3qxg - Revision history

OCA at 12:02, 14 March 2024

OCA — Thu, 14 Mar 2024 12:02:16 GMT

←Older revision		Revision as of 12:02, 14 March 2024
Line 1:		Line 1:

	==Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation==		==Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation==
-	<StructureSection load='3qxg' size='340' side='right'caption='[[3qxg]]' scene=''>	+	<StructureSection load='3qxg' size='340' side='right'caption='[[3qxg]], [[Resolution\|resolution]] 1.24Å' 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=3QXG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QXG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qxg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QXG 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=3qxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxg OCA], [https://pdbe.org/3qxg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qxg RCSB], [https://www.ebi.ac.uk/pdbsum/3qxg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxg ProSAT]</span></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]] 1.24Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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=3qxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxg OCA], [https://pdbe.org/3qxg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qxg RCSB], [https://www.ebi.ac.uk/pdbsum/3qxg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8A5V9_BACTN Q8A5V9_BACTN]

	==See Also==		==See Also==
Line 11:		Line 15:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacteroides thetaiotaomicron]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Almo SC]]		[[Category: Almo SC]]

OCA at 05:40, 15 June 2022

OCA — Wed, 15 Jun 2022 05:40:25 GMT

←Older revision		Revision as of 05:40, 15 June 2022
Line 1:		Line 1:

	==Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation==		==Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation==
-	<StructureSection load='3qxg' size='340' side='right' caption='[[3qxg]]~~, [[Resolution\|resolution]] 1.24Å~~' scene=''>	+	<StructureSection load='3qxg' size='340' side='right'caption='[[3qxg]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[3qxg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_thetaiotaomicron"_distaso_1912 "bacillus thetaiotaomicron" distaso 1912].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3QXG FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QXG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>	+	</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=3qxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxg OCA], [https://pdbe.org/3qxg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qxg RCSB], [https://www.ebi.ac.uk/pdbsum/3qxg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxg ProSAT]</span></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qu2\|3qu2]], [[3qu4\|3qu4]], [[3qu5\|3qu5]], [[3qu7\|3qu7]], [[3qu9\|3qu9]], [[3qub\|3qub]], [[3quc\|3quc]], [[3quq\|3quq]], [[3qut\|3qut]], [[3qyp\|3qyp]], [[3qx7\|3qx7]], [[3r9k\|3r9k]]</td></tr>	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_2127 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=818 "Bacillus thetaiotaomicron" Distaso 1912])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </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=3qxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxg OCA], [~~http~~://pdbe.org/3qxg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3qxg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3qxg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxg ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The explosion of protein sequence information requires that current strategies for function assignment evolve to complement experimental approaches with computationally based function prediction. This necessitates the development of strategies based on the identification of sequence markers in the form of specificity determinants and a more informed definition of orthologues. Herein, we have undertaken the function assignment of the unknown haloalkanoate dehalogenase superfamily member BT2127 (Uniprot accession code Q8A5 V9) from Bacteroides thetaiotaomicron using an integrated bioinformatics-structure-mechanism approach. The substrate specificity profile and steady-state rate constants of BT2127 (with a k(cat)/K(m) value for pyrophosphate of ~1 x 10(5) M(-1) s(-1)), together with the gene context, support the assigned in vivo function as an inorganic pyrophosphatase. The X-ray structural analysis of wild-type BT2127 and several variants generated by site-directed mutagenesis shows that substrate discrimination is based, in part, on active site space restrictions imposed by the cap domain (specifically by residues Tyr76 and Glu47). Structure-guided site-directed mutagenesis coupled with kinetic analysis of the mutant enzymes identified the residues required for catalysis, substrate binding, and domain-domain association. On the basis of this structure-function analysis, the catalytic residues Asp11, Asp13, Thr113, and Lys147 as well the metal binding residues Asp171, Asn172, and Glu47 were used as markers to confirm BT2127 orthologues identified via sequence searches. This bioinformatic analysis demonstrated that the biological range of BT2127 orthologue is restricted to the phylum Bacteroidetes/Chlorobi. The key structural determinants in the divergence of BT2127 and its closest homologue, beta-phosphoglucomutase, control the leaving group size (phosphate vs glucose phosphate) and the position of the Asp acid/base in the open versus closed conformations. HADSF pyrophosphatases represent a third mechanistic and fold type for bacterial pyrophosphatases.
-
-	Divergence of structure and function in the haloacid dehalogenase enzyme superfamily: Bacteroides thetaiotaomicron BT2127 is an inorganic pyrophosphatase.,Huang H, Patskovsky Y, Toro R, Farelli JD, Pandya C, Almo SC, Allen KN, Dunaway-Mariano D Biochemistry. 2011 Oct 18;50(41):8937-49. Epub 2011 Sep 21. PMID:21894910<ref>PMID:21894910</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3qxg" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]	+	*[[Inorganic pyrophosphatase 3D structures\|Inorganic pyrophosphatase 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus thetaiotaomicron distaso 1912]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Inorganic diphosphatase~~]]	+	[[Category: Almo SC]]
-	[[Category: Almo~~, S C~~]]	+	[[Category: Burley SK]]
-	[[Category: Burley~~, S K~~]]	+	[[Category: Dunaway-Mariano D]]
-	[[Category: Dunaway-Mariano, D]]	+	[[Category: Gerlt JA]]
-	~~[[Category: EFI, Enzyme Function Initiative~~]]	+	[[Category: Huang H]]
-	[[Category: Gerlt~~, J A~~]]	+	[[Category: Patskovsky Y]]
-	[[Category: Huang, H]]	+	[[Category: Toro R]]
-	~~[[Category: Structural genomic~~]]	+
-	[[Category: Patskovsky, Y]]	+
-	[[Category: Toro, R]]	+
-	~~[[Category: Efi]]~~	+
-	~~[[Category: Enzyme function initiative]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Magnesium binding site]]~~	+
-	~~[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Pyrophosphatase~~]]	+

