4zky - Revision history

OCA at 08:19, 27 September 2023

OCA — Wed, 27 Sep 2023 08:19:51 GMT

←Older revision		Revision as of 08:19, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4zky]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZKY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4zky]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZKY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.65Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=4zky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zky OCA], [https://pdbe.org/4zky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zky RCSB], [https://www.ebi.ac.uk/pdbsum/4zky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zky 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=4zky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zky OCA], [https://pdbe.org/4zky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zky RCSB], [https://www.ebi.ac.uk/pdbsum/4zky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zky ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:32, 18 May 2023

OCA — Thu, 18 May 2023 07:32:00 GMT

←Older revision		Revision as of 07:32, 18 May 2023
Line 3:		Line 3:
	<StructureSection load='4zky' size='340' side='right'caption='[[4zky]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='4zky' size='340' side='right'caption='[[4zky]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zky]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZKY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ZKY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zky]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZKY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyridoxal_5'-phosphate_synthase Pyridoxal 5'-phosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.5 1.4.3.5] </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=4zky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zky OCA], [https://pdbe.org/4zky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zky RCSB], [https://www.ebi.ac.uk/pdbsum/4zky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zky 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=4zky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zky OCA], [~~http~~://pdbe.org/4zky PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4zky RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4zky PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4zky ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0R6F1_MYCS2 A0R6F1_MYCS2]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pyridoxal 5'-phosphate synthase~~]]	+	[[Category: Mycolicibacterium smegmatis]]
-	[[Category: Ahmed~~, F H~~]]	+	[[Category: Ahmed FH]]
-	[[Category: Carr~~, P D~~]]	+	[[Category: Carr PD]]
-	[[Category: Jackson~~, C J~~]]	+	[[Category: Jackson CJ]]
-	[[Category: Lee~~, B M]]~~	+	[[Category: Lee BM]]
-	~~[[Category: F420]]~~	+
-	~~[[Category: Fdor]]~~	+
-	~~[[Category: Fdr]]~~	+
-	~~[[Category: Fdr-b]]~~	+
-	~~[[Category: Msmeg_6526]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Reductase~~]]	+

OCA at 07:36, 4 March 2020

OCA — Wed, 04 Mar 2020 07:36:35 GMT

←Older revision		Revision as of 07:36, 4 March 2020
Line 1:		Line 1:

	==Structure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis==		==Structure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis==
-	<StructureSection load='4zky' size='340' side='right' caption='[[4zky]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='4zky' size='340' side='right'caption='[[4zky]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4zky]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZKY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4zky]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZKY FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pyridoxal 5'-phosphate synthase]]		[[Category: Pyridoxal 5'-phosphate synthase]]
	[[Category: Ahmed, F H]]		[[Category: Ahmed, F H]]

OCA at 17:10, 18 August 2017

OCA — Fri, 18 Aug 2017 17:10:17 GMT

←Older revision		Revision as of 17:10, 18 August 2017
Line 1:		Line 1:
		+
	==Structure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis==		==Structure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis==
	<StructureSection load='4zky' size='340' side='right' caption='[[4zky]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='4zky' size='340' side='right' caption='[[4zky]], [[Resolution\|resolution]] 1.65Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyridoxal_5'-phosphate_synthase Pyridoxal 5'-phosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.5 1.4.3.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyridoxal_5'-phosphate_synthase Pyridoxal 5'-phosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.5 1.4.3.5] </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=4zky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zky OCA], [http://pdbe.org/4zky PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zky RCSB], [http://www.ebi.ac.uk/pdbsum/4zky 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=4zky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zky OCA], [http://pdbe.org/4zky PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zky RCSB], [http://www.ebi.ac.uk/pdbsum/4zky PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zky ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:10, 30 November 2015

OCA — Mon, 30 Nov 2015 19:10:47 GMT

←Older revision		Revision as of 19:10, 30 November 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis==
		+	<StructureSection load='4zky' size='340' side='right' caption='[[4zky]], [[Resolution\|resolution]] 1.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4zky]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZKY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyridoxal_5'-phosphate_synthase Pyridoxal 5'-phosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.5 1.4.3.5] </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=4zky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zky OCA], [http://pdbe.org/4zky PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zky RCSB], [http://www.ebi.ac.uk/pdbsum/4zky 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 4zky 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: Lee~~, B.M.~~, Carr, P.D., Ahmed, F.H., Jackson, C.J~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Structure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis~~	+	<div class="pdbe-citations 4zky" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: Ahmed, F.H]]	+	<references/>
-	[[Category: Jackson, C.J]]	+	__TOC__
-	[[Category: Lee, B.M]]	+	</StructureSection>
-	[[Category: ~~Carr, P.D~~]]	+	[[Category: Pyridoxal 5'-phosphate synthase]]
		+	[[Category: Ahmed, F H]]
		+	[[Category: Carr, P D]]
		+	[[Category: Jackson, C J]]
		+	[[Category: Lee, B M]]
		+	[[Category: F420]]
		+	[[Category: Fdor]]
		+	[[Category: Fdr]]
		+	[[Category: Fdr-b]]
		+	[[Category: Msmeg_6526]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Reductase]]

OCA at 07:45, 9 September 2015

OCA — Wed, 09 Sep 2015 07:45:36 GMT

←Older revision		Revision as of 07:45, 9 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

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

OCA at 11:04, 13 May 2015

OCA — Wed, 13 May 2015 11:04:31 GMT

←Older revision		Revision as of 11:04, 13 May 2015
Line 3:		Line 3:
	The entry 4zky is ON HOLD		The entry 4zky is ON HOLD

-	Authors: Lee, B.M., Carr, P.D, Ahmed, F.H., Jackson, C.J.	+	Authors: Lee, B.M., Carr, P.D., Ahmed, F.H., Jackson, C.J.

-	Description: Structure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis.	+	Description: Structure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Carr, P.D,~~ Ahmed, F.H]]	+	[[Category: Ahmed, F.H]]
	[[Category: Jackson, C.J]]		[[Category: Jackson, C.J]]
	[[Category: Lee, B.M]]		[[Category: Lee, B.M]]
		+	[[Category: Carr, P.D]]

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

OCA — Wed, 06 May 2015 11:53:49 GMT

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

←Older revision

Revision as of 11:53, 6 May 2015

OCA: New page: '''Unreleased structure''' The entry 4zky is ON HOLD Authors: Lee, B.M., Carr, P.D, Ahmed, F.H., Jackson, C.J. Description: Structure of F420 binding protein, MSMEG_6526, from Mycobact...

OCA — Wed, 06 May 2015 11:53:48 GMT

New page: '''Unreleased structure''' The entry 4zky is ON HOLD Authors: Lee, B.M., Carr, P.D, Ahmed, F.H., Jackson, C.J. Description: Structure of F420 binding protein, MSMEG_6526, from Mycobact...

New page

'''Unreleased structure'''

The entry 4zky is ON HOLD

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

Description: Structure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis.
[[Category: Unreleased Structures]]
[[Category: Carr, P.D, Ahmed, F.H]]
[[Category: Jackson, C.J]]
[[Category: Lee, B.M]]