4u72 - Revision history

OCA at 08:05, 22 March 2023

2023-03-22T08:05:56Z

←Older revision		Revision as of 08:05, 22 March 2023
Line 3:		Line 3:
	<StructureSection load='4u72' size='340' side='right'caption='[[4u72]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4u72' size='340' side='right'caption='[[4u72]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4u72]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U72 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4U72 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4u72]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U72 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4U72 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene>, <scene name='pdbligand=PIM:4-PHENYL-1H-IMIDAZOLE'>PIM</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene>, <scene name='pdbligand=PIM:4-PHENYL-1H-IMIDAZOLE'>PIM</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d0t\|2d0t]]</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=4u72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u72 OCA], [https://pdbe.org/4u72 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4u72 RCSB], [https://www.ebi.ac.uk/pdbsum/4u72 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4u72 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IDO1, IDO, INDO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Indoleamine_2,3-dioxygenase Indoleamine 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.52 1.13.11.52] </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=4u72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u72 OCA], [~~http~~://pdbe.org/4u72 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4u72 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4u72 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4u72 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/I23O1_HUMAN I23O1_HUMAN]] Catalyzes the cleavage of the pyrrol ring of tryptophan and incorporates both atoms of a molecule of oxygen.<ref>PMID:17671174</ref>	+	[https://www.uniprot.org/uniprot/I23O1_HUMAN I23O1_HUMAN] Catalyzes the cleavage of the pyrrol ring of tryptophan and incorporates both atoms of a molecule of oxygen.<ref>PMID:17671174</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Human indoleamine 2,3-dioxygenase (IDO) catalyzes the cleavage of the pyrrol ring of L-Trp and incorporates both atoms of a molecule of oxygen (O2). Here we report on the x-ray crystal structure of human IDO, complexed with the ligand inhibitor 4-phenylimidazole and cyanide. The overall structure of IDO shows two alpha-helical domains with the heme between them. A264 of the flexible loop in the heme distal side is in close proximity to the iron. A mutant analysis shows that none of the polar amino acid residues in the distal heme pocket are essential for activity, suggesting that, unlike the heme-containing monooxygenases (i.e., peroxidase and cytochrome P450), no protein group of IDO is essential in dioxygen activation or proton abstraction. These characteristics of the IDO structure provide support for a reaction mechanism involving the abstraction of a proton from the substrate by iron-bound dioxygen. Inactive mutants (F226A, F227A, and R231A) retain substrate-binding affinity, and an electron density map reveals that 2-(N-cyclohexylamino)ethane sulfonic acid is bound to these residues, mimicking the substrate. These findings suggest that strict shape complementarities between the indole ring of the substrate and the protein side chains are required, not for binding, but, rather, to permit the interaction between the substrate and iron-bound dioxygen in the first step of the reaction. This study provides the structural basis for a heme-containing dioxygenase mechanism, a missing piece in our understanding of heme chemistry.	+
-		+
-	Crystal structure of human indoleamine 2,3-dioxygenase: catalytic mechanism of O2 incorporation by a heme-containing dioxygenase.,Sugimoto H, Oda S, Otsuki T, Hino T, Yoshida T, Shiro Y Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2611-6. Epub 2006 Feb 13. PMID:16477023<ref>PMID:16477023</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4u72" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 28:		Line 16:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Indoleamine 2,3-dioxygenase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Horitani, M]]	+	[[Category: Horitani M]]
-	[[Category: Kometani, E]]	+	[[Category: Kometani E]]
-	[[Category: Shiro, Y]]	+	[[Category: Shiro Y]]
-	[[Category: Sugimoto, H]]	+	[[Category: Sugimoto H]]
-	~~[[Category: All alpha]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 15:58, 29 January 2020

2020-01-29T15:58:14Z

←Older revision		Revision as of 15:58, 29 January 2020
Line 23:		Line 23:

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

OCA at 15:01, 10 May 2019

2019-05-10T15:01:20Z

←Older revision		Revision as of 15:01, 10 May 2019
Line 1:		Line 1:
		+
	==Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (A260G mutant)==		==Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (A260G mutant)==
-	<StructureSection load='4u72' size='340' side='right' caption='[[4u72]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='4u72' size='340' side='right'caption='[[4u72]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4u72]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U72 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U72 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4u72]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U72 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U72 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene>, <scene name='pdbligand=PIM:4-PHENYL-1H-IMIDAZOLE'>PIM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene>, <scene name='pdbligand=PIM:4-PHENYL-1H-IMIDAZOLE'>PIM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d0t\|2d0t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d0t\|2d0t]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IDO1, IDO, INDO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Indoleamine_2,3-dioxygenase Indoleamine 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.52 1.13.11.52] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Indoleamine_2,3-dioxygenase Indoleamine 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.52 1.13.11.52] </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=4u72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u72 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4u72 RCSB], [http://www.ebi.ac.uk/pdbsum/4u72 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=4u72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u72 OCA], [http://pdbe.org/4u72 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4u72 RCSB], [http://www.ebi.ac.uk/pdbsum/4u72 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4u72 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 20:
	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 4u72" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase\|Dioxygenase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Indoleamine 2,3-dioxygenase]]		[[Category: Indoleamine 2,3-dioxygenase]]
		+	[[Category: Large Structures]]
	[[Category: Horitani, M]]		[[Category: Horitani, M]]
	[[Category: Kometani, E]]		[[Category: Kometani, E]]

