4ybn - Revision history

OCA at 07:56, 27 September 2023

2023-09-27T07:56:16Z

←Older revision		Revision as of 07:56, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ybn]] 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=4YBN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YBN FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ybn]] 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=4YBN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YBN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=4ybn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybn OCA], [https://pdbe.org/4ybn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ybn RCSB], [https://www.ebi.ac.uk/pdbsum/4ybn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybn 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=4ybn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybn OCA], [https://pdbe.org/4ybn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ybn RCSB], [https://www.ebi.ac.uk/pdbsum/4ybn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybn ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:07, 3 May 2023

2023-05-03T08:07:26Z

←Older revision		Revision as of 08:07, 3 May 2023
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	<StructureSection load='4ybn' size='340' side='right'caption='[[4ybn]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4ybn' size='340' side='right'caption='[[4ybn]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ybn]] 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=4YBN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YBN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ybn]] 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=4YBN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YBN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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_4975, MSMEI_4848, LJ00_24605 ([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=4ybn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybn OCA], [https://pdbe.org/4ybn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ybn RCSB], [https://www.ebi.ac.uk/pdbsum/4ybn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybn 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=4ybn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybn OCA], [~~http~~://pdbe.org/4ybn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ybn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ybn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybn ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0R238_MYCS2 A0R238_MYCS2]
	<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: ~~Mycs2~~]]	+	[[Category: Mycolicibacterium smegmatis MC2 155]]
-	[[Category: Ahmed~~, F H~~]]	+	[[Category: Ahmed FH]]
-	[[Category: Carr~~, P D~~]]	+	[[Category: Carr PD]]
-	[[Category: Jackson~~, C J]]~~	+	[[Category: Jackson CJ]]
-	~~[[Category: Fad]]~~	+
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Split beta-barrel~~]]	+

OCA at 07:21, 12 June 2019

2019-06-12T07:21:03Z

←Older revision		Revision as of 07:21, 12 June 2019
Line 1:		Line 1:
		+
	==Structure of the FAD and Heme binding protein msmeg_4975 from Mycobacterium smegmatis==		==Structure of the FAD and Heme binding protein msmeg_4975 from Mycobacterium smegmatis==
-	<StructureSection load='4ybn' size='340' side='right' caption='[[4ybn]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='4ybn' size='340' side='right'caption='[[4ybn]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ybn]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YBN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ybn]] 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=4YBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YBN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=4ybn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybn OCA], [http://pdbe.org/4ybn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ybn RCSB], [http://www.ebi.ac.uk/pdbsum/4ybn PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MSMEG_4975, MSMEI_4848, LJ00_24605 ([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=4ybn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybn OCA], [http://pdbe.org/4ybn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ybn RCSB], [http://www.ebi.ac.uk/pdbsum/4ybn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybn 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: Large Structures]]
		+	[[Category: Mycs2]]
	[[Category: Ahmed, F H]]		[[Category: Ahmed, F H]]
	[[Category: Carr, P D]]		[[Category: Carr, P D]]

OCA at 05:26, 22 October 2015

2015-10-22T05:26:22Z

←Older revision		Revision as of 05:26, 22 October 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of the FAD and Heme binding protein msmeg_4975 from Mycobacterium smegmatis==
		+	<StructureSection load='4ybn' size='340' side='right' caption='[[4ybn]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ybn]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YBN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=4ybn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybn OCA], [http://pdbe.org/4ybn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ybn RCSB], [http://www.ebi.ac.uk/pdbsum/4ybn 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 4ybn 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 the FAD and Heme binding protein msmeg_4975 from Mycobacterium smegmatis~~	+	<div class="pdbe-citations 4ybn" 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: Fad]]
		+	[[Category: Heme]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Split beta-barrel]]

OCA at 10:34, 18 March 2015

2015-03-18T10:34:23Z

←Older revision		Revision as of 10:34, 18 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

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

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

2015-02-25T12:57:21Z

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

←Older revision

Revision as of 12:57, 25 February 2015

OCA: New page: '''Unreleased structure''' The entry 4ybn is ON HOLD Authors: Ahmed, F.H., Carr, P.D., Jackson, C.J. Description: Structure of the FAD and Heme binding protein msmeg_4975 from Mycobact...

2015-02-25T12:57:20Z

New page: '''Unreleased structure''' The entry 4ybn is ON HOLD Authors: Ahmed, F.H., Carr, P.D., Jackson, C.J. Description: Structure of the FAD and Heme binding protein msmeg_4975 from Mycobact...

New page

'''Unreleased structure'''

The entry 4ybn is ON HOLD

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

Description: Structure of the FAD and Heme binding protein msmeg_4975 from Mycobacterium smegmatis
[[Category: Unreleased Structures]]
[[Category: Ahmed, F.H]]
[[Category: Jackson, C.J]]
[[Category: Carr, P.D]]