5xxm - Revision history

OCA at 10:20, 27 March 2024

OCA — Wed, 27 Mar 2024 10:20:51 GMT

←Older revision		Revision as of 10:20, 27 March 2024
Line 1:		Line 1:

	==Crystal structure of GH3 beta-glucosidase from Bacteroides thetaiotaomicron in complex with gluconolactone==		==Crystal structure of GH3 beta-glucosidase from Bacteroides thetaiotaomicron in complex with gluconolactone==
-	<StructureSection load='5xxm' size='340' side='right' caption='[[5xxm]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5xxm' size='340' side='right'caption='[[5xxm]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xxm]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bactn Bactn~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XXM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XXM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xxm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XXM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LGC:(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE'>LGC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 1.7Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_3567 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LGC:(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE'>LGC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></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=5xxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xxm OCA], [~~http~~://pdbe.org/5xxm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xxm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xxm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xxm 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=5xxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xxm OCA], [https://pdbe.org/5xxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xxm RCSB], [https://www.ebi.ac.uk/pdbsum/5xxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xxm ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q8A1U1_BACTN Q8A1U1_BACTN]
-	~~BT_3567 protein, a putative beta-glucosidase from Bacteroides thetaiotaomicron, exhibits higher activity toward Sop3-5 (Sopn , n~~: degree of polymerization of beta-1,2-glucooligosaccharides) than toward Sop2 , unlike a known beta-glucosidase from Listeria innocua which predominantly prefers Sop2 . In the complex structure determined by soaking of a D286N mutant crystal with Sop4 , a Sop3 moiety was observed at subsites -1 to +2. The glucose moiety at subsite +2 forms a hydrogen bond with Asn81, which is replaced with Gly in the L. innocua beta-glucosidase. ~~The Km values of the N81G mutant for Sop3-5 are much higher than those of the wild-type, suggesting that Asn81 contributes to the binding to substrates longer than Sop3~~ .	+

-	Function and structure relationships of a beta-1,2-glucooligosaccharide-degrading beta-glucosidase.,Ishiguro R, Tanaka N, Abe K, Nakajima M, Maeda T, Miyanaga A, Takahashi Y, Sugimoto N, Nakai H, Taguchi H FEBS Lett. 2017 Dec;591(23):3926-3936. doi: 10.1002/1873-3468.12911. Epub 2017, Nov 24. PMID:29131329<ref>PMID:29131329</ref>	+	==See Also==
-		+	*[[Beta-glucosidase 3D structures\|Beta-glucosidase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 5xxm" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bactn~~]]	+	[[Category: Bacteroides thetaiotaomicron VPI-5482]]
-	[[Category: Abe, K]]	+	[[Category: Large Structures]]
-	[[Category: Ishiguro, R]]	+	[[Category: Abe K]]
-	[[Category: Maeda, T]]	+	[[Category: Ishiguro R]]
-	[[Category: Miyanaga, A]]	+	[[Category: Maeda T]]
-	[[Category: Nakai, H]]	+	[[Category: Miyanaga A]]
-	[[Category: Nakajima, M]]	+	[[Category: Nakai H]]
-	[[Category: Sugimoto, N]]	+	[[Category: Nakajima M]]
-	[[Category: Taguchi, H]]	+	[[Category: Sugimoto N]]
-	[[Category: Takahash, Y]]	+	[[Category: Taguchi H]]
-	[[Category: Tanaka, N]]	+	[[Category: Takahash Y]]
-	~~[[Category: Beta-glucosidase]]~~	+	[[Category: Tanaka N]]
-	~~[[Category: Glycoside hydrolase family 3]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 08:58, 27 December 2017

OCA — Wed, 27 Dec 2017 08:58:13 GMT

←Older revision		Revision as of 08:58, 27 December 2017
Line 3:		Line 3:
	<StructureSection load='5xxm' size='340' side='right' caption='[[5xxm]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5xxm' size='340' side='right' caption='[[5xxm]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xxm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XXM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xxm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bactn Bactn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XXM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LGC:(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE'>LGC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LGC:(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE'>LGC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_3567 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])</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=5xxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xxm OCA], [http://pdbe.org/5xxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xxm RCSB], [http://www.ebi.ac.uk/pdbsum/5xxm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xxm 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=5xxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xxm OCA], [http://pdbe.org/5xxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xxm RCSB], [http://www.ebi.ac.uk/pdbsum/5xxm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xxm ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bactn]]
	[[Category: Abe, K]]		[[Category: Abe, K]]
	[[Category: Ishiguro, R]]		[[Category: Ishiguro, R]]

