1ix4 - Revision history

OCA at 06:02, 3 April 2024

OCA — Wed, 03 Apr 2024 06:02:45 GMT

←Older revision		Revision as of 06:02, 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=1ix4 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=1ix4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Heme oxygenase (HO) catalyzes heme degradation by utilizing O(2) and reducing equivalents to produce biliverdin IX alpha, iron, and CO. To avoid product inhibition, the heme[bond]HO complex (heme[bond]HO) is structured to markedly increase its affinity for O(2) while suppressing its affinity for CO. We determined the crystal structures of rat ferrous heme[bond]HO and heme[bond]HO bound to CO, CN(-), and NO at 2.3, 1.8, 2.0, and 1.7 A resolution, respectively. The heme pocket of ferrous heme-HO has the same conformation as that of the previously determined ferric form, but no ligand is visible on the distal side of the ferrous heme. Fe[bond]CO and Fe[bond]CN(-) are tilted, whereas the Fe[bond]NO is bent. The structure of heme[bond]HO bound to NO is identical to that bound to N(3)(-), which is also bent as in the case of O(2). Notably, in the CO- and CN(-)-bound forms, the heme and its ligands shift toward the alpha-meso carbon, and the distal F-helix shifts in the opposite direction. These shifts allow CO or CN(-) to bind in a tilted fashion without a collision between the distal ligand and Gly139 O and cause disruption of one salt bridge between the heme and basic residue. The structural identity of the ferrous and ferric states of heme[bond]HO indicates that these shifts are not produced on reduction of heme iron. Neither such conformational changes nor a heme shift occurs on NO or N(3)(-) binding. Heme[bond]HO therefore recognizes CO and O(2) by their binding geometries. The marked reduction in the ratio of affinities of CO to O(2) for heme[bond]HO achieved by an increase in O(2) affinity [Migita, C. T., Matera, K. M., Ikeda-Saito, M., Olson, J. S., Fujii, H., Yoshimura, T., Zhou, H., and Yoshida, T. (1998) J. Biol. Chem. 273, 945-949] is explained by hydrogen bonding and polar interactions that are favorable for O(2) binding, as well as by characteristic structural changes in the CO-bound form.
-
-	Crystal structures of ferrous and CO-, CN(-)-, and NO-bound forms of rat heme oxygenase-1 (HO-1) in complex with heme: structural implications for discrimination between CO and O2 in HO-1.,Sugishima M, Sakamoto H, Noguchi M, Fukuyama K Biochemistry. 2003 Aug 26;42(33):9898-905. PMID:12924938<ref>PMID:12924938</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ix4" style="background-color:#fffaf0;"></div>

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

OCA at 23:38, 27 December 2023

OCA — Wed, 27 Dec 2023 23:38:30 GMT

←Older revision		Revision as of 23:38, 27 December 2023
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	<StructureSection load='1ix4' size='340' side='right'caption='[[1ix4]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1ix4' size='340' side='right'caption='[[1ix4]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ix4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IX4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IX4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ix4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IX4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IX4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>~~, ~~<scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1dve\|1dve]], [[1ivj\|1ivj]], [[1qq8\|1qq8]], [[1j77\|1j77]], [[1ix3\|1ix3]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3]~~ </~~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=1ix4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ix4 OCA], [https://pdbe.org/1ix4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ix4 RCSB], [https://www.ebi.ac.uk/pdbsum/1ix4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ix4 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=1ix4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ix4 OCA], [https://pdbe.org/1ix4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ix4 RCSB], [https://www.ebi.ac.uk/pdbsum/1ix4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ix4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/HMOX1_RAT HMOX1_RAT]] Heme oxygenase cleaves the heme ring at the alpha methene bridge to form biliverdin. Biliverdin is subsequently converted to bilirubin by biliverdin reductase. Under physiological conditions, the activity of heme oxygenase is highest in the spleen, where senescent erythrocytes are sequestrated and destroyed.	+	[https://www.uniprot.org/uniprot/HMOX1_RAT HMOX1_RAT] Heme oxygenase cleaves the heme ring at the alpha methene bridge to form biliverdin. Biliverdin is subsequently converted to bilirubin by biliverdin reductase. Under physiological conditions, the activity of heme oxygenase is highest in the spleen, where senescent erythrocytes are sequestrated and destroyed.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Buffalo rat]]
-	[[Category: Heme oxygenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fukuyama, K]]	+	[[Category: Rattus norvegicus]]
-	[[Category: Hayashi, S]]	+	[[Category: Fukuyama K]]
-	[[Category: Noguchi, M]]	+	[[Category: Hayashi S]]
-	[[Category: Omata, Y]]	+	[[Category: Noguchi M]]
-	[[Category: Sakamoto, H]]	+	[[Category: Omata Y]]
-	[[Category: Sugishima, M]]	+	[[Category: Sakamoto H]]
-	~~[[Category: Hemeprotein]]~~	+	[[Category: Sugishima M]]
-	~~[[Category: Inhibitor complex]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:07, 4 August 2021

