1m85 - Revision history

OCA at 08:32, 10 April 2024

OCA — Wed, 10 Apr 2024 08:32:43 GMT

←Older revision		Revision as of 08:32, 10 April 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1m85]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_mirabilis Proteus mirabilis]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2cae 2cae] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cae 1cae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M85 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M85 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1m85]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_mirabilis Proteus mirabilis]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2cae 2cae] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cae 1cae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M85 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M85 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 2Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~OMT~~:~~S-DIOXYMETHIONINE~~'>~~OMT~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OMT:S-DIOXYMETHIONINE'>OMT</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"><div style~~=~~'overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2caf\|2caf]], [[2cah\|2cah]], [[1e93\|1e93]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Catalase Catalase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6]~~ </~~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=1m85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m85 OCA], [https://pdbe.org/1m85 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m85 RCSB], [https://www.ebi.ac.uk/pdbsum/1m85 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m85 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=1m85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m85 OCA], [https://pdbe.org/1m85 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m85 RCSB], [https://www.ebi.ac.uk/pdbsum/1m85 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m85 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CATA_PROMI CATA_PROMI]] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.	+	[https://www.uniprot.org/uniprot/CATA_PROMI CATA_PROMI] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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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=1m85 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=1m85 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A catalase from a peroxide resistant mutant of Proteus mirabilis binds NADPH tightly. Interestingly, this enzyme can be stripped of NADPH without loss of the catalatic activity. It is the only known non-mammalian catalase able to bind NADPH. The structure without cofactor was solved by molecular replacement using the structure of beef liver catalase as a model. The structure was refined to an R-factor of 19.3% in the range 8 to 2.2 A resolution. According to the sequence, a methionine sulphone was positioned in the haem active site. This oxidized form of methionine is particular to Proteus mirabilis catalase and likely to produce some steric hindrance in the active site. Two important water molecules are positioned in the haem distal site. These two water molecules are not located in the structure of beef liver catalase, but are supposed to account for the catalytic mechanism. The liganded form was obtained by soaking crystals of the unliganded form into an NADPH solution. The structure was refined to an R-factor of 15.9% in the range of 8 to 3.1 A resolution using the unliganded structure as a model. The NADPH was clearly located in the electron density map with the same conformation as in beef liver catalase. The NADPH binding induces slight structural changes. However, the imidazole ring of a histidine residue (His284) rotates about 50 degrees to accommodate the cofactor. The electron transfer from NADPH to the haem molecule was examined and several pathways are proposed.
-
-	Crystal structure of Proteus mirabilis PR catalase with and without bound NADPH.,Gouet P, Jouve HM, Dideberg O J Mol Biol. 1995 Jun 23;249(5):933-54. PMID:7791219<ref>PMID:7791219</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1m85" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Catalase 3D structures\|Catalase 3D structures]]		*[[Catalase 3D structures\|Catalase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Catalase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Proteus mirabilis]]		[[Category: Proteus mirabilis]]
-	[[Category: Dideberg, O]]	+	[[Category: Dideberg O]]
-	[[Category: Gouet, P]]	+	[[Category: Gouet P]]
-	[[Category: Jouve, H M]]	+	[[Category: Jouve H-M]]
-	~~[[Category: Methionine sulfone]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 06:53, 18 August 2021

OCA — Wed, 18 Aug 2021 06:53:55 GMT

OCA at 12:41, 13 November 2019

OCA — Wed, 13 Nov 2019 12:41:37 GMT

←Older revision		Revision as of 12:41, 13 November 2019
Line 1:		Line 1:

	==Structure of Proteus mirabilis catalase for the native form==		==Structure of Proteus mirabilis catalase for the native form==
-	<StructureSection load='1m85' size='340' side='right' caption='[[1m85]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1m85' size='340' side='right'caption='[[1m85]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1m85]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Proteus_mirabilis Proteus mirabilis]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2cae 2cae] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cae 1cae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M85 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M85 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1m85]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Proteus_mirabilis Proteus mirabilis]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2cae 2cae] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cae 1cae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M85 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M85 FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 1m85" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1m85" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Catalase 3D structures\|Catalase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Catalase]]		[[Category: Catalase]]
		+	[[Category: Large Structures]]
	[[Category: Proteus mirabilis]]		[[Category: Proteus mirabilis]]
	[[Category: Dideberg, O]]		[[Category: Dideberg, O]]

