1wpn - Revision history

OCA at 13:33, 13 March 2024

OCA — Wed, 13 Mar 2024 13:33:26 GMT

←Older revision		Revision as of 13:33, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='1wpn' size='340' side='right'caption='[[1wpn]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='1wpn' size='340' side='right'caption='[[1wpn]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wpn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WPN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wpn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WPN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.3Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1wpm\|1wpm]], [[1wpp\|1wpp]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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~~'>~~[https://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=1wpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpn OCA], [https://pdbe.org/1wpn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wpn RCSB], [https://www.ebi.ac.uk/pdbsum/1wpn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wpn 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=1wpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpn OCA], [https://pdbe.org/1wpn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wpn RCSB], [https://www.ebi.ac.uk/pdbsum/1wpn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wpn ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PPAC_BACSU PPAC_BACSU]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1wpn ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1wpn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Family II inorganic pyrophosphatases (PPases) constitute a new evolutionary group of PPases, with a different fold and mechanism than the common family I enzyme; they are related to the "DHH" family of phosphoesterases. Biochemical studies have shown that Mn(2+) and Co(2+) preferentially activate family II PPases; Mg(2+) partially activates; and Zn(2+) can either activate or inhibit (Zyryanov et al., Biochemistry, 43, 14395-14402, accompanying paper in this issue). The three solved family II PPase structures did not explain the differences between the PPase families nor the metal ion differences described above. We therefore solved three new family II PPase structures: Bacillus subtilis PPase (Bs-PPase) dimer core bound to Mn(2+) at 1.3 A resolution, and, at 2.05 A resolution, metal-free Bs-PPase and Streptococcus gordonii (Sg-PPase) containing sulfate and Zn(2+). Comparison of the new and old structures of various family II PPases demonstrates why the family II enzyme prefers Mn(2+) or Co(2+), as an activator rather than Mg(2+). Both M1 and M2 undergo significant changes upon substrate binding, changing from five-coordinate to octahedral geometry. Mn(2+) and Co(2+), which readily adopt different coordination states and geometries, are thus favored. Combining our structures with biochemical data, we identified M2 as the high-affinity metal site. Zn(2+) activates in the M1 site, where octahedral geometry is not essential for catalysis, but inhibits in the M2 site, because it is unable to assume octahedral geometry but remains trigonal bipyramidal. Finally, we propose that Lys205-Gln81-Gln80 form a hydrophilic channel to speed product release from the active site.
-
-	Structural studies of metal ions in family II pyrophosphatases: the requirement for a Janus ion.,Fabrichniy IP, Lehtio L, Salminen A, Zyryanov AB, Baykov AA, Lahti R, Goldman A Biochemistry. 2004 Nov 16;43(45):14403-11. PMID:15533045<ref>PMID:15533045</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1wpn" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Inorganic pyrophosphatase 3D structures\|Inorganic pyrophosphatase 3D structures]]		*[[Inorganic pyrophosphatase 3D structures\|Inorganic pyrophosphatase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~globigii migula 1900]]~~	+	[[Category: Bacillus subtilis]]
-	~~[[Category: Inorganic diphosphatase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Baykov~~, A A~~]]	+	[[Category: Baykov AA]]
-	[[Category: Fabrichniy~~, I P~~]]	+	[[Category: Fabrichniy IP]]
-	[[Category: Goldman, A]]	+	[[Category: Goldman A]]
-	[[Category: Lahti, R]]	+	[[Category: Lahti R]]
-	[[Category: Lehtio, L]]	+	[[Category: Lehtio L]]
-	[[Category: Salminen, A]]	+	[[Category: Salminen A]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inorganic pyrophosphatase]]~~	+
-	~~[[Category: Metal binding~~]]	+