OCA — Wed, 04 Aug 2021 11:07:15 GMT

←Older revision		Revision as of 11:07, 4 August 2021
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	<StructureSection load='1ix4' size='340' side='right'caption='[[1ix4]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1ix4' size='340' side='right'caption='[[1ix4]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ix4]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IX4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1IX4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ix4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IX4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IX4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dve\|1dve]], [[1ivj\|1ivj]], [[1qq8\|1qq8]], [[1j77\|1j77]], [[1ix3\|1ix3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dve\|1dve]], [[1ivj\|1ivj]], [[1qq8\|1qq8]], [[1j77\|1j77]], [[1ix3\|1ix3]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </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=1ix4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ix4 OCA], [~~http~~://pdbe.org/1ix4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ix4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ix4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ix4 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=1ix4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ix4 OCA], [https://pdbe.org/1ix4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ix4 RCSB], [https://www.ebi.ac.uk/pdbsum/1ix4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ix4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/HMOX1_RAT HMOX1_RAT]] Heme oxygenase cleaves the heme ring at the alpha methene bridge to form biliverdin. Biliverdin is subsequently converted to bilirubin by biliverdin reductase. Under physiological conditions, the activity of heme oxygenase is highest in the spleen, where senescent erythrocytes are sequestrated and destroyed.	+	[[https://www.uniprot.org/uniprot/HMOX1_RAT HMOX1_RAT]] Heme oxygenase cleaves the heme ring at the alpha methene bridge to form biliverdin. Biliverdin is subsequently converted to bilirubin by biliverdin reductase. Under physiological conditions, the activity of heme oxygenase is highest in the spleen, where senescent erythrocytes are sequestrated and destroyed.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:36, 30 October 2019

OCA — Wed, 30 Oct 2019 10:36:46 GMT

←Older revision		Revision as of 10:36, 30 October 2019
Line 1:		Line 1:

	==Crystal Structure of Rat Heme Oxygenase-1 in complex with Heme bound to Carbon Monoxide==		==Crystal Structure of Rat Heme Oxygenase-1 in complex with Heme bound to Carbon Monoxide==
-	<StructureSection load='1ix4' size='340' side='right' caption='[[1ix4]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1ix4' size='340' side='right'caption='[[1ix4]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ix4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IX4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IX4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ix4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IX4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IX4 FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 1ix4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ix4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Heme oxygenase 3D structures\|Heme oxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 39:
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
	[[Category: Heme oxygenase]]		[[Category: Heme oxygenase]]
		+	[[Category: Large Structures]]
	[[Category: Fukuyama, K]]		[[Category: Fukuyama, K]]
	[[Category: Hayashi, S]]		[[Category: Hayashi, S]]