OCA at 12:22, 2 September 2015

2015-09-02T12:22:55Z

←Older revision		Revision as of 12:22, 2 September 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (A260G mutant)==
		+	<StructureSection load='4u72' size='340' side='right' caption='[[4u72]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4u72]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U72 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U72 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene>, <scene name='pdbligand=PIM:4-PHENYL-1H-IMIDAZOLE'>PIM</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d0t\|2d0t]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Indoleamine_2,3-dioxygenase Indoleamine 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.52 1.13.11.52] </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=4u72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u72 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4u72 RCSB], [http://www.ebi.ac.uk/pdbsum/4u72 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/I23O1_HUMAN I23O1_HUMAN]] Catalyzes the cleavage of the pyrrol ring of tryptophan and incorporates both atoms of a molecule of oxygen.<ref>PMID:17671174</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human indoleamine 2,3-dioxygenase (IDO) catalyzes the cleavage of the pyrrol ring of L-Trp and incorporates both atoms of a molecule of oxygen (O2). Here we report on the x-ray crystal structure of human IDO, complexed with the ligand inhibitor 4-phenylimidazole and cyanide. The overall structure of IDO shows two alpha-helical domains with the heme between them. A264 of the flexible loop in the heme distal side is in close proximity to the iron. A mutant analysis shows that none of the polar amino acid residues in the distal heme pocket are essential for activity, suggesting that, unlike the heme-containing monooxygenases (i.e., peroxidase and cytochrome P450), no protein group of IDO is essential in dioxygen activation or proton abstraction. These characteristics of the IDO structure provide support for a reaction mechanism involving the abstraction of a proton from the substrate by iron-bound dioxygen. Inactive mutants (F226A, F227A, and R231A) retain substrate-binding affinity, and an electron density map reveals that 2-(N-cyclohexylamino)ethane sulfonic acid is bound to these residues, mimicking the substrate. These findings suggest that strict shape complementarities between the indole ring of the substrate and the protein side chains are required, not for binding, but, rather, to permit the interaction between the substrate and iron-bound dioxygen in the first step of the reaction. This study provides the structural basis for a heme-containing dioxygenase mechanism, a missing piece in our understanding of heme chemistry.

-	~~The entry 4u72 is ON HOLD until Paper Publication~~	+	Crystal structure of human indoleamine 2,3-dioxygenase: catalytic mechanism of O2 incorporation by a heme-containing dioxygenase.,Sugimoto H, Oda S, Otsuki T, Hino T, Yoshida T, Shiro Y Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2611-6. Epub 2006 Feb 13. PMID:16477023<ref>PMID:16477023</ref>

-	~~Authors: Sugimoto~~, H.~~, Horitani, M~~.~~, Kometani, E., Shiro, Y~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of 4-phenylimidazole bound form of human indoleamine~~ 2,3-dioxygenase ~~(A260G mutant)~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Indoleamine 2,3-dioxygenase]]
		+	[[Category: Horitani, M]]
		+	[[Category: Kometani, E]]
	[[Category: Shiro, Y]]		[[Category: Shiro, Y]]
	[[Category: Sugimoto, H]]		[[Category: Sugimoto, H]]
-	[[Category: ~~Kometani, E~~]]	+	[[Category: All alpha]]
-	[[Category: ~~Horitani, M~~]]	+	[[Category: Metal-binding]]
		+	[[Category: Oxidoreductase]]

OCA at 18:12, 24 December 2014

2014-12-24T18:12:23Z

←Older revision		Revision as of 18:12, 24 December 2014
Line 6:		Line 6:

	Description: Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (A260G mutant)		Description: Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (A260G mutant)
		+	[[Category: Unreleased Structures]]
		+	[[Category: Shiro, Y]]
		+	[[Category: Sugimoto, H]]
		+	[[Category: Kometani, E]]
		+	[[Category: Horitani, M]]

OCA at 07:16, 27 August 2014

2014-08-27T07:16:35Z

←Older revision		Revision as of 07:16, 27 August 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4u72 is ON HOLD	+	The entry 4u72 is ON HOLD until Paper Publication

	Authors: Sugimoto, H., Horitani, M., Kometani, E., Shiro, Y.		Authors: Sugimoto, H., Horitani, M., Kometani, E., Shiro, Y.

	Description: Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (A260G mutant)		Description: Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (A260G mutant)

OCA at 15:03, 20 August 2014

2014-08-20T15:03:07Z

←Older revision		Revision as of 15:03, 20 August 2014
Line 3:		Line 3:
	The entry 4u72 is ON HOLD		The entry 4u72 is ON HOLD

-	Authors: Sugimoto, ~~Hiroshi~~, Horitani, ~~Masaki~~, Kometani, ~~Erisa~~, Shiro, ~~Yoshitsugu~~	+	Authors: Sugimoto, H., Horitani, M., Kometani, E., Shiro, Y.

	Description: Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (A260G mutant)		Description: Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (A260G mutant)

OCA: Protected "4u72" [edit=sysop:move=sysop]

2014-08-07T01:32:45Z

Protected "4u72" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:32, 7 August 2014

OCA: New page: '''Unreleased structure''' The entry 4u72 is ON HOLD Authors: Sugimoto, Hiroshi, Horitani, Masaki, Kometani, Erisa, Shiro, Yoshitsugu Description: Crystal structure of 4-phenylimidazol...

2014-08-07T01:32:43Z

New page: '''Unreleased structure''' The entry 4u72 is ON HOLD Authors: Sugimoto, Hiroshi, Horitani, Masaki, Kometani, Erisa, Shiro, Yoshitsugu Description: Crystal structure of 4-phenylimidazol...

New page

'''Unreleased structure'''

The entry 4u72 is ON HOLD

Authors: Sugimoto, Hiroshi, Horitani, Masaki, Kometani, Erisa, Shiro, Yoshitsugu

Description: Crystal structure of 4-phenylimidazole bound form of human indoleamine 2,3-dioxygenase (A260G mutant)