OCA at 10:14, 11 August 2016

OCA — Thu, 11 Aug 2016 10:14:14 GMT

←Older revision		Revision as of 10:14, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation==		==Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation==
	<StructureSection load='3qxg' size='340' side='right' caption='[[3qxg]], [[Resolution\|resolution]] 1.24Å' scene=''>		<StructureSection load='3qxg' size='340' side='right' caption='[[3qxg]], [[Resolution\|resolution]] 1.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3qxg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacteroides_thetaiotaomicron Bacteroides~~ thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3qxg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_thetaiotaomicron"_distaso_1912 "bacillus thetaiotaomicron" distaso 1912]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qu2\|3qu2]], [[3qu4\|3qu4]], [[3qu5\|3qu5]], [[3qu7\|3qu7]], [[3qu9\|3qu9]], [[3qub\|3qub]], [[3quc\|3quc]], [[3quq\|3quq]], [[3qut\|3qut]], [[3qyp\|3qyp]], [[3qx7\|3qx7]], [[3r9k\|3r9k]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qu2\|3qu2]], [[3qu4\|3qu4]], [[3qu5\|3qu5]], [[3qu7\|3qu7]], [[3qu9\|3qu9]], [[3qub\|3qub]], [[3quc\|3quc]], [[3quq\|3quq]], [[3qut\|3qut]], [[3qyp\|3qyp]], [[3qx7\|3qx7]], [[3r9k\|3r9k]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_2127 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=818 ~~Bacteroides~~ thetaiotaomicron])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_2127 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=818 "Bacillus thetaiotaomicron" Distaso 1912])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </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=3qxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxg RCSB], [http://www.ebi.ac.uk/pdbsum/3qxg 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=3qxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxg OCA], [http://pdbe.org/3qxg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qxg RCSB], [http://www.ebi.ac.uk/pdbsum/3qxg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxg ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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 3qxg" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacteroides~~ thetaiotaomicron]]	+	[[Category: Bacillus thetaiotaomicron distaso 1912]]
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]

