1wpm - Revision history

OCA at 13:33, 13 March 2024

OCA — Wed, 13 Mar 2024 13:33:24 GMT

←Older revision		Revision as of 13:33, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='1wpm' size='340' side='right'caption='[[1wpm]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='1wpm' size='340' side='right'caption='[[1wpm]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wpm]] 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=1WPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WPM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wpm]] 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=1WPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WPM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 2.05Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1wpn\|1wpn]], [[1wpp\|1wpp]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=1wpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpm OCA], [https://pdbe.org/1wpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wpm RCSB], [https://www.ebi.ac.uk/pdbsum/1wpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wpm 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=1wpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpm OCA], [https://pdbe.org/1wpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wpm RCSB], [https://www.ebi.ac.uk/pdbsum/1wpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wpm 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=1wpm 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=1wpm 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 1wpm" 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]]~~	+
-	~~[[Category: Ppase~~]]	+

OCA at 09:04, 21 April 2021

OCA — Wed, 21 Apr 2021 09:04:08 GMT

←Older revision		Revision as of 09:04, 21 April 2021
Line 3:		Line 3:
	<StructureSection load='1wpm' size='340' side='right'caption='[[1wpm]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='1wpm' size='340' side='right'caption='[[1wpm]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wpm]] 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=1WPM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1WPM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wpm]] 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=1WPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WPM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=PG4:TETRAETHYLENE+GLYCOL'>PG4</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">[[1wpn\|1wpn]], [[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;'>[[1wpn\|1wpn]], [[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=1wpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpm OCA], [~~http~~://pdbe.org/1wpm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1wpm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1wpm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1wpm 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=1wpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpm OCA], [https://pdbe.org/1wpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wpm RCSB], [https://www.ebi.ac.uk/pdbsum/1wpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wpm 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 13:07, 17 July 2019

OCA — Wed, 17 Jul 2019 13:07:58 GMT

←Older revision		Revision as of 13:07, 17 July 2019
Line 1:		Line 1:

	==Structure of Bacillus subtilis inorganic pyrophosphatase==		==Structure of Bacillus subtilis inorganic pyrophosphatase==
-	<StructureSection load='1wpm' size='340' side='right' caption='[[1wpm]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='1wpm' size='340' side='right'caption='[[1wpm]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wpm]] 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=1WPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WPM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wpm]] 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=1WPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WPM 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/1wpm_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wp/1wpm_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 1wpm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1wpm" 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 10:39, 12 October 2017

OCA — Thu, 12 Oct 2017 10:39:58 GMT

←Older revision		Revision as of 10:39, 12 October 2017
Line 1:		Line 1:
		+
	==Structure of Bacillus subtilis inorganic pyrophosphatase==		==Structure of Bacillus subtilis inorganic pyrophosphatase==
	<StructureSection load='1wpm' size='340' side='right' caption='[[1wpm]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='1wpm' size='340' side='right' caption='[[1wpm]], [[Resolution\|resolution]] 2.05Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wpn\|1wpn]], [[1wpp\|1wpp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wpn\|1wpn]], [[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=1wpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpm OCA], [http://pdbe.org/1wpm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wpm RCSB], [http://www.ebi.ac.uk/pdbsum/1wpm 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=1wpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpm OCA], [http://pdbe.org/1wpm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wpm RCSB], [http://www.ebi.ac.uk/pdbsum/1wpm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wpm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<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=1wpm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1wpm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1wpm" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:18, 11 September 2015

OCA — Fri, 11 Sep 2015 11:18:19 GMT

←Older revision		Revision as of 11:18, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1wpm' size='340' side='right' caption='[[1wpm]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='1wpm' size='340' side='right' caption='[[1wpm]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wpm]] 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=1WPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WPM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wpm]] 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=1WPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WPM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=PG4:TETRAETHYLENE+GLYCOL'>PG4</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">[[1wpn\|1wpn]], [[1wpp\|1wpp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wpn\|1wpn]], [[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=1wpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wpm RCSB], [http://www.ebi.ac.uk/pdbsum/1wpm 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=1wpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpm OCA], [http://pdbe.org/1wpm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wpm RCSB], [http://www.ebi.ac.uk/pdbsum/1wpm 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 1wpm" 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 13:30, 6 January 2015

OCA — Tue, 06 Jan 2015 13:30:28 GMT

←Older revision		Revision as of 13:30, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wpm]] 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=1WPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WPM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wpm]] 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=1WPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WPM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wpn\|1wpn]], [[1wpp\|1wpp]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wpn\|1wpn]], [[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=1wpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wpm RCSB], [http://www.ebi.ac.uk/pdbsum/1wpm 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=1wpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wpm RCSB], [http://www.ebi.ac.uk/pdbsum/1wpm 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]]
	[[Category: Ppase]]		[[Category: Ppase]]

OCA at 20:11, 28 September 2014

OCA — Sun, 28 Sep 2014 20:11:47 GMT

←Older revision		Revision as of 20:11, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1wpm.~~png~~\|~~left~~\|200px]]	+	==Structure of Bacillus subtilis inorganic pyrophosphatase==
		+	<StructureSection load='1wpm' size='340' side='right' caption='[[1wpm]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1wpm]] 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=1WPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WPM FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wpn\|1wpn]], [[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=1wpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wpm RCSB], [http://www.ebi.ac.uk/pdbsum/1wpm 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/1wpm_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_1wpm\| PDB=1wpm \| 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>

-	~~===Structure~~ 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==~~	+
-	~~[[1wpm]] 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=1WPM 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 18:29, 20 October 2012

OCA — Sat, 20 Oct 2012 18:29:36 GMT

←Older revision		Revision as of 18:29, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1wpm]] 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=1WPM OCA].	+	[[1wpm]] 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=1WPM OCA].

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

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

OCA — Fri, 27 Jul 2012 04:15:33 GMT

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

←Older revision

Revision as of 04:15, 27 July 2012

OCA at 04:15, 27 July 2012

OCA — Fri, 27 Jul 2012 04:15:31 GMT

←Older revision		Revision as of 04:15, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1wpm.png\|left\|200px]]		[[Image:1wpm.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1wpm", 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_1wpm\| PDB=1wpm \| SCENE= }}		{{STRUCTURE_1wpm\| PDB=1wpm \| SCENE= }}

	===Structure of Bacillus subtilis inorganic pyrophosphatase===		===Structure of Bacillus subtilis inorganic pyrophosphatase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15533045}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15533045 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15533045}}		{{ABSTRACT_PUBMED_15533045}}

	==About this Structure==		==About this Structure==
-	~~1WPM~~ is a 2 ~~chains~~ structure of ~~sequences~~ 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=1WPM OCA].	+	[[1wpm]] 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=1WPM OCA].
		+
		+	==See Also==
		+	*[[Inorganic pyrophosphatase\|Inorganic pyrophosphatase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15533045~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015533045</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Inorganic diphosphatase]]		[[Category: Inorganic diphosphatase]]
Line 32:		Line 23:
	[[Category: Lehtio, L.]]		[[Category: Lehtio, L.]]
	[[Category: Salminen, A.]]		[[Category: Salminen, A.]]
		+	[[Category: Hydrolase]]
	[[Category: Inorganic pyrophosphatase]]		[[Category: Inorganic pyrophosphatase]]
	[[Category: Metal binding]]		[[Category: Metal binding]]
	[[Category: Ppase]]		[[Category: Ppase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 20:47:36 2009''