OCA at 09:04, 21 April 2021

OCA — Wed, 21 Apr 2021 09:04:13 GMT

←Older revision		Revision as of 09:04, 21 April 2021
Line 3:		Line 3:
	<StructureSection load='1wpn' size='340' side='right'caption='[[1wpn]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='1wpn' size='340' side='right'caption='[[1wpn]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wpn]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1WPN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wpn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WPN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wpm\|1wpm]], [[1wpp\|1wpp]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wpm\|1wpm]], [[1wpp\|1wpp]]</div></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'>[https://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [https://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=1wpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpn OCA], [~~http~~://pdbe.org/1wpn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1wpn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1wpn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1wpn 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=1wpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpn OCA], [https://pdbe.org/1wpn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wpn RCSB], [https://www.ebi.ac.uk/pdbsum/1wpn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wpn ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]	+	*[[Inorganic pyrophosphatase 3D structures\|Inorganic pyrophosphatase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:24, 17 July 2019

OCA — Wed, 17 Jul 2019 13:24:37 GMT

←Older revision		Revision as of 13:24, 17 July 2019
Line 1:		Line 1:

	==Crystal structure of the N-terminal core of Bacillus subtilis inorganic pyrophosphatase==		==Crystal structure of the N-terminal core of Bacillus subtilis inorganic pyrophosphatase==
-	<StructureSection load='1wpn' size='340' side='right' caption='[[1wpn]], [[Resolution\|resolution]] 1.30Å' scene=''>	+	<StructureSection load='1wpn' size='340' side='right'caption='[[1wpn]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wpn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WPN FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wpn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WPN FirstGlance]. <br>
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wp/1wpn_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wp/1wpn_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1wpn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1wpn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	[[Category: Bacillus globigii migula 1900]]		[[Category: Bacillus globigii migula 1900]]
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
		+	[[Category: Large Structures]]
	[[Category: Baykov, A A]]		[[Category: Baykov, A A]]
	[[Category: Fabrichniy, I P]]		[[Category: Fabrichniy, I P]]

OCA at 13:50, 12 October 2017

OCA — Thu, 12 Oct 2017 13:50:14 GMT

←Older revision		Revision as of 13:50, 12 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of the N-terminal core of Bacillus subtilis inorganic pyrophosphatase==		==Crystal structure of the N-terminal core of Bacillus subtilis inorganic pyrophosphatase==
	<StructureSection load='1wpn' size='340' side='right' caption='[[1wpn]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='1wpn' size='340' side='right' caption='[[1wpn]], [[Resolution\|resolution]] 1.30Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wpm\|1wpm]], [[1wpp\|1wpp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wpm\|1wpm]], [[1wpp\|1wpp]]</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=1wpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpn OCA], [http://pdbe.org/1wpn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wpn RCSB], [http://www.ebi.ac.uk/pdbsum/1wpn 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=1wpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpn OCA], [http://pdbe.org/1wpn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wpn RCSB], [http://www.ebi.ac.uk/pdbsum/1wpn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wpn ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1wpn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1wpn" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:17, 8 February 2016

OCA — Mon, 08 Feb 2016 06:17:55 GMT

←Older revision		Revision as of 06:17, 8 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1wpn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:43, 10 September 2015

OCA — Thu, 10 Sep 2015 08:43:04 GMT

←Older revision		Revision as of 08:43, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1wpn' size='340' side='right' caption='[[1wpn]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='1wpn' size='340' side='right' caption='[[1wpn]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wpn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_subtilis Bacillus subtilis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WPN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wpn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WPN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wpm\|1wpm]], [[1wpp\|1wpp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wpm\|1wpm]], [[1wpp\|1wpp]]</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=1wpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wpn RCSB], [http://www.ebi.ac.uk/pdbsum/1wpn 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=1wpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpn OCA], [http://pdbe.org/1wpn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wpn RCSB], [http://www.ebi.ac.uk/pdbsum/1wpn PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 1wpn" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
	[[Category: Baykov, A A]]		[[Category: Baykov, A A]]