OCA at 13:31, 6 November 2014

OCA — Thu, 06 Nov 2014 13:31:24 GMT

←Older revision		Revision as of 13:31, 6 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3qxg.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation==
		+	<StructureSection load='3qxg' size='340' side='right' caption='[[3qxg]], [[Resolution\|resolution]] 1.24Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3qxg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXG FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qu2\|3qu2]], [[3qu4\|3qu4]], [[3qu5\|3qu5]], [[3qu7\|3qu7]], [[3qu9\|3qu9]], [[3qub\|3qub]], [[3quc\|3quc]], [[3quq\|3quq]], [[3qut\|3qut]], [[3qyp\|3qyp]], [[3qx7\|3qx7]], [[3r9k\|3r9k]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BT_2127 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=818 Bacteroides thetaiotaomicron])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </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=3qxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qxg RCSB], [http://www.ebi.ac.uk/pdbsum/3qxg PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The explosion of protein sequence information requires that current strategies for function assignment evolve to complement experimental approaches with computationally based function prediction. This necessitates the development of strategies based on the identification of sequence markers in the form of specificity determinants and a more informed definition of orthologues. Herein, we have undertaken the function assignment of the unknown haloalkanoate dehalogenase superfamily member BT2127 (Uniprot accession code Q8A5 V9) from Bacteroides thetaiotaomicron using an integrated bioinformatics-structure-mechanism approach. The substrate specificity profile and steady-state rate constants of BT2127 (with a k(cat)/K(m) value for pyrophosphate of ~1 x 10(5) M(-1) s(-1)), together with the gene context, support the assigned in vivo function as an inorganic pyrophosphatase. The X-ray structural analysis of wild-type BT2127 and several variants generated by site-directed mutagenesis shows that substrate discrimination is based, in part, on active site space restrictions imposed by the cap domain (specifically by residues Tyr76 and Glu47). Structure-guided site-directed mutagenesis coupled with kinetic analysis of the mutant enzymes identified the residues required for catalysis, substrate binding, and domain-domain association. On the basis of this structure-function analysis, the catalytic residues Asp11, Asp13, Thr113, and Lys147 as well the metal binding residues Asp171, Asn172, and Glu47 were used as markers to confirm BT2127 orthologues identified via sequence searches. This bioinformatic analysis demonstrated that the biological range of BT2127 orthologue is restricted to the phylum Bacteroidetes/Chlorobi. The key structural determinants in the divergence of BT2127 and its closest homologue, beta-phosphoglucomutase, control the leaving group size (phosphate vs glucose phosphate) and the position of the Asp acid/base in the open versus closed conformations. HADSF pyrophosphatases represent a third mechanistic and fold type for bacterial pyrophosphatases.

-	~~{{STRUCTURE_3qxg\| PDB=3qxg \| SCENE= }}~~	+	Divergence of structure and function in the haloacid dehalogenase enzyme superfamily: Bacteroides thetaiotaomicron BT2127 is an inorganic pyrophosphatase.,Huang H, Patskovsky Y, Toro R, Farelli JD, Pandya C, Almo SC, Allen KN, Dunaway-Mariano D Biochemistry. 2011 Oct 18;50(41):8937-49. Epub 2011 Sep 21. PMID:21894910<ref>PMID:21894910</ref>

-	~~===Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium~~, a ~~closed cap conformation===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_21894910}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3qxg]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3QXG OCA].~~	+

	==See Also==		==See Also==
	*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]		*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:021894910<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bacteroides thetaiotaomicron]]		[[Category: Bacteroides thetaiotaomicron]]
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
-	[[Category: Almo, S C.]]	+	[[Category: Almo, S C]]
-	[[Category: Burley, S K.]]	+	[[Category: Burley, S K]]
-	[[Category: Dunaway-Mariano, D.]]	+	[[Category: Dunaway-Mariano, D]]
-	[[Category: EFI, Enzyme Function Initiative.]]	+	[[Category: EFI, Enzyme Function Initiative]]
-	[[Category: Gerlt, J A.]]	+	[[Category: Gerlt, J A]]
-	[[Category: Huang, H.]]	+	[[Category: Huang, H]]
-	[[Category: ~~NYSGXRC, New York SGX Research Center for~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Patskovsky, Y.]]	+	[[Category: Patskovsky, Y]]
-	[[Category: Toro, R.]]	+	[[Category: Toro, R]]
	[[Category: Efi]]		[[Category: Efi]]
	[[Category: Enzyme function initiative]]		[[Category: Enzyme function initiative]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Magnesium binding site]]		[[Category: Magnesium binding site]]
-	[[Category: New ~~york sgx research center~~ for ~~structural genomic]]~~	+	[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
-	~~[[Category: Nysgxrc~~]]	+	[[Category: PSI, Protein structure initiative]]
-	[[Category: Protein structure initiative]]	+
-	~~[[Category: Psi-2~~]]	+
	[[Category: Pyrophosphatase]]		[[Category: Pyrophosphatase]]

OCA at 19:05, 20 October 2012

OCA — Sat, 20 Oct 2012 19:05:05 GMT

←Older revision		Revision as of 19:05, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3qxg]] is a 2 chain structure ~~of [[Inorganic pyrophosphatase]]~~ with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXG OCA].	+	[[3qxg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXG OCA].

