1bzo - Revision history

OCA at 05:57, 3 April 2024

OCA — Wed, 03 Apr 2024 05:57:02 GMT

←Older revision		Revision as of 05:57, 3 April 2024
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	</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=1bzo 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=1bzo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Prokaryotic Cu,Zn superoxide dismutases are characterized by a distinct quaternary structure, as compared to that of the homologous eukaryotic enzymes. Here we report a newly determined crystal structure of the dimeric Cu,Zn superoxide dismutase from Photobacterium leiognathi (crystallized in space group R32, refined at 2.5 A resolution, R-factor 0.19) and analyse it in comparison with that of the monomeric enzyme from Escherichia coli. The dimeric assembly, observed also in a previously studied monoclinic crystal form of P. leiognathi Cu,Zn superoxide dismutase, is based on a ring-shaped subunit contact region, defining a solvated interface cavity. Three clusters of neighbouring residues play a direct role in the stabilization of the quaternary assembly. The present analysis, extended to the amino acid sequences of the other 11 known prokaryotic Cu,Zn superoxide dismutases, shows that at least in five other prokaryotic enzymes the interface residue clusters are under strong evolutionary constraint, suggesting the attainment of a quaternary structure coincident with that of P. leiognathi Cu,Zn superoxide dismutase. Calculation of electrostatic fields for both the enzymes from E. coli and P. leiognathi shows that the monomeric/dimeric association behaviour displayed by prokaryotic Cu, Zn superoxide dismutases is related to the distribution of surface charged residues. Moreover, Brownian dynamics simulations reproduce closely the observed enzyme:substrate association rates, highlighting the role of the active site neighbouring residues in determining the dismutase catalytic properties.
-
-	Evolutionary constraints for dimer formation in prokaryotic Cu,Zn superoxide dismutase.,Bordo D, Matak D, Djinovic-Carugo K, Rosano C, Pesce A, Bolognesi M, Stroppolo ME, Falconi M, Battistoni A, Desideri A J Mol Biol. 1999 Jan 8;285(1):283-96. PMID:9878406<ref>PMID:9878406</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1bzo" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Superoxide dismutase 3D structures\|Superoxide dismutase 3D structures]]		*[[Superoxide dismutase 3D structures\|Superoxide dismutase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 23:22, 27 December 2023

OCA — Wed, 27 Dec 2023 23:22:47 GMT

←Older revision		Revision as of 23:22, 27 December 2023
Line 3:		Line 3:
	<StructureSection load='1bzo' size='340' side='right'caption='[[1bzo]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1bzo' size='340' side='right'caption='[[1bzo]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bzo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BZO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BZO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bzo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Photobacterium_leiognathi_subsp._leiognathi Photobacterium leiognathi subsp. leiognathi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BZO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BZO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.1Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1bzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bzo OCA], [https://pdbe.org/1bzo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bzo RCSB], [https://www.ebi.ac.uk/pdbsum/1bzo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bzo 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=1bzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bzo OCA], [https://pdbe.org/1bzo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bzo RCSB], [https://www.ebi.ac.uk/pdbsum/1bzo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bzo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SODC_PHOLE SODC_PHOLE]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.	+	[https://www.uniprot.org/uniprot/SODC_PHOLE SODC_PHOLE] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Superoxide dismutase~~]]	+	[[Category: Photobacterium leiognathi subsp. leiognathi]]
-	[[Category: Battistoni, A]]	+	[[Category: Battistoni A]]
-	[[Category: Bolognesi, M]]	+	[[Category: Bolognesi M]]
-	[[Category: Bordo, D]]	+	[[Category: Bordo D]]
-	[[Category: Desideri, A]]	+	[[Category: Desideri A]]
-	[[Category: Djinovic-Carugo, K]]	+	[[Category: Djinovic-Carugo K]]
-	[[Category: Falconi, M]]	+	[[Category: Falconi M]]
-	[[Category: Matak, D]]	+	[[Category: Matak D]]
-	[[Category: Pesce, A]]	+	[[Category: Pesce A]]
-	[[Category: Rosano, C]]	+	[[Category: Rosano C]]
-	[[Category: Stroppolo~~, M E]]~~	+	[[Category: Stroppolo ME]]
-	~~[[Category: Monomeric cu]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Protein electrostatic]]~~	+
-	~~[[Category: Protein-subunit recognition]]~~	+
-	~~[[Category: Zn superoxide dismutase~~]]	+

