6byg - Revision history

OCA at 14:25, 13 March 2024

OCA — Wed, 13 Mar 2024 14:25:00 GMT

←Older revision		Revision as of 14:25, 13 March 2024
Line 1:		Line 1:

	==Crystal structure of the nucleophile mutant (E575A) of the GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri==		==Crystal structure of the nucleophile mutant (E575A) of the GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri==
-	<StructureSection load='6byg' size='340' side='right' caption='[[6byg]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='6byg' size='340' side='right'caption='[[6byg]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6byg]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Xanac Xanac~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BYG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BYG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6byg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_citri_pv._citri_str._306 Xanthomonas citri pv. citri str. 306]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BYG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BYG 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>~~</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]] 1.999Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~XAC3075 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=190486 XANAC])~~</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></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=6byg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6byg OCA], [~~http~~://pdbe.org/6byg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6byg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6byg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6byg 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=6byg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6byg OCA], [https://pdbe.org/6byg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6byg RCSB], [https://www.ebi.ac.uk/pdbsum/6byg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6byg ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q8PI23_XANAC Q8PI23_XANAC]
-	The classical microbial strategy for depolymerization of beta-mannan polysaccharides involves the synergistic action of at least two enzymes, endo-1,4-beta-mannanases and beta-mannosidases. In this work, we describe the first exo-beta-mannanase from the GH2 family, isolated from Xanthomonas axonopodis pv. citri (XacMan2A), which can efficiently hydrolyze both manno-oligosaccharides and beta-mannan into mannose. It represents a valuable process simplification in the microbial carbon uptake that could be of potential industrial interest. Biochemical assays revealed a progressive increase in the hydrolysis rates from mannobiose to mannohexaose, which distinguishes XacMan2A from the known GH2 beta-mannosidases. Crystallographic analysis indicates that the active-site topology of XacMan2A underwent profound structural changes at the positive-subsite region, by the removal of the physical barrier canonically observed in GH2 beta-mannosidases, generating a more open and accessible active site with additional productive positive subsites. Besides that, XacMan2A contains two residue substitutions in relation to typical GH2 beta-mannosidases, Gly(439) and Gly(556), which alter the active site volume and are essential to its mode of action. Interestingly, the only other mechanistically characterized mannose-releasing exo-beta-mannanase so far is from the GH5 family, and its mode of action was attributed to the emergence of a blocking loop at the negative-subsite region of a cleft-like active site, whereas in XacMan2A, the same activity can be explained by the removal of steric barriers at the positive-subsite region in an originally pocket-like active site. Therefore, the GH2 exo-beta-mannanase represents a distinct molecular route to this rare activity, expanding our knowledge about functional convergence mechanisms in carbohydrate-active enzymes.	+
-		+
-	Structural basis of exo-beta-mannanase activity in the GH2 family.,Domingues MN, Souza FHM, Vieira PS, de Morais MAB, Zanphorlin LM, Dos Santos CR, Pirolla RAS, Honorato RV, de Oliveira PSL, Gozzo FC, Murakami MT J Biol Chem. 2018 Aug 31;293(35):~~13636-13649. doi: 10.1074~~/~~jbc.RA118.002374. Epub, 2018 Jul 11. PMID:29997257<ref>PMID:29997257<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6byg" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
-	*[[Mannosidase\|Mannosidase]]	+	*[[Mannosidase 3D structures\|Mannosidase 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Xanac~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Domingues, M N]]~~	+	[[Category: Xanthomonas citri pv. citri str. 306]]
-	~~[[Category: Morais, M A~~.B]]	+	[[Category: Domingues MN]]
-	[[Category: ~~Murakami, M T~~]]	+	[[Category: Morais MAB]]
-	[[Category: ~~Vieira, P S~~]]	+	[[Category: Murakami MT]]
-	[[Category: ~~Carbohydrate~~]]	+	[[Category: Vieira PS]]
-	[[Category: ~~Hydrolase-carbohydrate complex~~]]	+