OCA at 09:22, 17 January 2018

OCA — Wed, 17 Jan 2018 09:22:49 GMT

←Older revision		Revision as of 09:22, 17 January 2018
Line 1:		Line 1:
		+
	==Crystal Structure of Rat Heme Oxygenase-1 in complex with Heme bound to Carbon Monoxide==		==Crystal Structure of Rat Heme Oxygenase-1 in complex with Heme bound to Carbon Monoxide==
	<StructureSection load='1ix4' size='340' side='right' caption='[[1ix4]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1ix4' size='340' side='right' caption='[[1ix4]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dve\|1dve]], [[1ivj\|1ivj]], [[1qq8\|1qq8]], [[1j77\|1j77]], [[1ix3\|1ix3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dve\|1dve]], [[1ivj\|1ivj]], [[1qq8\|1qq8]], [[1j77\|1j77]], [[1ix3\|1ix3]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </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=1ix4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ix4 OCA], [http://pdbe.org/1ix4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ix4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ix4 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=1ix4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ix4 OCA], [http://pdbe.org/1ix4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ix4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ix4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ix4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ix/1ix4_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ix/1ix4_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 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1ix4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ix4" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Heme oxygenase\|Heme oxygenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:13, 9 February 2016

OCA — Tue, 09 Feb 2016 14:13:53 GMT

←Older revision		Revision as of 14:13, 9 February 2016
Line 18:		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=1ix4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:01, 10 September 2015

OCA — Thu, 10 Sep 2015 23:01:34 GMT

←Older revision		Revision as of 23:01, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1ix4' size='340' side='right' caption='[[1ix4]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1ix4' size='340' side='right' caption='[[1ix4]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ix4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rattus_norvegicus Rattus norvegicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IX4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IX4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ix4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IX4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IX4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dve\|1dve]], [[1ivj\|1ivj]], [[1qq8\|1qq8]], [[1j77\|1j77]], [[1ix3\|1ix3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dve\|1dve]], [[1ivj\|1ivj]], [[1qq8\|1qq8]], [[1j77\|1j77]], [[1ix3\|1ix3]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </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=1ix4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ix4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ix4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ix4 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=1ix4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ix4 OCA], [http://pdbe.org/1ix4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ix4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ix4 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1ix4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
	[[Category: Heme oxygenase]]		[[Category: Heme oxygenase]]
-	[[Category: Rattus norvegicus]]
	[[Category: Fukuyama, K]]		[[Category: Fukuyama, K]]
	[[Category: Hayashi, S]]		[[Category: Hayashi, S]]

OCA at 07:19, 25 December 2014

OCA — Thu, 25 Dec 2014 07:19:08 GMT

←Older revision		Revision as of 07:19, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ix4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IX4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IX4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ix4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IX4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IX4 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dve\|1dve]], [[1ivj\|1ivj]], [[1qq8\|1qq8]], [[1j77\|1j77]], [[1ix3\|1ix3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dve\|1dve]], [[1ivj\|1ivj]], [[1qq8\|1qq8]], [[1j77\|1j77]], [[1ix3\|1ix3]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </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=1ix4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ix4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ix4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ix4 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=1ix4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ix4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ix4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ix4 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HMOX1_RAT HMOX1_RAT]] Heme oxygenase cleaves the heme ring at the alpha methene bridge to form biliverdin. Biliverdin is subsequently converted to bilirubin by biliverdin reductase. Under physiological conditions, the activity of heme oxygenase is highest in the spleen, where senescent erythrocytes are sequestrated and destroyed.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Heme oxygenase]]		[[Category: Heme oxygenase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Fukuyama, K.]]	+	[[Category: Fukuyama, K]]
-	[[Category: Hayashi, S.]]	+	[[Category: Hayashi, S]]
-	[[Category: Noguchi, M.]]	+	[[Category: Noguchi, M]]
-	[[Category: Omata, Y.]]	+	[[Category: Omata, Y]]
-	[[Category: Sakamoto, H.]]	+	[[Category: Sakamoto, H]]
-	[[Category: Sugishima, M.]]	+	[[Category: Sugishima, M]]
	[[Category: Hemeprotein]]		[[Category: Hemeprotein]]
	[[Category: Inhibitor complex]]		[[Category: Inhibitor complex]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 09:06, 28 September 2014

