4fdt - Revision history

OCA at 11:15, 1 March 2024

OCA — Fri, 01 Mar 2024 11:15:20 GMT

←Older revision		Revision as of 11:15, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4fdt]] 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=4FDT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FDT FirstGlance]. <br>		<table><tr><td colspan='2'>[[4fdt]] 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=4FDT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FDT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.93Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4fdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fdt OCA], [https://pdbe.org/4fdt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fdt RCSB], [https://www.ebi.ac.uk/pdbsum/4fdt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fdt 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=4fdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fdt OCA], [https://pdbe.org/4fdt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fdt RCSB], [https://www.ebi.ac.uk/pdbsum/4fdt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fdt ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q89YI8_BACTN Q89YI8_BACTN]		[https://www.uniprot.org/uniprot/Q89YI8_BACTN Q89YI8_BACTN]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Dietary InsP6 can modulate eukaryotic cell proliferation and has complex nutritive consequences, but its metabolism in the mammalian gastrointestinal tract is poorly understood. Therefore, we performed phylogenetic analyses of the gastrointestinal microbiome in order to search for candidate InsP6 phosphatases. We determined that prominent gut bacteria express homologs of the mammalian InsP6 phosphatase (MINPP) and characterized the enzyme from Bacteroides thetaiotaomicron (BtMinpp). We show that BtMinpp has exceptionally high catalytic activity, which we rationalize on the basis of mutagenesis studies and by determining its crystal structure at 1.9 A resolution. We demonstrate that BtMinpp is packaged inside outer membrane vesicles (OMVs) protecting the enzyme from degradation by gastrointestinal proteases. Moreover, we uncover an example of cross-kingdom cell-to-cell signaling, showing that the BtMinpp-OMVs interact with intestinal epithelial cells to promote intracellular Ca(2+) signaling. Our characterization of BtMinpp offers several directions for understanding how the microbiome serves human gastrointestinal physiology.
-
-	A Bacterial Homolog of a Eukaryotic Inositol Phosphate Signaling Enzyme Mediates Cross-kingdom Dialog in the Mammalian Gut.,Stentz R, Osborne S, Horn N, Li AW, Hautefort I, Bongaerts R, Rouyer M, Bailey P, Shears SB, Hemmings AM, Brearley CA, Carding SR Cell Rep. 2014 Feb 27;6(4):646-56. doi: 10.1016/j.celrep.2014.01.021. Epub 2014, Feb 13. PMID:24529702<ref>PMID:24529702</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4fdt" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 04:51, 7 October 2022

OCA — Fri, 07 Oct 2022 04:51:00 GMT

←Older revision		Revision as of 04:51, 7 October 2022
Line 1:		Line 1:

	==Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase==		==Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase==
-	<StructureSection load='4fdt' size='340' side='right' caption='[[4fdt]], [[Resolution\|resolution]] 1.93Å' scene=''>	+	<StructureSection load='4fdt' size='340' side='right'caption='[[4fdt]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4fdt]] 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=4FDT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4FDT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4fdt]] 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=4FDT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FDT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fdu\|4fdu]]</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=4fdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fdt OCA], [https://pdbe.org/4fdt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fdt RCSB], [https://www.ebi.ac.uk/pdbsum/4fdt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fdt ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_4744 ([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=4fdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fdt OCA], [~~http~~://pdbe.org/4fdt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4fdt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4fdt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4fdt ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q89YI8_BACTN Q89YI8_BACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bactn~~]]	+	[[Category: Bacteroides thetaiotaomicron VPI-5482]]
-	[[Category: ~~Hemmings, A M~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Li, A W.H~~]]	+	[[Category: Hemmings AM]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Li AWH]]
-	~~[[Category: Phosphatase~~]]	+

OCA at 12:19, 11 August 2016

OCA — Thu, 11 Aug 2016 12:19:00 GMT

←Older revision		Revision as of 12:19, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase==		==Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase==
	<StructureSection load='4fdt' size='340' side='right' caption='[[4fdt]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='4fdt' size='340' side='right' caption='[[4fdt]], [[Resolution\|resolution]] 1.93Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fdu\|4fdu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fdu\|4fdu]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_4744 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_4744 ([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=4fdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fdt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fdt RCSB], [http://www.ebi.ac.uk/pdbsum/4fdt 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=4fdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fdt OCA], [http://pdbe.org/4fdt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fdt RCSB], [http://www.ebi.ac.uk/pdbsum/4fdt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fdt ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4fdt" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:29, 4 January 2015

OCA — Sun, 04 Jan 2015 14:29:13 GMT

←Older revision		Revision as of 14:29, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4fdt\| PDB=4fdt \| SCENE= }}~~	+	==Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase==
-	===Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase===	+	<StructureSection load='4fdt' size='340' side='right' caption='[[4fdt]], [[Resolution\|resolution]] 1.93Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24529702}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4fdt]] 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=4FDT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FDT FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4fdu\|4fdu]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_4744 ([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=4fdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fdt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fdt RCSB], [http://www.ebi.ac.uk/pdbsum/4fdt PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Dietary InsP6 can modulate eukaryotic cell proliferation and has complex nutritive consequences, but its metabolism in the mammalian gastrointestinal tract is poorly understood. Therefore, we performed phylogenetic analyses of the gastrointestinal microbiome in order to search for candidate InsP6 phosphatases. We determined that prominent gut bacteria express homologs of the mammalian InsP6 phosphatase (MINPP) and characterized the enzyme from Bacteroides thetaiotaomicron (BtMinpp). We show that BtMinpp has exceptionally high catalytic activity, which we rationalize on the basis of mutagenesis studies and by determining its crystal structure at 1.9 A resolution. We demonstrate that BtMinpp is packaged inside outer membrane vesicles (OMVs) protecting the enzyme from degradation by gastrointestinal proteases. Moreover, we uncover an example of cross-kingdom cell-to-cell signaling, showing that the BtMinpp-OMVs interact with intestinal epithelial cells to promote intracellular Ca(2+) signaling. Our characterization of BtMinpp offers several directions for understanding how the microbiome serves human gastrointestinal physiology.