OCA at 15:12, 3 March 2021

OCA — Wed, 03 Mar 2021 15:12:47 GMT

←Older revision		Revision as of 15:12, 3 March 2021
Line 3:		Line 3:
	<StructureSection load='1bzo' size='340' side='right'caption='[[1bzo]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1bzo' size='340' side='right'caption='[[1bzo]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bzo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BZO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1BZO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bzo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BZO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BZO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=1bzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bzo OCA], [~~http~~://pdbe.org/1bzo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1bzo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1bzo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1bzo 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=1bzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bzo OCA], [https://pdbe.org/1bzo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bzo RCSB], [https://www.ebi.ac.uk/pdbsum/1bzo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bzo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SODC_PHOLE SODC_PHOLE]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.	+	[[https://www.uniprot.org/uniprot/SODC_PHOLE SODC_PHOLE]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Superoxide ~~Dismutase~~\|Superoxide ~~Dismutase~~]]	+	*[[Superoxide dismutase 3D structures\|Superoxide dismutase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:05, 29 May 2019

OCA — Wed, 29 May 2019 07:05:41 GMT

←Older revision		Revision as of 07:05, 29 May 2019
Line 1:		Line 1:

	==THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU,ZN SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY X-RAY CRYSTALLOGRAPHY.==		==THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU,ZN SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY X-RAY CRYSTALLOGRAPHY.==
-	<StructureSection load='1bzo' size='340' side='right' caption='[[1bzo]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1bzo' size='340' side='right'caption='[[1bzo]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bzo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BZO FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bzo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BZO FirstGlance]. <br>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bz/1bzo_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bz/1bzo_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 36:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]
	[[Category: Battistoni, A]]		[[Category: Battistoni, A]]

OCA at 11:16, 24 August 2017

OCA — Thu, 24 Aug 2017 11:16:48 GMT

←Older revision		Revision as of 11:16, 24 August 2017
Line 1:		Line 1:
		+
	==THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU,ZN SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY X-RAY CRYSTALLOGRAPHY.==		==THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU,ZN SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY X-RAY CRYSTALLOGRAPHY.==
	<StructureSection load='1bzo' size='340' side='right' caption='[[1bzo]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1bzo' size='340' side='right' caption='[[1bzo]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bzo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"photobacterium_leiognathi_subsp._leiognathi"_(boisvert_et_al._1967)_ast_and_dunlap_2004 "photobacterium leiognathi subsp. leiognathi" (boisvert et al. 1967) ast and dunlap 2004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BZO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bzo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BZO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=1bzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bzo OCA], [http://pdbe.org/1bzo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bzo RCSB], [http://www.ebi.ac.uk/pdbsum/1bzo 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=1bzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bzo OCA], [http://pdbe.org/1bzo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bzo RCSB], [http://www.ebi.ac.uk/pdbsum/1bzo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1bzo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	<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=1bzo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:35, 11 September 2015

OCA — Fri, 11 Sep 2015 10:35:27 GMT

←Older revision		Revision as of 10:35, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1bzo' size='340' side='right' caption='[[1bzo]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1bzo' size='340' side='right' caption='[[1bzo]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bzo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Photobacterium_leiognathi Photobacterium~~ leiognathi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BZO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bzo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"photobacterium_leiognathi_subsp._leiognathi"_(boisvert_et_al._1967)_ast_and_dunlap_2004 "photobacterium leiognathi subsp. leiognathi" (boisvert et al. 1967) ast and dunlap 2004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BZO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=1bzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bzo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bzo RCSB], [http://www.ebi.ac.uk/pdbsum/1bzo 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=1bzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bzo OCA], [http://pdbe.org/1bzo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bzo RCSB], [http://www.ebi.ac.uk/pdbsum/1bzo PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1bzo" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Photobacterium leiognathi]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]
	[[Category: Battistoni, A]]		[[Category: Battistoni, A]]

OCA at 15:17, 25 December 2014

OCA — Thu, 25 Dec 2014 15:17:40 GMT

←Older revision		Revision as of 15:17, 25 December 2014
Line 7:		Line 7:
	<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=1bzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bzo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bzo RCSB], [http://www.ebi.ac.uk/pdbsum/1bzo 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=1bzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bzo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bzo RCSB], [http://www.ebi.ac.uk/pdbsum/1bzo PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SODC_PHOLE SODC_PHOLE]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:42, 22 December 2014