OCA at 12:50, 6 January 2015

OCA — Tue, 06 Jan 2015 12:50:57 GMT

←Older revision		Revision as of 12:50, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wpn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WPN FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wpn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WPN FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wpm\|1wpm]], [[1wpp\|1wpp]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wpm\|1wpm]], [[1wpp\|1wpp]]</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wpn RCSB], [http://www.ebi.ac.uk/pdbsum/1wpn 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=1wpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wpn RCSB], [http://www.ebi.ac.uk/pdbsum/1wpn PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
-	[[Category: Baykov, A A.]]	+	[[Category: Baykov, A A]]
-	[[Category: Fabrichniy, I P.]]	+	[[Category: Fabrichniy, I P]]
-	[[Category: Goldman, A.]]	+	[[Category: Goldman, A]]
-	[[Category: Lahti, R.]]	+	[[Category: Lahti, R]]
-	[[Category: Lehtio, L.]]	+	[[Category: Lehtio, L]]
-	[[Category: Salminen, A.]]	+	[[Category: Salminen, A]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Inorganic pyrophosphatase]]		[[Category: Inorganic pyrophosphatase]]
	[[Category: Metal binding]]		[[Category: Metal binding]]

OCA at 23:27, 28 September 2014

OCA — Sun, 28 Sep 2014 23:27:16 GMT

←Older revision		Revision as of 23:27, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1wpn.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the N-terminal core of Bacillus subtilis inorganic pyrophosphatase==
		+	<StructureSection load='1wpn' size='340' side='right' caption='[[1wpn]], [[Resolution\|resolution]] 1.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1wpn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WPN FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wpm\|1wpm]], [[1wpp\|1wpp]]</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wpn RCSB], [http://www.ebi.ac.uk/pdbsum/1wpn PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wp/1wpn_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Family II inorganic pyrophosphatases (PPases) constitute a new evolutionary group of PPases, with a different fold and mechanism than the common family I enzyme; they are related to the "DHH" family of phosphoesterases. Biochemical studies have shown that Mn(2+) and Co(2+) preferentially activate family II PPases; Mg(2+) partially activates; and Zn(2+) can either activate or inhibit (Zyryanov et al., Biochemistry, 43, 14395-14402, accompanying paper in this issue). The three solved family II PPase structures did not explain the differences between the PPase families nor the metal ion differences described above. We therefore solved three new family II PPase structures: Bacillus subtilis PPase (Bs-PPase) dimer core bound to Mn(2+) at 1.3 A resolution, and, at 2.05 A resolution, metal-free Bs-PPase and Streptococcus gordonii (Sg-PPase) containing sulfate and Zn(2+). Comparison of the new and old structures of various family II PPases demonstrates why the family II enzyme prefers Mn(2+) or Co(2+), as an activator rather than Mg(2+). Both M1 and M2 undergo significant changes upon substrate binding, changing from five-coordinate to octahedral geometry. Mn(2+) and Co(2+), which readily adopt different coordination states and geometries, are thus favored. Combining our structures with biochemical data, we identified M2 as the high-affinity metal site. Zn(2+) activates in the M1 site, where octahedral geometry is not essential for catalysis, but inhibits in the M2 site, because it is unable to assume octahedral geometry but remains trigonal bipyramidal. Finally, we propose that Lys205-Gln81-Gln80 form a hydrophilic channel to speed product release from the active site.

-	~~{{STRUCTURE_1wpn\| PDB=1wpn \| SCENE= }}~~	+	Structural studies of metal ions in family II pyrophosphatases: the requirement for a Janus ion.,Fabrichniy IP, Lehtio L, Salminen A, Zyryanov AB, Baykov AA, Lahti R, Goldman A Biochemistry. 2004 Nov 16;43(45):14403-11. PMID:15533045<ref>PMID:15533045</ref>

-	~~===Crystal structure~~ of the ~~N-terminal core of Bacillus subtilis inorganic pyrophosphatase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15533045}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1wpn]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_subtilis Bacillus subtilis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1WPN OCA].~~	+

	==See Also==		==See Also==
	*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]		*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015533045<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]

OCA at 09:13, 20 October 2012

OCA — Sat, 20 Oct 2012 09:13:03 GMT

←Older revision		Revision as of 09:13, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1wpn]] is a 2 chain structure ~~of [[Inorganic pyrophosphatase]]~~ with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPN OCA].	+	[[1wpn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPN OCA].

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

OCA: Protected "1wpn" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2012 22:08:36 GMT

Protected "1wpn" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:08, 25 July 2012