6ld0 - Revision history

OCA at 10:57, 22 November 2023

2023-11-22T10:57:08Z

←Older revision		Revision as of 10:57, 22 November 2023
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	<StructureSection load='6ld0' size='340' side='right'caption='[[6ld0]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6ld0' size='340' side='right'caption='[[6ld0]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ld0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bifdb Bifdb~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LD0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ld0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_dentium_Bd1 Bifidobacterium dentium Bd1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LD0 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=E8X:(2~{S},3~{S},4~{R},5~{R})~~-~~2-hexyl-4~~,~~5-bis(oxidanyl)piperidine-3-carboxylic+acid'>E8X</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]] 1.901Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>lacZ1, BDP_2112 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=401473 BIFDB])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E8X:(2~{S},3~{S},4~{R},5~{R})-2-hexyl-4,5-bis(oxidanyl)piperidine-3-carboxylic+acid'>E8X</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~~-~~galactosidase Beta~~-~~galactosidase]~~, ~~with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=~~3~~.2.1.23 3.2.1.23]~~ </~~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=6ld0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ld0 OCA], [https://pdbe.org/6ld0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ld0 RCSB], [https://www.ebi.ac.uk/pdbsum/6ld0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ld0 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=6ld0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ld0 OCA], [https://pdbe.org/6ld0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ld0 RCSB], [https://www.ebi.ac.uk/pdbsum/6ld0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ld0 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D2Q7B1_BIFDB D2Q7B1_BIFDB]
	<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-galactosidase]]~~	+	[[Category: Bifidobacterium dentium Bd1]]
-	~~[[Category: Bifdb~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hsieh, T J]]	+	[[Category: Hsieh T-J]]
-	[[Category: Lin, C H]]	+	[[Category: Lin C-H]]
-	[[Category: Lin, H Y]]	+	[[Category: Lin H-Y]]
-	~~[[Category: Carbohydrate]]~~	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Inhibitor~~]]	+

OCA at 06:11, 11 August 2021

2021-08-11T06:11:39Z

←Older revision		Revision as of 06:11, 11 August 2021
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	==Structure of Bifidobacterium dentium beta-glucuronidase complexed with C6-hexyl uronic isofagomine==		==Structure of Bifidobacterium dentium beta-glucuronidase complexed with C6-hexyl uronic isofagomine==
-	<StructureSection load='6ld0' size='340' side='right'caption='[[6ld0]]' scene=''>	+	<StructureSection load='6ld0' size='340' side='right'caption='[[6ld0]], [[Resolution\|resolution]] 1.90Å' 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=6LD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LD0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ld0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifdb Bifdb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LD0 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=6ld0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ld0 OCA], [https://pdbe.org/6ld0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ld0 RCSB], [https://www.ebi.ac.uk/pdbsum/6ld0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ld0 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=E8X:(2~{S},3~{S},4~{R},5~{R})-2-hexyl-4,5-bis(oxidanyl)piperidine-3-carboxylic+acid'>E8X</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lacZ1, BDP_2112 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=401473 BIFDB])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </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=6ld0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ld0 OCA], [https://pdbe.org/6ld0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ld0 RCSB], [https://www.ebi.ac.uk/pdbsum/6ld0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ld0 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Irinotecan inhibits cell proliferation and thus is used for the primary treatment of colorectal cancer. Metabolism of irinotecan involves incorporation of beta-glucuronic acid to facilitate excretion. During transit of the glucuronidated product through the gastrointestinal tract, an induced upregulation of gut microbial beta-glucuronidase (GUS) activity may cause severe diarrhea and thus force many patients to stop treatment. We herein report the development of uronic isofagomine (UIFG) derivatives that act as general, potent inhibitors of bacterial GUSs, especially those of Escherichia coli and Clostridium perfringens. The best inhibitor, C6-nonyl UIFG, is 23,300-fold more selective for E. coli GUS than for human GUS (Ki = 0.0045 and 105 muM, respectively). Structural evidence indicated that the loss of coordinated water molecules, with the consequent increase in entropy, contributes to the high affinity and selectivity for bacterial GUSs. The inhibitors also effectively reduced irinotecan-induced diarrhea in mice without damaging intestinal epithelial cells.
		+
		+	Entropy-driven binding of gut bacterial beta-glucuronidase inhibitors ameliorates irinotecan-induced toxicity.,Lin HY, Chen CY, Lin TC, Yeh LF, Hsieh WC, Gao S, Burnouf PA, Chen BM, Hsieh TJ, Dashnyam P, Kuo YH, Tu Z, Roffler SR, Lin CH Commun Biol. 2021 Mar 4;4(1):280. doi: 10.1038/s42003-021-01815-w. PMID:33664385<ref>PMID:33664385</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ld0" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Beta-galactosidase]]
		+	[[Category: Bifdb]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hsieh T-J]]	+	[[Category: Hsieh, T J]]
-	[[Category: Lin C-H]]	+	[[Category: Lin, C H]]
-	[[Category: Lin H-Y]]	+	[[Category: Lin, H Y]]
		+	[[Category: Carbohydrate]]
		+	[[Category: Complex]]
		+	[[Category: Glycosidase]]
		+	[[Category: Inhibitor]]

OCA at 07:52, 27 January 2021

2021-01-27T07:52:08Z

←Older revision		Revision as of 07:52, 27 January 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6ld0 is ~~ON HOLD until Jan 20 2022~~	+	==Structure of Bifidobacterium dentium beta-glucuronidase complexed with C6-hexyl uronic isofagomine==
-		+	<StructureSection load='6ld0' size='340' side='right'caption='[[6ld0]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LD0 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=6ld0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ld0 OCA], [https://pdbe.org/6ld0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ld0 RCSB], [https://www.ebi.ac.uk/pdbsum/6ld0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ld0 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Hsieh T-J]]
		+	[[Category: Lin C-H]]
		+	[[Category: Lin H-Y]]

OCA at 05:06, 25 November 2020

2020-11-25T05:06:54Z

←Older revision		Revision as of 05:06, 25 November 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ld0 is ON HOLD until ~~Paper Publication~~	+	The entry 6ld0 is ON HOLD until Jan 20 2022

	Authors:		Authors:

OCA at 05:36, 18 December 2019

2019-12-18T05:36:55Z

←Older revision		Revision as of 05:36, 18 December 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ld0 is ON HOLD	+	The entry 6ld0 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6ld0" [edit=sysop:move=sysop]

2019-11-27T05:07:58Z

Protected "6ld0" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:07, 27 November 2019

OCA: New page: '''Unreleased structure''' The entry 6ld0 is ON HOLD Authors: Description: Category: Unreleased Structures

2019-11-27T05:07:56Z

New page: '''Unreleased structure''' The entry 6ld0 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ld0 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]