OCA at 07:01, 13 December 2017

OCA — Wed, 13 Dec 2017 07:01:18 GMT

←Older revision		Revision as of 07:01, 13 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xxm is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of GH3 beta-glucosidase from Bacteroides thetaiotaomicron in complex with gluconolactone==
		+	<StructureSection load='5xxm' size='340' side='right' caption='[[5xxm]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xxm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XXM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LGC:(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE'>LGC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></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=5xxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xxm OCA], [http://pdbe.org/5xxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xxm RCSB], [http://www.ebi.ac.uk/pdbsum/5xxm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xxm ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BT_3567 protein, a putative beta-glucosidase from Bacteroides thetaiotaomicron, exhibits higher activity toward Sop3-5 (Sopn , n: degree of polymerization of beta-1,2-glucooligosaccharides) than toward Sop2 , unlike a known beta-glucosidase from Listeria innocua which predominantly prefers Sop2 . In the complex structure determined by soaking of a D286N mutant crystal with Sop4 , a Sop3 moiety was observed at subsites -1 to +2. The glucose moiety at subsite +2 forms a hydrogen bond with Asn81, which is replaced with Gly in the L. innocua beta-glucosidase. The Km values of the N81G mutant for Sop3-5 are much higher than those of the wild-type, suggesting that Asn81 contributes to the binding to substrates longer than Sop3 .

-	~~Authors: Nakajima~~, M., Ishiguro, R., Tanaka, N., Abe, K., Maeda, T., Miyanaga, A~~., Takahash~~, Y., Sugimoto, N., Nakai, H., Taguchi, H.	+	Function and structure relationships of a beta-1,2-glucooligosaccharide-degrading beta-glucosidase.,Ishiguro R, Tanaka N, Abe K, Nakajima M, Maeda T, Miyanaga A, Takahashi Y, Sugimoto N, Nakai H, Taguchi H FEBS Lett. 2017 Dec;591(23):3926-3936. doi: 10.1002/1873-3468.12911. Epub 2017, Nov 24. PMID:29131329<ref>PMID:29131329</ref>

-	~~Description: Crystal structure~~ of ~~GH3 beta~~-~~glucosidase from Bacteroides thetaiotaomicron in complex with gluconolactone~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5xxm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Abe, K]]
		+	[[Category: Ishiguro, R]]
		+	[[Category: Maeda, T]]
		+	[[Category: Miyanaga, A]]
	[[Category: Nakai, H]]		[[Category: Nakai, H]]
	[[Category: Nakajima, M]]		[[Category: Nakajima, M]]
-	[[Category: Taguchi, H]]
	[[Category: Sugimoto, N]]		[[Category: Sugimoto, N]]
-	[[Category: ~~Ishiguro~~, R]]	+	[[Category: Taguchi, H]]
	[[Category: Takahash, Y]]		[[Category: Takahash, Y]]
	[[Category: Tanaka, N]]		[[Category: Tanaka, N]]
-	[[Category: ~~Maeda, T~~]]	+	[[Category: Beta-glucosidase]]
-	[[Category: ~~Miyanaga, A~~]]	+	[[Category: Glycoside hydrolase family 3]]
-	[[Category: ~~Abe, K~~]]	+	[[Category: Hydrolase]]

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

OCA — Wed, 27 Sep 2017 15:53:35 GMT

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

←Older revision

Revision as of 15:53, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xxm is ON HOLD until Paper Publication Authors: Nakajima, M., Ishiguro, R., Tanaka, N., Abe, K., Maeda, T., Miyanaga, A., Takahash, Y., Sugimoto, N...

OCA — Wed, 27 Sep 2017 15:53:34 GMT

New page: '''Unreleased structure''' The entry 5xxm is ON HOLD until Paper Publication Authors: Nakajima, M., Ishiguro, R., Tanaka, N., Abe, K., Maeda, T., Miyanaga, A., Takahash, Y., Sugimoto, N...

New page

'''Unreleased structure'''

The entry 5xxm is ON HOLD until Paper Publication

Authors: Nakajima, M., Ishiguro, R., Tanaka, N., Abe, K., Maeda, T., Miyanaga, A., Takahash, Y., Sugimoto, N., Nakai, H., Taguchi, H.

Description: Crystal structure of GH3 beta-glucosidase from Bacteroides thetaiotaomicron in complex with gluconolactone
[[Category: Unreleased Structures]]
[[Category: Nakai, H]]
[[Category: Nakajima, M]]
[[Category: Taguchi, H]]
[[Category: Sugimoto, N]]
[[Category: Ishiguro, R]]
[[Category: Takahash, Y]]
[[Category: Tanaka, N]]
[[Category: Maeda, T]]
[[Category: Miyanaga, A]]
[[Category: Abe, K]]