	==See Also==		==See Also==

OCA at 06:13, 27 July 2012

OCA — Fri, 27 Jul 2012 06:13:53 GMT

←Older revision		Revision as of 06:13, 27 July 2012
Line 1:		Line 1:
	[[Image:3qxg.png\|left\|200px]]		[[Image:3qxg.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3qxg", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3qxg\| PDB=3qxg \| SCENE= }}		{{STRUCTURE_3qxg\| PDB=3qxg \| SCENE= }}

	===Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation===		===Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21894910}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21894910 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_21894910}}		{{ABSTRACT_PUBMED_21894910}}

	==About this Structure==		==About this Structure==
-	[[3qxg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXG OCA].	+	[[3qxg]] is a 2 chain structure of [[Inorganic pyrophosphatase]] with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXG OCA].
		+
		+	==See Also==
		+	*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]

	==Reference==		==Reference==

OCA at 10:31, 16 November 2011

OCA — Wed, 16 Nov 2011 10:31:22 GMT

←Older revision		Revision as of 10:31, 16 November 2011
Line 1:		Line 1:
-	[[Image:3qxg.~~jpg~~\|left\|200px]]	+	[[Image:3qxg.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation===		===Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21894910}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21894910 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21894910}}

	==About this Structure==		==About this Structure==
	[[3qxg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXG OCA].		[[3qxg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXG OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021894910</ref><references group="xtra"/>
	[[Category: Bacteroides thetaiotaomicron]]		[[Category: Bacteroides thetaiotaomicron]]
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
Line 25:		Line 34:
	[[Category: Patskovsky, Y.]]		[[Category: Patskovsky, Y.]]
	[[Category: Toro, R.]]		[[Category: Toro, R.]]
		+	[[Category: Efi]]
		+	[[Category: Enzyme function initiative]]
		+	[[Category: Hydrolase]]
		+	[[Category: Magnesium binding site]]
		+	[[Category: New york sgx research center for structural genomic]]
		+	[[Category: Nysgxrc]]
		+	[[Category: Protein structure initiative]]
		+	[[Category: Psi-2]]
		+	[[Category: Pyrophosphatase]]

OCA at 07:29, 27 April 2011

OCA — Wed, 27 Apr 2011 07:29:36 GMT

←Older revision		Revision as of 07:29, 27 April 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3qxg.jpg\|left\|200px]]

-	The ~~entry 3qxg~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3qxg", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3qxg\| PDB=3qxg \| SCENE= }}

-	~~Authors: Patskovsky~~, ~~Y., Huang, H., Toro, R., Gerlt, J.A., Burley, S.K., Dunaway-Mariano, D., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)~~	+	===Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation===

-	~~Description: Crystal~~ structure ~~of pyrophosphatase~~ from ~~bacteroides~~ thetaiotaomicron ~~complexed with calcium~~, ~~a closed cap conformation~~	+
		+	==About this Structure==
		+	[[3qxg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXG OCA].
		+	[[Category: Bacteroides thetaiotaomicron]]
		+	[[Category: Inorganic diphosphatase]]
		+	[[Category: Almo, S C.]]
		+	[[Category: Burley, S K.]]
		+	[[Category: Dunaway-Mariano, D.]]
		+	[[Category: EFI, Enzyme Function Initiative.]]
		+	[[Category: Gerlt, J A.]]
		+	[[Category: Huang, H.]]
		+	[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics.]]
		+	[[Category: Patskovsky, Y.]]
		+	[[Category: Toro, R.]]

OCA at 08:05, 16 March 2011

OCA — Wed, 16 Mar 2011 08:05:02 GMT

←Older revision		Revision as of 08:05, 16 March 2011
Line 3:		Line 3:
	The entry 3qxg is ON HOLD		The entry 3qxg is ON HOLD

-	Authors: Patskovsky, Y., Huang, H., Toro, R., Gerlt, J.A., Burley, S.K., Dunaway-Mariano, D., Almo, S.C., New York ~~Sgx~~ Research Center for Structural Genomics ~~(Nysgxrc), New York Structural GenomiX Research Consortium~~ (NYSGXRC)	+	Authors: Patskovsky, Y., Huang, H., Toro, R., Gerlt, J.A., Burley, S.K., Dunaway-Mariano, D., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

-	Description: ~~CRYSTAL STRUCTURE OF PYROPHOSPHATASE FROM BACTEROIDES THETAIOTAOMICRON COMPLEXED WITH CALCIUM~~, ~~A CLOSED CAP CONFORMATION~~	+	Description: Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation

OCA: Protected "3qxg" [edit=sysop:move=sysop]

OCA — Wed, 09 Mar 2011 06:10:02 GMT

Protected "3qxg" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:10, 9 March 2011