4kia - Revision history

OCA at 14:30, 8 November 2023

OCA — Wed, 08 Nov 2023 14:30:16 GMT

←Older revision		Revision as of 14:30, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kia]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_monocytogenes_EGD-e Listeria monocytogenes EGD-e]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KIA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KIA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kia]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_monocytogenes_EGD-e Listeria monocytogenes EGD-e]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KIA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KIA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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]] 1.75Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4kia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kia OCA], [https://pdbe.org/4kia PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kia RCSB], [https://www.ebi.ac.uk/pdbsum/4kia PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kia 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=4kia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kia OCA], [https://pdbe.org/4kia PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kia RCSB], [https://www.ebi.ac.uk/pdbsum/4kia PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kia ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:53, 7 December 2022

OCA — Wed, 07 Dec 2022 08:53:45 GMT

←Older revision		Revision as of 08:53, 7 December 2022
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	<StructureSection load='4kia' size='340' side='right'caption='[[4kia]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='4kia' size='340' side='right'caption='[[4kia]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kia]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lismo Lismo~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KIA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4KIA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kia]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_monocytogenes_EGD-e Listeria monocytogenes EGD-e]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KIA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KIA FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lmo2213 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=169963 LISMO])~~</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=4kia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kia OCA], [https://pdbe.org/4kia PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kia RCSB], [https://www.ebi.ac.uk/pdbsum/4kia PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kia ProSAT]</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=4kia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kia OCA], [~~http~~://pdbe.org/4kia PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4kia RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4kia PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4kia ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/HMO_LISMO HMO_LISMO] Catalyzes the degradation of heme to biliverdin in the presence of a suitable electron donor such as ascorbate, with the subsequent release of iron. Hardly any CO is released by the heme degradation reaction. Binds heme (PubMed:24598731). Allows bacterial pathogens to use the host heme as an iron source. Release of iron from heme may play a crucial role in the pathogenicity of L.monocytogenes (Probable).<ref>PMID:24598731</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lismo~~]]	+	[[Category: Listeria monocytogenes EGD-e]]
-	[[Category: Duong, T]]	+	[[Category: Duong T]]
-	[[Category: Kim~~, K K~~]]	+	[[Category: Kim KK]]
-	[[Category: Kim, T]]	+	[[Category: Kim T]]
-	~~[[Category: Ferredoxin fold]]~~	+
-	~~[[Category: Heme binding]]~~	+
-	~~[[Category: Heme-degrading enzyme]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 08:38, 1 January 2020

OCA — Wed, 01 Jan 2020 08:38:03 GMT

←Older revision		Revision as of 08:38, 1 January 2020
Line 1:		Line 1:

	==Crystal structure of LmHde, heme-degrading enzyme, from Listeria monocytogenes==		==Crystal structure of LmHde, heme-degrading enzyme, from Listeria monocytogenes==
-	<StructureSection load='4kia' size='340' side='right' caption='[[4kia]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='4kia' size='340' side='right'caption='[[4kia]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kia]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lismo Lismo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KIA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kia]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lismo Lismo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KIA FirstGlance]. <br>
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	<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=4kia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kia OCA], [http://pdbe.org/4kia PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kia RCSB], [http://www.ebi.ac.uk/pdbsum/4kia PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kia ProSAT]</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=4kia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kia OCA], [http://pdbe.org/4kia PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kia RCSB], [http://www.ebi.ac.uk/pdbsum/4kia PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kia ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial pathogens have evolved diverse types of efficient machinery to acquire haem, the most abundant source of iron in the human body, and degrade it for the utilization of iron. Gram-positive bacteria commonly encode IsdG-family proteins as haem-degrading monooxygenases. Listeria monocytogenes is predicted to possess an IsdG-type protein (Lmo2213), but the residues involved in haem monooxygenase activity are not well conserved and there is an extra N-terminal domain in Lmo2213. Therefore, its function and mechanism of action cannot be predicted. In this study, the crystal structure of Lmo2213 was determined at 1.75 A resolution and its haem-binding and haem-degradation activities were confirmed. Structure-based mutational and functional assays of this protein, designated as an Isd-type L. monocytogenes haem-degrading enzyme (Isd-LmHde), identified that Glu71, Tyr87 and Trp129 play important roles in haem degradation and that the N-terminal domain is also critical for its haem-degrading activity. The haem-degradation product of Isd-LmHde is verified to be biliverdin, which is also known to be the degradation product of other bacterial haem oxygenases. This study, the first structural and functional report of the haem-degradation system in L. monocytogenes, sheds light on the concealed haem-utilization system in this life-threatening human pathogen.
		+
		+	Structural and functional characterization of an Isd-type haem-degradation enzyme from Listeria monocytogenes.,Duong T, Park K, Kim T, Kang SW, Hahn MJ, Hwang HY, Jang I, Oh HB, Kim KK Acta Crystallogr D Biol Crystallogr. 2014 Mar;70(Pt 3):615-26. doi:, 10.1107/S1399004713030794. Epub 2014 Feb 15. PMID:24598731<ref>PMID:24598731</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4kia" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lismo]]		[[Category: Lismo]]
	[[Category: Duong, T]]		[[Category: Duong, T]]