OCA at 08:15, 31 January 2018

OCA — Wed, 31 Jan 2018 08:15:46 GMT

←Older revision		Revision as of 08:15, 31 January 2018
Line 1:		Line 1:
		+
	==Structure of Proteus mirabilis catalase for the native form==		==Structure of Proteus mirabilis catalase for the native form==
	<StructureSection load='1m85' size='340' side='right' caption='[[1m85]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1m85' size='340' side='right' caption='[[1m85]], [[Resolution\|resolution]] 2.00Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2caf\|2caf]], [[2cah\|2cah]], [[1e93\|1e93]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2caf\|2caf]], [[2cah\|2cah]], [[1e93\|1e93]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </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=1m85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m85 OCA], [http://pdbe.org/1m85 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m85 RCSB], [http://www.ebi.ac.uk/pdbsum/1m85 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=1m85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m85 OCA], [http://pdbe.org/1m85 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m85 RCSB], [http://www.ebi.ac.uk/pdbsum/1m85 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m85 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m8/1m85_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m8/1m85_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 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 1m85" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1m85" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Catalase\|Catalase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 00:44, 10 February 2016

OCA — Wed, 10 Feb 2016 00:44:19 GMT

←Older revision		Revision as of 00:44, 10 February 2016
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	<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=1m85 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:40, 11 September 2015

OCA — Fri, 11 Sep 2015 03:40:25 GMT

←Older revision		Revision as of 03:40, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1m85' size='340' side='right' caption='[[1m85]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1m85' size='340' side='right' caption='[[1m85]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m85]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Proteus_mirabilis Proteus mirabilis]. This structure supersedes the now removed PDB entries and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cae 1cae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M85 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M85 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m85]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Proteus_mirabilis Proteus mirabilis]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2cae 2cae] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cae 1cae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M85 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M85 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMT:S-DIOXYMETHIONINE'>OMT</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMT:S-DIOXYMETHIONINE'>OMT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2caf\|2caf]], [[2cah\|2cah]], [[1e93\|1e93]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2caf\|2caf]], [[2cah\|2cah]], [[1e93\|1e93]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </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=1m85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m85 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m85 RCSB], [http://www.ebi.ac.uk/pdbsum/1m85 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=1m85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m85 OCA], [http://pdbe.org/1m85 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m85 RCSB], [http://www.ebi.ac.uk/pdbsum/1m85 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 1m85" style="background-color:#fffaf0;"></div>

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

OCA at 10:36, 25 December 2014

OCA — Thu, 25 Dec 2014 10:36:24 GMT

←Older revision		Revision as of 10:36, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1m85]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Proteus_mirabilis Proteus mirabilis]. This structure supersedes the now removed PDB entries and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cae 1cae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M85 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M85 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1m85]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Proteus_mirabilis Proteus mirabilis]. This structure supersedes the now removed PDB entries and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cae 1cae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M85 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M85 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMT:S-DIOXYMETHIONINE'>OMT</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMT:S-DIOXYMETHIONINE'>OMT</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2caf\|2caf]], [[2cah\|2cah]], [[1e93\|1e93]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2caf\|2caf]], [[2cah\|2cah]], [[1e93\|1e93]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </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=1m85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m85 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m85 RCSB], [http://www.ebi.ac.uk/pdbsum/1m85 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=1m85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m85 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m85 RCSB], [http://www.ebi.ac.uk/pdbsum/1m85 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CATA_PROMI CATA_PROMI]] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Catalase]]		[[Category: Catalase]]
	[[Category: Proteus mirabilis]]		[[Category: Proteus mirabilis]]
-	[[Category: Dideberg, O.]]	+	[[Category: Dideberg, O]]
-	[[Category: Gouet, P.]]	+	[[Category: Gouet, P]]
-	[[Category: Jouve, H M.]]	+	[[Category: Jouve, H M]]
	[[Category: Methionine sulfone]]		[[Category: Methionine sulfone]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 11:27, 3 October 2014

OCA — Fri, 03 Oct 2014 11:27:48 GMT

←Older revision		Revision as of 11:27, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1m85~~\| ~~PDB~~=1m85 \| ~~SCENE~~= }}	+	==Structure of Proteus mirabilis catalase for the native form==
-	===~~Structure~~ of Proteus mirabilis catalase for the ~~native~~ form~~===~~	+	<StructureSection load='1m85' size='340' side='right' caption='[[1m85]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_7791219}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1m85]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Proteus_mirabilis Proteus mirabilis]. This structure supersedes the now removed PDB entries and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cae 1cae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M85 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M85 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMT:S-DIOXYMETHIONINE'>OMT</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2caf\|2caf]], [[2cah\|2cah]], [[1e93\|1e93]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </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=1m85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m85 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m85 RCSB], [http://www.ebi.ac.uk/pdbsum/1m85 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/m8/1m85_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 ==
		+	A catalase from a peroxide resistant mutant of Proteus mirabilis binds NADPH tightly. Interestingly, this enzyme can be stripped of NADPH without loss of the catalatic activity. It is the only known non-mammalian catalase able to bind NADPH. The structure without cofactor was solved by molecular replacement using the structure of beef liver catalase as a model. The structure was refined to an R-factor of 19.3% in the range 8 to 2.2 A resolution. According to the sequence, a methionine sulphone was positioned in the haem active site. This oxidized form of methionine is particular to Proteus mirabilis catalase and likely to produce some steric hindrance in the active site. Two important water molecules are positioned in the haem distal site. These two water molecules are not located in the structure of beef liver catalase, but are supposed to account for the catalytic mechanism. The liganded form was obtained by soaking crystals of the unliganded form into an NADPH solution. The structure was refined to an R-factor of 15.9% in the range of 8 to 3.1 A resolution using the unliganded structure as a model. The NADPH was clearly located in the electron density map with the same conformation as in beef liver catalase. The NADPH binding induces slight structural changes. However, the imidazole ring of a histidine residue (His284) rotates about 50 degrees to accommodate the cofactor. The electron transfer from NADPH to the haem molecule was examined and several pathways are proposed.