OCA at 09:25, 30 January 2019

OCA — Wed, 30 Jan 2019 09:25:00 GMT

←Older revision		Revision as of 09:25, 30 January 2019
Line 3:		Line 3:
	<StructureSection load='6byg' size='340' side='right' caption='[[6byg]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6byg' size='340' side='right' caption='[[6byg]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6byg]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BYG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BYG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6byg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Xanac Xanac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BYG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BYG 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></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></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">XAC3075 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190486 XANAC])</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=6byg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6byg OCA], [http://pdbe.org/6byg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6byg RCSB], [http://www.ebi.ac.uk/pdbsum/6byg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6byg 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=6byg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6byg OCA], [http://pdbe.org/6byg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6byg RCSB], [http://www.ebi.ac.uk/pdbsum/6byg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6byg ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The classical microbial strategy for depolymerization of beta-mannan polysaccharides involves the synergistic action of at least two enzymes, endo-1,4-beta-mannanases and beta-mannosidases. In this work, we describe the first exo-beta-mannanase from the GH2 family, isolated from Xanthomonas axonopodis pv. citri (XacMan2A), which can efficiently hydrolyze both manno-oligosaccharides and beta-mannan into mannose. It represents a valuable process simplification in the microbial carbon uptake that could be of potential industrial interest. Biochemical assays revealed a progressive increase in the hydrolysis rates from mannobiose to mannohexaose, which distinguishes XacMan2A from the known GH2 beta-mannosidases. Crystallographic analysis indicates that the active-site topology of XacMan2A underwent profound structural changes at the positive-subsite region, by the removal of the physical barrier canonically observed in GH2 beta-mannosidases, generating a more open and accessible active site with additional productive positive subsites. Besides that, XacMan2A contains two residue substitutions in relation to typical GH2 beta-mannosidases, Gly(439) and Gly(556), which alter the active site volume and are essential to its mode of action. Interestingly, the only other mechanistically characterized mannose-releasing exo-beta-mannanase so far is from the GH5 family, and its mode of action was attributed to the emergence of a blocking loop at the negative-subsite region of a cleft-like active site, whereas in XacMan2A, the same activity can be explained by the removal of steric barriers at the positive-subsite region in an originally pocket-like active site. Therefore, the GH2 exo-beta-mannanase represents a distinct molecular route to this rare activity, expanding our knowledge about functional convergence mechanisms in carbohydrate-active enzymes.
		+
		+	Structural basis of exo-beta-mannanase activity in the GH2 family.,Domingues MN, Souza FHM, Vieira PS, de Morais MAB, Zanphorlin LM, Dos Santos CR, Pirolla RAS, Honorato RV, de Oliveira PSL, Gozzo FC, Murakami MT J Biol Chem. 2018 Aug 31;293(35):13636-13649. doi: 10.1074/jbc.RA118.002374. Epub, 2018 Jul 11. PMID:29997257<ref>PMID:29997257</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6byg" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Mannosidase\|Mannosidase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Xanac]]
	[[Category: Domingues, M N]]		[[Category: Domingues, M N]]
	[[Category: Morais, M A.B]]		[[Category: Morais, M A.B]]

OCA at 07:35, 18 July 2018

OCA — Wed, 18 Jul 2018 07:35:46 GMT

←Older revision		Revision as of 07:35, 18 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6byg is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of the nucleophile mutant (E575A) of the GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri==
-		+	<StructureSection load='6byg' size='340' side='right' caption='[[6byg]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~: ~~Domingues~~, M.N., ~~Vieira~~, P.S., ~~Morais, M~~.A.B., ~~Murakami, M~~.T.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6byg]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BYG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BYG FirstGlance]. <br>
-	~~Description: Structure from nucleophile E575A mutant protein XAC3075~~	+	</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></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=6byg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6byg OCA], [http://pdbe.org/6byg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6byg RCSB], [http://www.ebi.ac.uk/pdbsum/6byg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6byg ProSAT]</span></td></tr>
-	[[Category: ~~Murakami~~, M.T]]	+	</table>
-	[[Category: ~~Morais~~, M~~.A.B~~]]	+	__TOC__
-	[[Category: Vieira, P.S]]	+	</StructureSection>
-	[[Category: ~~Domingues, M.N~~]]	+	[[Category: Domingues, M N]]
		+	[[Category: Morais, M A.B]]
		+	[[Category: Murakami, M T]]
		+	[[Category: Vieira, P S]]
		+	[[Category: Carbohydrate]]
		+	[[Category: Hydrolase-carbohydrate complex]]

OCA at 04:57, 28 February 2018

OCA — Wed, 28 Feb 2018 04:57:51 GMT

←Older revision		Revision as of 04:57, 28 February 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Domingues, M.N., Vieira, P.S., Morais, M.A.B., Murakami, M.T.		Authors: Domingues, M.N., Vieira, P.S., Morais, M.A.B., Murakami, M.T.

OCA at 07:11, 10 January 2018

OCA — Wed, 10 Jan 2018 07:11:17 GMT

←Older revision		Revision as of 07:11, 10 January 2018
Line 5:		Line 5:
	Authors: Domingues, M.N., Vieira, P.S., Morais, M.A.B., Murakami, M.T.		Authors: Domingues, M.N., Vieira, P.S., Morais, M.A.B., Murakami, M.T.

-	Description: Structure from nucleophile mutant protein XAC3075 ~~and biochemical characterization~~	+	Description: Structure from nucleophile E575A mutant protein XAC3075
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Murakami, M.T]]		[[Category: Murakami, M.T]]
		+	[[Category: Morais, M.A.B]]
	[[Category: Vieira, P.S]]		[[Category: Vieira, P.S]]
	[[Category: Domingues, M.N]]		[[Category: Domingues, M.N]]
-	[[Category: Morais, M.A.B]]

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

OCA — Wed, 27 Dec 2017 07:23:42 GMT

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

←Older revision

Revision as of 07:23, 27 December 2017

OCA: New page: '''Unreleased structure''' The entry 6byg is ON HOLD Authors: Domingues, M.N., Vieira, P.S., Morais, M.A.B., Murakami, M.T. Description: Structure from nucleophile mutant protein XAC30...

OCA — Wed, 27 Dec 2017 07:23:41 GMT

New page: '''Unreleased structure''' The entry 6byg is ON HOLD Authors: Domingues, M.N., Vieira, P.S., Morais, M.A.B., Murakami, M.T. Description: Structure from nucleophile mutant protein XAC30...

New page

'''Unreleased structure'''

The entry 6byg is ON HOLD

Authors: Domingues, M.N., Vieira, P.S., Morais, M.A.B., Murakami, M.T.

Description: Structure from nucleophile mutant protein XAC3075 and biochemical characterization
[[Category: Unreleased Structures]]
[[Category: Murakami, M.T]]
[[Category: Vieira, P.S]]
[[Category: Domingues, M.N]]
[[Category: Morais, M.A.B]]