6u3l - Revision history

OCA at 14:56, 13 March 2024

2024-03-13T14:56:25Z

←Older revision		Revision as of 14:56, 13 March 2024
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	<StructureSection load='6u3l' size='340' side='right'caption='[[6u3l]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='6u3l' size='340' side='right'caption='[[6u3l]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6u3l]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_12478 Atcc 12478~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6pie 6pie]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U3L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6U3L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u3l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_kansasii Mycobacterium kansasii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6pie 6pie]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U3L FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EDO:~~1~~,2-ETHANEDIOL'>EDO</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='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[6pie\|6pie]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">BZL29_7639 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1768 ATCC 12478])~~</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=6u3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u3l OCA], [https://pdbe.org/6u3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u3l RCSB], [https://www.ebi.ac.uk/pdbsum/6u3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u3l 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=6u3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u3l OCA], [~~http~~://pdbe.org/6u3l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6u3l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6u3l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6u3l ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/X7XZL2_MYCKA X7XZL2_MYCKA]
-	Pathogenic and opportunistic mycobacteria have a distinct class of non-heme di-iron hemerythrin-like proteins (HLPs). The first to be isolated was the Rv2633c protein, which plays a role in infection by Mycobacterium tuberculosis (Mtb), but could not be crystallized. This work presents the first crystal structure of an ortholog of Rv2633c, the mycobacterial HLP from Mycobacterium kansasii (Mka). This structure differs from those of hemerythrins and other known HLPs. It is comprised of five a-helices, whereas all other HLP domains have four. In contrast to other HLPs, the HLP domain is not fused to an additional protein domain. The residues ligating and surrounding the di-iron site are also unique among HLPs. Notably; a tyrosine occupies the position normally held by one of the histidine ligands in hemerythrin. This structure was used to construct a homology model of Rv2633c. The structure of five a-helices is conserved and the di-iron site ligands are identical in Rv2633c. Two residues near the ends of helices in the Mka HLP structure are replaced with prolines in Rv2633c model. This may account for structural perturbations that decrease the solubility of Rv2633c relative to Mka HLP. Clusters of residues that differ in charge or polarity between Rv2633c and Mka HLP that point outward from the helical core could reflect a specificity for potential differential interactions with other protein partners in vivo, which are related to function. The Mka HLP exhibited weaker catalase activity than Rv2633c. Evidence was obtained for interaction of Mka HLP irons with nitric oxide.	+
-		+
-	Crystal structure of a hemerythrin-like protein from Mycobacterium kansasii and homology model of the orthologous Rv2633c protein of M. tuberculosis.,Ma Z, Abendroth J, Buchko GW, Rohde KH, Davidson VL Biochem J. 2020 Jan 8. pii: ~~221812. doi: 10.1042~~/~~BCJ20190827. PMID:31913442<ref>PMID:31913442<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6u3l" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 12478]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Structural genomic]]~~	+	[[Category: Mycobacterium kansasii]]
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Ssgcid~~]]	+

OCA at 04:45, 13 February 2020

2020-02-13T04:45:47Z

←Older revision		Revision as of 04:45, 13 February 2020
Line 3:		Line 3:
	<StructureSection load='6u3l' size='340' side='right'caption='[[6u3l]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='6u3l' size='340' side='right'caption='[[6u3l]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6u3l]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6pie 6pie]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U3L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U3L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6u3l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12478 Atcc 12478]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6pie 6pie]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U3L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U3L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6pie\|6pie]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6pie\|6pie]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BZL29_7639 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1768 ATCC 12478])</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=6u3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u3l OCA], [http://pdbe.org/6u3l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u3l RCSB], [http://www.ebi.ac.uk/pdbsum/6u3l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u3l 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=6u3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u3l OCA], [http://pdbe.org/6u3l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u3l RCSB], [http://www.ebi.ac.uk/pdbsum/6u3l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u3l ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 12478]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Protein binding]]		[[Category: Protein binding]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]

OCA at 16:21, 22 January 2020

2020-01-22T16:21:31Z

←Older revision		Revision as of 16:21, 22 January 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6u3l is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Hemerythrin HHE cation binding domain-containing protein: Rv2633c homolog from Mycobacterium kansasii==
		+	<StructureSection load='6u3l' size='340' side='right'caption='[[6u3l]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6u3l]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6pie 6pie]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U3L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6U3L FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6pie\|6pie]]</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=6u3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u3l OCA], [http://pdbe.org/6u3l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u3l RCSB], [http://www.ebi.ac.uk/pdbsum/6u3l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u3l ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pathogenic and opportunistic mycobacteria have a distinct class of non-heme di-iron hemerythrin-like proteins (HLPs). The first to be isolated was the Rv2633c protein, which plays a role in infection by Mycobacterium tuberculosis (Mtb), but could not be crystallized. This work presents the first crystal structure of an ortholog of Rv2633c, the mycobacterial HLP from Mycobacterium kansasii (Mka). This structure differs from those of hemerythrins and other known HLPs. It is comprised of five a-helices, whereas all other HLP domains have four. In contrast to other HLPs, the HLP domain is not fused to an additional protein domain. The residues ligating and surrounding the di-iron site are also unique among HLPs. Notably; a tyrosine occupies the position normally held by one of the histidine ligands in hemerythrin. This structure was used to construct a homology model of Rv2633c. The structure of five a-helices is conserved and the di-iron site ligands are identical in Rv2633c. Two residues near the ends of helices in the Mka HLP structure are replaced with prolines in Rv2633c model. This may account for structural perturbations that decrease the solubility of Rv2633c relative to Mka HLP. Clusters of residues that differ in charge or polarity between Rv2633c and Mka HLP that point outward from the helical core could reflect a specificity for potential differential interactions with other protein partners in vivo, which are related to function. The Mka HLP exhibited weaker catalase activity than Rv2633c. Evidence was obtained for interaction of Mka HLP irons with nitric oxide.

-	~~Authors~~:	+	Crystal structure of a hemerythrin-like protein from Mycobacterium kansasii and homology model of the orthologous Rv2633c protein of M. tuberculosis.,Ma Z, Abendroth J, Buchko GW, Rohde KH, Davidson VL Biochem J. 2020 Jan 8. pii: 221812. doi: 10.1042/BCJ20190827. PMID:31913442<ref>PMID:31913442</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6u3l" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Structural genomic]]
		+	[[Category: Protein binding]]
		+	[[Category: Ssgcid]]

OCA at 03:52, 10 October 2019

2019-10-10T03:52:20Z

←Older revision		Revision as of 03:52, 10 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6u3l is ON HOLD	+	The entry 6u3l is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6u3l" [edit=sysop:move=sysop]

2019-08-28T14:06:47Z

Protected "6u3l" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:06, 28 August 2019

OCA: New page: '''Unreleased structure''' The entry 6u3l is ON HOLD Authors: Description: Category: Unreleased Structures

2019-08-28T14:06:45Z

New page: '''Unreleased structure''' The entry 6u3l is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6u3l is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]