-	~~==Function==~~	+	Crystal structure of Proteus mirabilis PR catalase with and without bound NADPH.,Gouet P, Jouve HM, Dideberg O J Mol Biol. 1995 Jun 23;249(5):933-54. PMID:7791219<ref>PMID:7791219</ref>
-	~~[[http://www~~.~~uniprot~~.~~org/uniprot/CATA_PROMI CATA_PROMI]] Decomposes hydrogen peroxide into water and oxygen~~; ~~serves to protect cells from the toxic effects of hydrogen peroxide~~.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[1m85]] is~~ a ~~1 chain structure with sequence from [http://en.wikipedia.org/wiki/Proteus_mirabilis Proteus mirabilis]. This structure supersedes~~ the ~~now removed PDB entries and [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/send-pdb?obs=1&id=1cae 1cae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M85 OCA].~~	+	</div>

	==See Also==		==See Also==
	*[[Catalase\|Catalase]]		*[[Catalase\|Catalase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:007791219</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Catalase]]		[[Category: Catalase]]
	[[Category: Proteus mirabilis]]		[[Category: Proteus mirabilis]]

OCA at 08:33, 16 April 2014

OCA — Wed, 16 Apr 2014 08:33:25 GMT

←Older revision		Revision as of 08:33, 16 April 2014
Line 1:		Line 1:
-	[[Image:1m85.png\|left\|200px]]
-
	{{STRUCTURE_1m85\| PDB=1m85 \| SCENE= }}		{{STRUCTURE_1m85\| PDB=1m85 \| SCENE= }}
-
	===Structure of Proteus mirabilis catalase for the native form===		===Structure of Proteus mirabilis catalase for the native form===
		+	{{ABSTRACT_PUBMED_7791219}}

-	~~{{ABSTRACT_PUBMED_7791219}}~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/CATA_PROMI CATA_PROMI]] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.

	==About this Structure==		==About this Structure==
Line 14:		Line 13:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:007791219</ref><references group="xtra"/>	+	<ref group="xtra">PMID:007791219</ref><references group="xtra"/><references/>
	[[Category: Catalase]]		[[Category: Catalase]]
	[[Category: Proteus mirabilis]]		[[Category: Proteus mirabilis]]

OCA at 15:42, 20 October 2012

OCA — Sat, 20 Oct 2012 15:42:45 GMT

←Older revision		Revision as of 15:42, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1m85]] is a 1 chain structure ~~of [[Catalase]]~~ with sequence from [http://en.wikipedia.org/wiki/Proteus_mirabilis Proteus mirabilis]. This structure supersedes the now removed PDB entries and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cae 1cae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M85 OCA].	+	[[1m85]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Proteus_mirabilis Proteus mirabilis]. This structure supersedes the now removed PDB entries and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cae 1cae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M85 OCA].

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

←Older revision		Revision as of 06:53, 18 August 2021
Line 3:		Line 3:
	<StructureSection load='1m85' size='340' side='right'caption='[[1m85]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1m85' size='340' side='right'caption='[[1m85]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m85]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Proteus_mirabilis Proteus mirabilis]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2cae 2cae] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cae 1cae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M85 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1M85 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m85]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Proteus_mirabilis Proteus mirabilis]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2cae 2cae] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cae 1cae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M85 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M85 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMT:S-DIOXYMETHIONINE'>OMT</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OMT:S-DIOXYMETHIONINE'>OMT</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2caf\|2caf]], [[2cah\|2cah]], [[1e93\|1e93]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2caf\|2caf]], [[2cah\|2cah]], [[1e93\|1e93]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Catalase Catalase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Catalase Catalase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </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=1m85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m85 OCA], [~~http~~://pdbe.org/1m85 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1m85 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1m85 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1m85 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=1m85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m85 OCA], [https://pdbe.org/1m85 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m85 RCSB], [https://www.ebi.ac.uk/pdbsum/1m85 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m85 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CATA_PROMI CATA_PROMI]] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.	+	[[https://www.uniprot.org/uniprot/CATA_PROMI CATA_PROMI]] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]