OCA — Mon, 22 Dec 2014 08:42:57 GMT

←Older revision		Revision as of 08:42, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bzo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Photobacterium_leiognathi Photobacterium leiognathi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BZO FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bzo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Photobacterium_leiognathi Photobacterium leiognathi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BZO FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=1bzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bzo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bzo RCSB], [http://www.ebi.ac.uk/pdbsum/1bzo 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=1bzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bzo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bzo RCSB], [http://www.ebi.ac.uk/pdbsum/1bzo 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 34:		Line 34:
	[[Category: Photobacterium leiognathi]]		[[Category: Photobacterium leiognathi]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]
-	[[Category: Battistoni, A.]]	+	[[Category: Battistoni, A]]
-	[[Category: Bolognesi, M.]]	+	[[Category: Bolognesi, M]]
-	[[Category: Bordo, D.]]	+	[[Category: Bordo, D]]
-	[[Category: Desideri, A.]]	+	[[Category: Desideri, A]]
-	[[Category: Djinovic-Carugo, K.]]	+	[[Category: Djinovic-Carugo, K]]
-	[[Category: Falconi, M.]]	+	[[Category: Falconi, M]]
-	[[Category: Matak, D.]]	+	[[Category: Matak, D]]
-	[[Category: Pesce, A.]]	+	[[Category: Pesce, A]]
-	[[Category: Rosano, C.]]	+	[[Category: Rosano, C]]
-	[[Category: Stroppolo, M E.]]	+	[[Category: Stroppolo, M E]]
	[[Category: Monomeric cu]]		[[Category: Monomeric cu]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 09:43, 13 August 2014

OCA — Wed, 13 Aug 2014 09:43:05 GMT

←Older revision		Revision as of 09:43, 13 August 2014
Line 1:		Line 1:
-	[[~~Image~~:1bzo.~~png\|left~~\|200px]]	+	==THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU,ZN SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY X-RAY CRYSTALLOGRAPHY.==
		+	<StructureSection load='1bzo' size='340' side='right' caption='[[1bzo]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1bzo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Photobacterium_leiognathi Photobacterium leiognathi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BZO FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </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=1bzo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bzo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bzo RCSB], [http://www.ebi.ac.uk/pdbsum/1bzo 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/bz/1bzo_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 ==
		+	Prokaryotic Cu,Zn superoxide dismutases are characterized by a distinct quaternary structure, as compared to that of the homologous eukaryotic enzymes. Here we report a newly determined crystal structure of the dimeric Cu,Zn superoxide dismutase from Photobacterium leiognathi (crystallized in space group R32, refined at 2.5 A resolution, R-factor 0.19) and analyse it in comparison with that of the monomeric enzyme from Escherichia coli. The dimeric assembly, observed also in a previously studied monoclinic crystal form of P. leiognathi Cu,Zn superoxide dismutase, is based on a ring-shaped subunit contact region, defining a solvated interface cavity. Three clusters of neighbouring residues play a direct role in the stabilization of the quaternary assembly. The present analysis, extended to the amino acid sequences of the other 11 known prokaryotic Cu,Zn superoxide dismutases, shows that at least in five other prokaryotic enzymes the interface residue clusters are under strong evolutionary constraint, suggesting the attainment of a quaternary structure coincident with that of P. leiognathi Cu,Zn superoxide dismutase. Calculation of electrostatic fields for both the enzymes from E. coli and P. leiognathi shows that the monomeric/dimeric association behaviour displayed by prokaryotic Cu, Zn superoxide dismutases is related to the distribution of surface charged residues. Moreover, Brownian dynamics simulations reproduce closely the observed enzyme:substrate association rates, highlighting the role of the active site neighbouring residues in determining the dismutase catalytic properties.

-	~~{{STRUCTURE_1bzo\| PDB=1bzo \| SCENE= }}~~	+	Evolutionary constraints for dimer formation in prokaryotic Cu,Zn superoxide dismutase.,Bordo D, Matak D, Djinovic-Carugo K, Rosano C, Pesce A, Bolognesi M, Stroppolo ME, Falconi M, Battistoni A, Desideri A J Mol Biol. 1999 Jan 8;285(1):283-96. PMID:9878406<ref>PMID:9878406</ref>

-	~~===THREE-DIMENSIONAL STRUCTURE OF PROKARYOTIC CU~~,~~ZN SUPEROXIDE DISMUTASE FROM P.LEIOGNATHI, SOLVED BY X-RAY CRYSTALLOGRAPHY.===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9878406}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1bzo]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Photobacterium_leiognathi Photobacterium leiognathi]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1BZO OCA].~~	+

	==See Also==		==See Also==
	*[[Superoxide Dismutase\|Superoxide Dismutase]]		*[[Superoxide Dismutase\|Superoxide Dismutase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:009878406<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Photobacterium leiognathi]]		[[Category: Photobacterium leiognathi]]
	[[Category: Superoxide dismutase]]		[[Category: Superoxide dismutase]]

OCA at 18:13, 20 October 2012

OCA — Sat, 20 Oct 2012 18:13:54 GMT

←Older revision		Revision as of 18:13, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1bzo]] is a 1 chain structure ~~of [[Superoxide Dismutase]]~~ with sequence from [http://en.wikipedia.org/wiki/Photobacterium_leiognathi Photobacterium leiognathi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BZO OCA].	+	[[1bzo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Photobacterium_leiognathi Photobacterium leiognathi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BZO OCA].

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