OCA — Sun, 28 Sep 2014 09:06:53 GMT

←Older revision		Revision as of 09:06, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1ix4.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Rat Heme Oxygenase-1 in complex with Heme bound to Carbon Monoxide==
		+	<StructureSection load='1ix4' size='340' side='right' caption='[[1ix4]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ix4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IX4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IX4 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dve\|1dve]], [[1ivj\|1ivj]], [[1qq8\|1qq8]], [[1j77\|1j77]], [[1ix3\|1ix3]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </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=1ix4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ix4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ix4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ix4 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/ix/1ix4_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 ==
		+	Heme oxygenase (HO) catalyzes heme degradation by utilizing O(2) and reducing equivalents to produce biliverdin IX alpha, iron, and CO. To avoid product inhibition, the heme[bond]HO complex (heme[bond]HO) is structured to markedly increase its affinity for O(2) while suppressing its affinity for CO. We determined the crystal structures of rat ferrous heme[bond]HO and heme[bond]HO bound to CO, CN(-), and NO at 2.3, 1.8, 2.0, and 1.7 A resolution, respectively. The heme pocket of ferrous heme-HO has the same conformation as that of the previously determined ferric form, but no ligand is visible on the distal side of the ferrous heme. Fe[bond]CO and Fe[bond]CN(-) are tilted, whereas the Fe[bond]NO is bent. The structure of heme[bond]HO bound to NO is identical to that bound to N(3)(-), which is also bent as in the case of O(2). Notably, in the CO- and CN(-)-bound forms, the heme and its ligands shift toward the alpha-meso carbon, and the distal F-helix shifts in the opposite direction. These shifts allow CO or CN(-) to bind in a tilted fashion without a collision between the distal ligand and Gly139 O and cause disruption of one salt bridge between the heme and basic residue. The structural identity of the ferrous and ferric states of heme[bond]HO indicates that these shifts are not produced on reduction of heme iron. Neither such conformational changes nor a heme shift occurs on NO or N(3)(-) binding. Heme[bond]HO therefore recognizes CO and O(2) by their binding geometries. The marked reduction in the ratio of affinities of CO to O(2) for heme[bond]HO achieved by an increase in O(2) affinity [Migita, C. T., Matera, K. M., Ikeda-Saito, M., Olson, J. S., Fujii, H., Yoshimura, T., Zhou, H., and Yoshida, T. (1998) J. Biol. Chem. 273, 945-949] is explained by hydrogen bonding and polar interactions that are favorable for O(2) binding, as well as by characteristic structural changes in the CO-bound form.

-	~~{{STRUCTURE_1ix4\| PDB=1ix4 \| SCENE= }}~~	+	Crystal structures of ferrous and CO-, CN(-)-, and NO-bound forms of rat heme oxygenase-1 (HO-1) in complex with heme: structural implications for discrimination between CO and O2 in HO-1.,Sugishima M, Sakamoto H, Noguchi M, Fukuyama K Biochemistry. 2003 Aug 26;42(33):9898-905. PMID:12924938<ref>PMID:12924938</ref>

-	~~===Crystal Structure~~ of ~~Rat Heme Oxygenase-1 in complex with Heme bound to Carbon Monoxide===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12924938}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1ix4]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rattus_norvegicus Rattus norvegicus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1IX4 OCA].~~	+

	==See Also==		==See Also==
	*[[Heme oxygenase\|Heme oxygenase]]		*[[Heme oxygenase\|Heme oxygenase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012924938<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Heme oxygenase]]		[[Category: Heme oxygenase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]

OCA at 14:06, 20 October 2012

OCA — Sat, 20 Oct 2012 14:06:53 GMT

←Older revision		Revision as of 14:06, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1ix4]] is a 1 chain structure ~~of [[Heme oxygenase]]~~ with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IX4 OCA].	+	[[1ix4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IX4 OCA].

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