5bnc - Revision history

OCA at 08:27, 27 September 2023

OCA — Wed, 27 Sep 2023 08:27:50 GMT

←Older revision		Revision as of 08:27, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5bnc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BNC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BNC FirstGlance]. <br>		<table><tr><td colspan='2'>[[5bnc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BNC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BNC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2.25Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5bnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bnc OCA], [https://pdbe.org/5bnc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bnc RCSB], [https://www.ebi.ac.uk/pdbsum/5bnc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bnc 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=5bnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bnc OCA], [https://pdbe.org/5bnc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bnc RCSB], [https://www.ebi.ac.uk/pdbsum/5bnc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bnc ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:00, 7 June 2023

OCA — Wed, 07 Jun 2023 06:00:45 GMT

←Older revision		Revision as of 06:00, 7 June 2023
Line 1:		Line 1:

	==Structure of heme binding protein MSMEG_6519 from Mycobacterium smegmatis==		==Structure of heme binding protein MSMEG_6519 from Mycobacterium smegmatis==
-	<StructureSection load='5bnc' size='340' side='right' caption='[[5bnc]], [[Resolution\|resolution]] 2.25Å' scene=''>	+	<StructureSection load='5bnc' size='340' side='right'caption='[[5bnc]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bnc]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Mycs2 Mycs2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BNC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5BNC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bnc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BNC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BNC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MSMEG_6519, MSMEI_6345, LJ00_32225 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</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=5bnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bnc OCA], [https://pdbe.org/5bnc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bnc RCSB], [https://www.ebi.ac.uk/pdbsum/5bnc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bnc 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=5bnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bnc OCA], [~~http~~://pdbe.org/5bnc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5bnc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5bnc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5bnc ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0R6E4_MYCS2 A0R6E4_MYCS2]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Mycs2~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Ahmed, F H~~]]	+	[[Category: Mycolicibacterium smegmatis MC2 155]]
-	[[Category: ~~Carr, P D~~]]	+	[[Category: Ahmed FH]]
-	[[Category: ~~Jackson, C J~~]]	+	[[Category: Carr PD]]
-	[[Category: ~~Heme binding protein]]~~	+	[[Category: Jackson CJ]]
-	~~[[Category: Heme oxygenase]]~~	+
-	~~[[Category: Split beta-barrel~~]]	+

OCA at 09:08, 1 November 2017

OCA — Wed, 01 Nov 2017 09:08:56 GMT

←Older revision		Revision as of 09:08, 1 November 2017
Line 1:		Line 1:
		+
	==Structure of heme binding protein MSMEG_6519 from Mycobacterium smegmatis==		==Structure of heme binding protein MSMEG_6519 from Mycobacterium smegmatis==
	<StructureSection load='5bnc' size='340' side='right' caption='[[5bnc]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='5bnc' size='340' side='right' caption='[[5bnc]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bnc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BNC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BNC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bnc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BNC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BNC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5bnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bnc OCA], [http://pdbe.org/5bnc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bnc RCSB], [http://www.ebi.ac.uk/pdbsum/5bnc PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MSMEG_6519, MSMEI_6345, LJ00_32225 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</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=5bnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bnc OCA], [http://pdbe.org/5bnc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bnc RCSB], [http://www.ebi.ac.uk/pdbsum/5bnc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bnc ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Mycs2]]
	[[Category: Ahmed, F H]]		[[Category: Ahmed, F H]]
	[[Category: Carr, P D]]		[[Category: Carr, P D]]

OCA at 05:22, 22 October 2015

OCA — Thu, 22 Oct 2015 05:22:59 GMT

←Older revision		Revision as of 05:22, 22 October 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of heme binding protein MSMEG_6519 from Mycobacterium smegmatis==
		+	<StructureSection load='5bnc' size='340' side='right' caption='[[5bnc]], [[Resolution\|resolution]] 2.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5bnc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BNC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BNC FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5bnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bnc OCA], [http://pdbe.org/5bnc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bnc RCSB], [http://www.ebi.ac.uk/pdbsum/5bnc PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The deazaflavin cofactor F420 enhances the persistence of mycobacteria during hypoxia, oxidative stress, and antibiotic treatment. However, the identities and functions of the mycobacterial enzymes that utilize F420 under these conditions have yet to be resolved. In this work, we used sequence similarity networks to analyze the distribution of the largest F420-dependent protein family in mycobacteria. We show that these enzymes are part of a larger split beta-barrel enzyme superfamily (flavin/deazaflavin oxidoreductases, FDORs) that include previously characterized pyridoxamine/pyridoxine-5'-phosphate oxidases and heme oxygenases. We show that these proteins variously utilize F420, flavin mononucleotide, flavin adenine dinucleotide, and heme cofactors. Functional annotation using phylogenetic, structural, and spectroscopic methods revealed their involvement in heme degradation, biliverdin reduction, fatty acid modification, and quinone reduction. Four novel crystal structures show that plasticity in substrate binding pockets and modifications to cofactor binding motifs enabled FDORs to carry out a variety of functions. This systematic classification and analysis provides a framework for further functional analysis of the roles of FDORs in mycobacterial pathogenesis and persistence.

-	~~The entry 5bnc is ON HOLD until Paper Publication~~	+	Sequence-Structure-Function Classification of a Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria.,Ahmed FH, Carr PD, Lee BM, Afriat-Jurnou L, Mohamed AE, Hong NS, Flanagan J, Taylor MC, Greening C, Jackson CJ J Mol Biol. 2015 Oct 3. pii: S0022-2836(15)00544-6. doi:, 10.1016/j.jmb.2015.09.021. PMID:26434506<ref>PMID:26434506</ref>

-	~~Authors: Ahmed~~, F.H.~~, Carr, P.D., Jackson, C.J~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Structure of heme binding protein MSMEG_6519 from Mycobacterium smegmatis~~	+	<div class="pdbe-citations 5bnc" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: ~~Ahmed~~, ~~F.H~~]]	+	<references/>
-	[[Category: Jackson, C.J]]	+	__TOC__
-	[[Category: ~~Carr, P.D~~]]	+	</StructureSection>
		+	[[Category: Ahmed, F H]]
		+	[[Category: Carr, P D]]
		+	[[Category: Jackson, C J]]
		+	[[Category: Heme binding protein]]
		+	[[Category: Heme oxygenase]]
		+	[[Category: Split beta-barrel]]

OCA: Protected "5bnc" [edit=sysop:move=sysop]

OCA — Wed, 03 Jun 2015 11:39:38 GMT

Protected "5bnc" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:39, 3 June 2015

OCA: New page: '''Unreleased structure''' The entry 5bnc is ON HOLD until Paper Publication Authors: Ahmed, F.H., Carr, P.D., Jackson, C.J. Description: Structure of heme binding protein MSMEG_6519 f...

OCA — Wed, 03 Jun 2015 11:39:37 GMT

New page: '''Unreleased structure''' The entry 5bnc is ON HOLD until Paper Publication Authors: Ahmed, F.H., Carr, P.D., Jackson, C.J. Description: Structure of heme binding protein MSMEG_6519 f...

New page

'''Unreleased structure'''

The entry 5bnc is ON HOLD until Paper Publication

Authors: Ahmed, F.H., Carr, P.D., Jackson, C.J.

Description: Structure of heme binding protein MSMEG_6519 from Mycobacterium smegmatis
[[Category: Unreleased Structures]]
[[Category: Ahmed, F.H]]
[[Category: Jackson, C.J]]
[[Category: Carr, P.D]]