6oj1 - Revision history

OCA at 07:11, 11 October 2023

OCA — Wed, 11 Oct 2023 07:11:18 GMT

←Older revision		Revision as of 07:11, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6oj1' size='340' side='right'caption='[[6oj1]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='6oj1' size='340' side='right'caption='[[6oj1]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6oj1]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aspfu Aspfu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJ1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6OJ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6oj1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_fumigatus_Af293 Aspergillus fumigatus Af293]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OJ1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 1.76Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AFUA_3G07890 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=330879 ASPFU])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=6oj1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oj1 OCA], [~~http~~://pdbe.org/6oj1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6oj1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6oj1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6oj1 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=6oj1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oj1 OCA], [https://pdbe.org/6oj1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6oj1 RCSB], [https://www.ebi.ac.uk/pdbsum/6oj1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6oj1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q4WX16_ASPFU Q4WX16_ASPFU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aspfu~~]]	+	[[Category: Aspergillus fumigatus Af293]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bamford~~, N C~~]]	+	[[Category: Bamford NC]]
-	[[Category: Howell~~, P L~~]]	+	[[Category: Howell PL]]
-	[[Category: Millan, C]]	+	[[Category: Millan C]]
-	[[Category: Subramanian~~, A S~~]]	+	[[Category: Subramanian AS]]
-	[[Category: Uson, I]]	+	[[Category: Uson I]]
-	~~[[Category: Galactosaminidase]]~~	+
-	~~[[Category: Glycoside hydrolase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 09:28, 8 January 2020

OCA — Wed, 08 Jan 2020 09:28:59 GMT

←Older revision		Revision as of 09:28, 8 January 2020
Line 3:		Line 3:
	<StructureSection load='6oj1' size='340' side='right'caption='[[6oj1]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='6oj1' size='340' side='right'caption='[[6oj1]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6oj1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OJ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6oj1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspfu Aspfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OJ1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AFUA_3G07890 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=330879 ASPFU])</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=6oj1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oj1 OCA], [http://pdbe.org/6oj1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oj1 RCSB], [http://www.ebi.ac.uk/pdbsum/6oj1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oj1 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=6oj1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oj1 OCA], [http://pdbe.org/6oj1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oj1 RCSB], [http://www.ebi.ac.uk/pdbsum/6oj1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oj1 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aspergillus fumigatus is an opportunistic fungal pathogen that causes both chronic and acute invasive infections. Galactosaminogalactan (GAG) is an integral component of the A. fumigatus biofilm matrix and a key virulence factor. GAG is a heterogeneous linear alpha-1,4-linked exopolysaccharide of galactose and GalNAc that is partially deacetylated after secretion. A cluster of five co-expressed genes has been linked to GAG biosynthesis and modification. One gene in this cluster, ega3, is annotated as encoding a putative alpha-1,4-galactosaminidase belonging to glycoside hydrolase family 114 (GH114). Herein, we show that recombinant Ega3 is an active glycoside hydrolase that disrupts GAG-dependent A. fumigatus and Pel polysaccharide-dependent Pseudomonas aeruginosa biofilms at nanomolar concentrations. Using MS and functional assays, we demonstrate that Ega3 is an endo-acting alpha-1,4-galactosaminidase whose activity depends on the conserved acidic residues, Asp-189 and Glu-247. X-ray crystallographic structural analysis of the apo Ega3 and an Ega3-galactosamine complex, at 1.76 and 2.09 A resolutions, revealed a modified (beta/alpha)8-fold with a deep electronegative cleft, which upon ligand binding is capped to form a tunnel. Our structural analysis coupled with in silico docking studies also uncovered the molecular determinants for galactosamine specificity and substrate binding at the -2 to +1 binding subsites. The findings in this study increase the structural and mechanistic understanding of the GH114 family, which has >600 members encoded by plant and opportunistic human pathogens, as well as in industrially used bacteria and fungi.
		+
		+	Ega3 from the fungal pathogen Aspergillus fumigatus is an endo-alpha-1,4-galactosaminidase that disrupts microbial biofilms.,Bamford NC, Le Mauff F, Subramanian AS, Yip P, Millan C, Zhang Y, Zacharias C, Forman A, Nitz M, Codee JDC, Uson I, Sheppard DC, Howell PL J Biol Chem. 2019 Sep 13;294(37):13833-13849. doi: 10.1074/jbc.RA119.009910. Epub, 2019 Aug 15. PMID:31416836<ref>PMID:31416836</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6oj1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aspfu]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Bamford, N C]]		[[Category: Bamford, N C]]

OCA at 16:41, 14 August 2019

OCA — Wed, 14 Aug 2019 16:41:20 GMT

←Older revision		Revision as of 16:41, 14 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6oj1 ~~is ON HOLD until Paper Publication~~	+	==Crystal Structure of Aspergillus fumigatus Ega3==
-		+	<StructureSection load='6oj1' size='340' side='right'caption='[[6oj1]], [[Resolution\|resolution]] 1.76Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6oj1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OJ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OJ1 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6oj1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6oj1 OCA], [http://pdbe.org/6oj1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6oj1 RCSB], [http://www.ebi.ac.uk/pdbsum/6oj1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6oj1 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Bamford, N C]]
		+	[[Category: Howell, P L]]
		+	[[Category: Millan, C]]
		+	[[Category: Subramanian, A S]]
		+	[[Category: Uson, I]]
		+	[[Category: Galactosaminidase]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]

OCA at 04:55, 24 April 2019

OCA — Wed, 24 Apr 2019 04:55:31 GMT

←Older revision		Revision as of 04:55, 24 April 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6oj1 is ON HOLD	+	The entry 6oj1 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6oj1" [edit=sysop:move=sysop]

OCA — Wed, 17 Apr 2019 04:16:18 GMT

Protected "6oj1" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:16, 17 April 2019

OCA: New page: '''Unreleased structure''' The entry 6oj1 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 17 Apr 2019 04:16:16 GMT

New page: '''Unreleased structure''' The entry 6oj1 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6oj1 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]