-	~~==About this Structure==~~	+	A Bacterial Homolog of a Eukaryotic Inositol Phosphate Signaling Enzyme Mediates Cross-kingdom Dialog in the Mammalian Gut.,Stentz R, Osborne S, Horn N, Li AW, Hautefort I, Bongaerts R, Rouyer M, Bailey P, Shears SB, Hemmings AM, Brearley CA, Carding SR Cell Rep. 2014 Feb 27;6(4):646-56. doi: 10.1016/j.celrep.2014.01.021. Epub 2014, Feb 13. PMID:24529702<ref>PMID:24529702</ref>
-	~~[[4fdt]] is~~ a ~~2 chain structure~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.~~il/oca-bin/ocashort?id=4FDT OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024529702</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Hemmings, A M.]]	+	== References ==
-	[[Category: Li, A W.H.]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bactn]]
		+	[[Category: Hemmings, A M]]
		+	[[Category: Li, A W.H]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Phosphatase]]		[[Category: Phosphatase]]

OCA at 13:45, 12 March 2014

OCA — Wed, 12 Mar 2014 13:45:11 GMT

←Older revision		Revision as of 13:45, 12 March 2014
Line 1:		Line 1:
	{{STRUCTURE_4fdt\| PDB=4fdt \| SCENE= }}		{{STRUCTURE_4fdt\| PDB=4fdt \| SCENE= }}
	===Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase===		===Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase===
		+	{{ABSTRACT_PUBMED_24529702}}

	==About this Structure==		==About this Structure==
	[[4fdt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FDT OCA].		[[4fdt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FDT OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:024529702</ref><references group="xtra"/><references/>
	[[Category: Hemmings, A M.]]		[[Category: Hemmings, A M.]]
	[[Category: Li, A W.H.]]		[[Category: Li, A W.H.]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Phosphatase]]		[[Category: Phosphatase]]

OCA at 07:44, 29 January 2014

OCA — Wed, 29 Jan 2014 07:44:32 GMT

←Older revision		Revision as of 07:44, 29 January 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4fdt\| PDB=4fdt \| SCENE= }}
		+	===Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase===

-	~~The entry~~ 4fdt is ~~ON HOLD until Jan 29 2015~~	+	==About this Structure==
-		+	[[4fdt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FDT OCA].
-	~~Authors~~: Li, A.W.H.~~, Hemmings, A.M.~~	+	[[Category: Hemmings, A M.]]
-		+	[[Category: Li, A W.H.]]
-	~~Description~~: ~~Crystal Structure of a Multiple Inositol Polyphosphate~~ Phosphatase	+	[[Category: Hydrolase]]
		+	[[Category: Phosphatase]]

OCA at 08:48, 8 January 2014

OCA — Wed, 08 Jan 2014 08:48:20 GMT

←Older revision		Revision as of 08:48, 8 January 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4fdt is ON HOLD until ~~Dec~~ 29 ~~2014~~	+	The entry 4fdt is ON HOLD until Jan 29 2015

	Authors: Li, A.W.H., Hemmings, A.M.		Authors: Li, A.W.H., Hemmings, A.M.

	Description: Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase		Description: Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase

OCA at 06:32, 4 December 2013

OCA — Wed, 04 Dec 2013 06:32:25 GMT

←Older revision		Revision as of 06:32, 4 December 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4fdt is ON HOLD until Dec 04 2014	+	The entry 4fdt is ON HOLD until Dec 29 2014

	Authors: Li, A.W.H., Hemmings, A.M.		Authors: Li, A.W.H., Hemmings, A.M.

	Description: Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase		Description: Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase

OCA at 09:21, 27 November 2013

OCA — Wed, 27 Nov 2013 09:21:22 GMT

←Older revision		Revision as of 09:21, 27 November 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4fdt is ON HOLD until ~~Nov 27~~ 2014	+	The entry 4fdt is ON HOLD until Dec 04 2014

	Authors: Li, A.W.H., Hemmings, A.M.		Authors: Li, A.W.H., Hemmings, A.M.

	Description: Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase		Description: Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase

OCA at 06:43, 16 May 2013

OCA — Thu, 16 May 2013 06:43:10 GMT

←Older revision		Revision as of 06:43, 16 May 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4fdt is ON HOLD until ~~Paper Publication~~	+	The entry 4fdt is ON HOLD until Nov 27 2014

	Authors: Li, A.W.H., Hemmings, A.M.		Authors: Li, A.W.H., Hemmings, A.M.

	Description: Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase		Description: Crystal Structure of a Multiple Inositol Polyphosphate Phosphatase