolyticum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Capra, N]]		[[Category: Capra, N]]

OCA at 15:43, 28 August 2019

2019-08-28T15:43:39Z

←Older revision		Revision as of 15:43, 28 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6s9v is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of sucrose 6F-phosphate phosphorylase from Thermoanaerobacter thermosaccharolyticum==
		+	<StructureSection load='6s9v' size='340' side='right'caption='[[6s9v]], [[Resolution\|resolution]] 1.83Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6s9v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S9V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6S9V FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sucrose_6(F)-phosphate_phosphorylase Sucrose 6(F)-phosphate phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.329 2.4.1.329] </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=6s9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s9v OCA], [http://pdbe.org/6s9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6s9v RCSB], [http://www.ebi.ac.uk/pdbsum/6s9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6s9v ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SUCPP_THETC SUCPP_THETC]] Catalyzes the reversible phosphorolysis of sucrose 6(F)-phosphate into alpha-D-glucose 1-phosphate (Glc1P) and D-fructose 6-phosphate. May be involved in a new pathway for the degradation of sucrose, which could become phosphorylated on its fructose moiety during uptake via a PTS system. To a lesser extent, can also reversibly act on sucrose in vitro (PubMed:24599311). Is also able to catalyze transglycosylation reactions in vitro (PubMed:26074151).<ref>PMID:24599311</ref> <ref>PMID:26074151</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In family GH13 of the carbohydrate-active enzyme database, subfamily 18 contains glycoside phosphorylases that act on alpha-sugars and glucosides. Because their phosphorolysis reactions are effectively reversible, these enzymes are of interest for the biocatalytic synthesis of various glycosidic compounds. Sucrose 6(F)-phosphate phosphorylases (SPPs) constitute one of the known substrate specificities. Here, we report the characterization of an SPP from Ilumatobacter coccineus with a far stricter specificity than the previously described promiscuous SPP from Thermoanaerobacterium thermosaccharolyticum. Crystal structures of both SPPs were determined to provide insight into their similarities and differences. The residues responsible for binding the fructose 6-phosphate group in subsite +1 were found to differ considerably between the two enzymes. Furthermore, several variants that introduce a higher degree of substrate promiscuity in the strict SPP from I. coccineus were designed. These results contribute to an expanded structural knowledge of enzymes in subfamily GH13_18 and facilitate their rational engineering.

-	~~Authors: Capra, N~~., Franceus, J., ~~Desmet~~, T., Thunnissen~~, A~~.M.W.H.	+	Structural Comparison of a Promiscuous and a Highly Specific Sucrose 6(F)-Phosphate Phosphorylase.,Franceus J, Capra N, Desmet T, Thunnissen AWH Int J Mol Sci. 2019 Aug 11;20(16). pii: ijms20163906. doi: 10.3390/ijms20163906. PMID:31405215<ref>PMID:31405215</ref>

-	~~Description: Crystal structure~~ of ~~sucrose 6F~~-~~phosphate phosphorylase from Thermoanaerobacter thermosaccharolyticum~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6s9v" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Capra, N]]		[[Category: Capra, N]]
-	[[Category: Franceus, J]]
	[[Category: Desmet, T]]		[[Category: Desmet, T]]
-	[[Category: Thunnissen, A.M.W.H]]	+	[[Category: Franceus, J]]
		+	[[Category: Thunnissen, A M.W H]]
		+	[[Category: Glycoside hydrolase family gh13-18]]
		+	[[Category: Glycoside phosphorylase]]
		+	[[Category: Sucrose 6-phosphate]]
		+	[[Category: Transferase]]

OCA at 04:16, 21 August 2019

2019-08-21T04:16:00Z

←Older revision		Revision as of 04:16, 21 August 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6s9v is ON HOLD	+	The entry 6s9v is ON HOLD until Paper Publication

	Authors: Capra, N., Franceus, J., Desmet, T., Thunnissen, A.M.W.H.		Authors: Capra, N., Franceus, J., Desmet, T., Thunnissen, A.M.W.H.

-	Description: Crystal structure of sucrose 6-phosphate phosphorylase from Thermoanaerobacter thermosaccharolyticum	+	Description: Crystal structure of sucrose 6F-phosphate phosphorylase from Thermoanaerobacter thermosaccharolyticum
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Franceus, J]]
-	[[Category: Thunnissen, A.M.W.H]]
	[[Category: Capra, N]]		[[Category: Capra, N]]
		+	[[Category: Franceus, J]]
	[[Category: Desmet, T]]		[[Category: Desmet, T]]
		+	[[Category: Thunnissen, A.M.W.H]]

OCA: Protected "6s9v" [edit=sysop:move=sysop]

2019-07-24T04:42:33Z

Protected "6s9v" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:42, 24 July 2019

OCA: New page: '''Unreleased structure''' The entry 6s9v is ON HOLD Authors: Capra, N., Franceus, J., Desmet, T., Thunnissen, A.M.W.H. Description: Crystal structure of sucrose 6-phosphate phosphoryl...

2019-07-24T04:42:31Z

New page: '''Unreleased structure''' The entry 6s9v is ON HOLD Authors: Capra, N., Franceus, J., Desmet, T., Thunnissen, A.M.W.H. Description: Crystal structure of sucrose 6-phosphate phosphoryl...

New page

'''Unreleased structure'''

The entry 6s9v is ON HOLD

Authors: Capra, N., Franceus, J., Desmet, T., Thunnissen, A.M.W.H.

Description: Crystal structure of sucrose 6-phosphate phosphorylase from Thermoanaerobacter thermosaccharolyticum
[[Category: Unreleased Structures]]
[[Category: Franceus, J]]
[[Category: Thunnissen, A.M.W.H]]
[[Category: Capra, N]]
[[Category: Desmet, T]]