6mgk - Revision history

OCA at 06:31, 11 October 2023

2023-10-11T06:31:19Z

←Older revision		Revision as of 06:31, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6mgk' size='340' side='right'caption='[[6mgk]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6mgk' size='340' side='right'caption='[[6mgk]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mgk]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_baa-93 Atcc baa-93~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MGK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MGK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mgk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_odorifer Paenibacillus odorifer]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MGK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</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]] 2.1Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSK60_29080 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=189426 ATCC BAA-93])~~</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=6mgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mgk OCA], [https://pdbe.org/6mgk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mgk RCSB], [https://www.ebi.ac.uk/pdbsum/6mgk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mgk 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=6mgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mgk OCA], [~~http~~://pdbe.org/6mgk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6mgk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6mgk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6mgk ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1R0YRH0_9BACL A0A1R0YRH0_9BACL]
	<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: Atcc baa-93]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arnal, G]]	+	[[Category: Paenibacillus odorifer]]
-	[[Category: Brumer, H]]	+	[[Category: Arnal G]]
-	[[Category: Nocek, B]]	+	[[Category: Brumer H]]
-	[[Category: Savchenko, A]]	+	[[Category: Nocek B]]
-	[[Category: Skarina, T]]	+	[[Category: Savchenko A]]
-	[[Category: Stogios~~, P J]]~~	+	[[Category: Skarina T]]
-	~~[[Category: Family gh74]]~~	+	[[Category: Stogios PJ]]
-	~~[[Category: Glycosylhydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Xyloglucanase~~]]	+

OCA at 09:05, 8 January 2020

2020-01-08T09:05:12Z

←Older revision		Revision as of 09:05, 8 January 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6mgk is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the catalytic domain from GH74 enzyme PoGH74 from Paenibacillus odorifer, in complex with XLX xyloglucan==
		+	<StructureSection load='6mgk' size='340' side='right'caption='[[6mgk]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6mgk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_baa-93 Atcc baa-93]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MGK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSK60_29080 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=189426 ATCC BAA-93])</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=6mgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mgk OCA], [http://pdbe.org/6mgk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mgk RCSB], [http://www.ebi.ac.uk/pdbsum/6mgk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mgk ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Paenibacillus odorifer produces a single multimodular enzyme containing a glycoside hydrolase (GH) family 74 module (AIQ73809). Recombinant production and characterization of the GH74 module (PoGH74cat) revealed a highly specific, processive endo-xyloglucanase that can hydrolyze the polysaccharide backbone at both branched and unbranched positions. X-ray crystal structures obtained for the free enzyme and oligosaccharide complexes evidenced an extensive hydrophobic binding platform - the first in GH74 extending from subsites -4 to +6 - and unique mobile active-site loops. Site-directed mutagenesis revealed that glycine-476 was uniquely responsible for the promiscuous backbone-cleaving activity of PoGH74cat; replacement with tyrosine, which is conserved in many GH74 members, resulted in exclusive hydrolysis at unbranched glucose units. Likewise, systematic replacement of the hydrophobic platform residues constituting the positive subsites indicated their relative contributions to the processive mode of action. Specifically, W347 (+3 subsite) and W348 (+5 subsite) are essential for processivity, while W406 (+2 subsite) and Y372 (+6 subsite) are not strictly essential, but aid processivity.

-	~~Authors:~~ Stogios, P.J., Skarina, T., ~~Nocek, B., Arnal, G.~~, Brumer, H.~~, Savchenko, A~~.	+	Structural enzymology reveals the molecular basis of substrate regiospecificity and processivity of an exemplar bacterial glycoside hydrolase family 74 endo-xyloglucanase.,Arnal G, Stogios PJ, Asohan J, Skarina T, Savchenko A, Brumer H Biochem J. 2018 Dec 19;475(24):3963-3978. doi: 10.1042/BCJ20180763. PMID:30463871<ref>PMID:30463871</ref>

-	~~Description: Crystal structure~~ of the ~~catalytic domain from GH74 enzyme PoGH74 from Paenibacillus odorifer, in complex with XLX xyloglucan~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Savchenko, A~~]]	+	<div class="pdbe-citations 6mgk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Atcc baa-93]]
		+	[[Category: Large Structures]]
	[[Category: Arnal, G]]		[[Category: Arnal, G]]
-	[[Category: Stogios, P.J]]
	[[Category: Brumer, H]]		[[Category: Brumer, H]]
-	[[Category: Skarina, T]]
	[[Category: Nocek, B]]		[[Category: Nocek, B]]
		+	[[Category: Savchenko, A]]
		+	[[Category: Skarina, T]]
		+	[[Category: Stogios, P J]]
		+	[[Category: Family gh74]]
		+	[[Category: Glycosylhydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Xyloglucanase]]

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

2018-09-26T06:29:13Z

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

←Older revision

Revision as of 06:29, 26 September 2018

OCA: New page: '''Unreleased structure''' The entry 6mgk is ON HOLD until Paper Publication Authors: Stogios, P.J., Skarina, T., Nocek, B., Arnal, G., Brumer, H., Savchenko, A. Description: Crystal s...

2018-09-26T06:29:12Z

New page: '''Unreleased structure''' The entry 6mgk is ON HOLD until Paper Publication Authors: Stogios, P.J., Skarina, T., Nocek, B., Arnal, G., Brumer, H., Savchenko, A. Description: Crystal s...

New page

'''Unreleased structure'''

The entry 6mgk is ON HOLD until Paper Publication

Authors: Stogios, P.J., Skarina, T., Nocek, B., Arnal, G., Brumer, H., Savchenko, A.

Description: Crystal structure of the catalytic domain from GH74 enzyme PoGH74 from Paenibacillus odorifer, in complex with XLX xyloglucan
[[Category: Unreleased Structures]]
[[Category: Savchenko, A]]
[[Category: Arnal, G]]
[[Category: Stogios, P.J]]
[[Category: Brumer, H]]
[[Category: Skarina, T]]
[[Category: Nocek, B]]