OCA at 07:38, 11 August 2016

OCA — Thu, 11 Aug 2016 07:38:52 GMT

←Older revision		Revision as of 07:38, 11 August 2016
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		+
	==Crystal structure of LmHde, heme-degrading enzyme, from Listeria monocytogenes==		==Crystal structure of LmHde, heme-degrading enzyme, from Listeria monocytogenes==
	<StructureSection load='4kia' size='340' side='right' caption='[[4kia]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='4kia' size='340' side='right' caption='[[4kia]], [[Resolution\|resolution]] 1.75Å' scene=''>
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	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lmo2213 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=169963 LISMO])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lmo2213 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=169963 LISMO])</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=4kia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kia OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kia RCSB], [http://www.ebi.ac.uk/pdbsum/4kia 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=4kia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kia OCA], [http://pdbe.org/4kia PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kia RCSB], [http://www.ebi.ac.uk/pdbsum/4kia PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kia ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 12:53, 4 January 2015

OCA — Sun, 04 Jan 2015 12:53:00 GMT

←Older revision		Revision as of 12:53, 4 January 2015
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-	~~{{STRUCTURE_4kia\| PDB=4kia \| SCENE= }}~~	+	==Crystal structure of LmHde, heme-degrading enzyme, from Listeria monocytogenes==
-	===Crystal structure of LmHde, heme-degrading enzyme, from Listeria monocytogenes===	+	<StructureSection load='4kia' size='340' side='right' caption='[[4kia]], [[Resolution\|resolution]] 1.75Å' scene=''>
-		+	== Structural highlights ==
-	==~~About this Structure~~==	+	<table><tr><td colspan='2'>[[4kia]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lismo Lismo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KIA FirstGlance]. <br>
-	[[4kia]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KIA OCA].	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	[[Category: Duong, T.]]	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lmo2213 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=169963 LISMO])</td></tr>
-	[[Category: Kim, K K.]]	+	<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=4kia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kia OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kia RCSB], [http://www.ebi.ac.uk/pdbsum/4kia PDBsum]</span></td></tr>
-	[[Category: Kim, T.]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Lismo]]
		+	[[Category: Duong, T]]
		+	[[Category: Kim, K K]]
		+	[[Category: Kim, T]]
	[[Category: Ferredoxin fold]]		[[Category: Ferredoxin fold]]
	[[Category: Heme binding]]		[[Category: Heme binding]]
	[[Category: Heme-degrading enzyme]]		[[Category: Heme-degrading enzyme]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 13:58, 12 March 2014

OCA — Wed, 12 Mar 2014 13:58:45 GMT

←Older revision		Revision as of 13:58, 12 March 2014
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-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4kia\| PDB=4kia \| SCENE= }}
		+	===Crystal structure of LmHde, heme-degrading enzyme, from Listeria monocytogenes===

-	~~The entry~~ 4kia is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[4kia]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KIA OCA].
-	~~Authors~~: ~~Kim, K~~.K., Duong, T., Kim, T.	+	[[Category: Duong, T.]]
-		+	[[Category: Kim, K K.]]
-	~~Description~~: ~~Crystal structure of LmHde, heme~~-degrading enzyme~~, from Listeria monocytogenes~~	+	[[Category: Kim, T.]]
		+	[[Category: Ferredoxin fold]]
		+	[[Category: Heme binding]]
		+	[[Category: Heme-degrading enzyme]]
		+	[[Category: Oxidoreductase]]

OCA at 08:55, 8 January 2014

OCA — Wed, 08 Jan 2014 08:55:13 GMT

←Older revision		Revision as of 08:55, 8 January 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Kim, K.K., Duong, T., Kim, T.		Authors: Kim, K.K., Duong, T., Kim, T.

	Description: Crystal structure of LmHde, heme-degrading enzyme, from Listeria monocytogenes		Description: Crystal structure of LmHde, heme-degrading enzyme, from Listeria monocytogenes

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

OCA — Wed, 08 May 2013 07:24:38 GMT

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

←Older revision

Revision as of 07:24, 8 May 2013

OCA: New page: '''Unreleased structure''' The entry 4kia is ON HOLD Authors: Kim, K.K., Duong, T., Kim, T. Description: Crystal structure of LmHde, heme-degrading enzyme, from Listeria monocytogenes

OCA — Wed, 08 May 2013 07:24:37 GMT

New page: '''Unreleased structure''' The entry 4kia is ON HOLD Authors: Kim, K.K., Duong, T., Kim, T. Description: Crystal structure of LmHde, heme-degrading enzyme, from Listeria monocytogenes

New page

'''Unreleased structure'''

The entry 4kia is ON HOLD

Authors: Kim, K.K., Duong, T., Kim, T.

Description: Crystal structure of LmHde, heme-degrading enzyme, from Listeria monocytogenes