5jug - Revision history

OCA at 07:24, 1 May 2024

OCA — Wed, 01 May 2024 07:24:50 GMT

←Older revision		Revision as of 07:24, 1 May 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A0A1L1QK16_9ACTN A0A1L1QK16_9ACTN]		[https://www.uniprot.org/uniprot/A0A1L1QK16_9ACTN A0A1L1QK16_9ACTN]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The enzymatic cleavage of beta-1,4-mannans is achieved by endo-beta-1,4-mannanases, enzymes involved in germination of seeds and microbial hemicellulose degradation, and which have increasing industrial and consumer product applications. beta-Mannanases occur in a range of families of the CAZy sequence-based glycoside hydrolase (GH) classification scheme including families 5, 26, and 113. In this work we reveal that beta-mannanases of the newly described GH family 134 differ from other mannanase families in both their mechanism and tertiary structure. A representative GH family 134 endo-beta-1,4-mannanase from a Streptomyces sp. displays a fold closely related to that of hen egg white lysozyme but acts with inversion of stereochemistry. A Michaelis complex with mannopentaose, and a product complex with mannotriose, reveal ligands with pyranose rings distorted in an unusual inverted chair conformation. Ab initio quantum mechanics/molecular mechanics metadynamics quantified the energetically accessible ring conformations and provided evidence in support of a 1C4 --> 3H4double dagger --> 3S1 conformational itinerary along the reaction coordinate. This work, in concert with that on GH family 124 cellulases, reveals how the lysozyme fold can be co-opted to catalyze the hydrolysis of different polysaccharides in a mechanistically distinct manner.
-
-	A beta-Mannanase with a Lysozyme-like Fold and a Novel Molecular Catalytic Mechanism.,Jin Y, Petricevic M, John A, Raich L, Jenkins H, Portela De Souza L, Cuskin F, Gilbert HJ, Rovira C, Goddard-Borger ED, Williams SJ, Davies GJ ACS Cent Sci. 2016 Dec 28;2(12):896-903. doi: 10.1021/acscentsci.6b00232. Epub, 2016 Nov 8. PMID:28058278<ref>PMID:28058278</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5jug" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:07, 20 September 2023

OCA — Wed, 20 Sep 2023 19:07:34 GMT

←Older revision		Revision as of 19:07, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='5jug' size='340' side='right'caption='[[5jug]], [[Resolution\|resolution]] 0.96Å' scene=''>		<StructureSection load='5jug' size='340' side='right'caption='[[5jug]], [[Resolution\|resolution]] 0.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jug]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Streptomyces_sp.~~_nrrl_b~~-16215 Streptomyces sp. ~~nrrl b~~-16215]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JUG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JUG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jug]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._NRRL_B-16215 Streptomyces sp. NRRL B-16215]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JUG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JUG FirstGlance]. <br>
-	</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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]] 0.96Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannan_endo-1,4-beta-mannosidase Mannan endo-1,4-beta-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.78 3.2.1.78] </span></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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5jug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jug OCA], [~~http~~://pdbe.org/5jug PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jug RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jug PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jug 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=5jug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jug OCA], [https://pdbe.org/5jug PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jug RCSB], [https://www.ebi.ac.uk/pdbsum/5jug PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jug ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1L1QK16_9ACTN A0A1L1QK16_9ACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Mannan endo-1,4-beta-mannosidase]]~~	+	[[Category: Streptomyces sp. NRRL B-16215]]
-	[[Category: Streptomyces sp. ~~nrrl b~~-16215]]	+	[[Category: Davies GJ]]
-	[[Category: Davies~~, G J~~]]	+	[[Category: Goddard-Borger ED]]
-	[[Category: Goddard-Borger~~, E D~~]]	+	[[Category: Jin Y]]
-	[[Category: Jin, Y]]	+	[[Category: Petricevic M]]
-	[[Category: Petricevic, M]]	+	[[Category: Williams SJ]]
-	[[Category: Williams~~, S J]]~~	+
-	~~[[Category: 4-mannanase]]~~	+
-	~~[[Category: Beta-1]]~~	+
-	~~[[Category: Carbohydrate degrading]]~~	+
-	~~[[Category: Glycosyl hydrolase]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 11:40, 17 June 2020

OCA — Wed, 17 Jun 2020 11:40:24 GMT

←Older revision		Revision as of 11:40, 17 June 2020
Line 1:		Line 1:

	==Structure of an inactive (E45Q) variant of a beta-1,4-mannanase, SsGH134, in complex with Man5==		==Structure of an inactive (E45Q) variant of a beta-1,4-mannanase, SsGH134, in complex with Man5==
-	<StructureSection load='5jug' size='340' side='right' caption='[[5jug]], [[Resolution\|resolution]] 0.96Å' scene=''>	+	<StructureSection load='5jug' size='340' side='right'caption='[[5jug]], [[Resolution\|resolution]] 0.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jug]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JUG OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JUG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jug]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp._nrrl_b-16215 Streptomyces sp. nrrl b-16215]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JUG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JUG 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>	+	</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannan_endo-1,4-beta-mannosidase Mannan endo-1,4-beta-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.78 3.2.1.78] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannan_endo-1,4-beta-mannosidase Mannan endo-1,4-beta-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.78 3.2.1.78] </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=5jug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jug OCA], [http://pdbe.org/5jug PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jug RCSB], [http://www.ebi.ac.uk/pdbsum/5jug PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jug ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5jug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jug OCA], [http://pdbe.org/5jug PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jug RCSB], [http://www.ebi.ac.uk/pdbsum/5jug PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jug ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Mannan endo-1,4-beta-mannosidase]]		[[Category: Mannan endo-1,4-beta-mannosidase]]
		+	[[Category: Streptomyces sp. nrrl b-16215]]
	[[Category: Davies, G J]]		[[Category: Davies, G J]]
	[[Category: Goddard-Borger, E D]]		[[Category: Goddard-Borger, E D]]

OCA at 07:45, 18 January 2017

OCA — Wed, 18 Jan 2017 07:45:11 GMT

←Older revision		Revision as of 07:45, 18 January 2017
Line 8:		Line 8:
	<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=5jug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jug OCA], [http://pdbe.org/5jug PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jug RCSB], [http://www.ebi.ac.uk/pdbsum/5jug PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jug 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=5jug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jug OCA], [http://pdbe.org/5jug PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jug RCSB], [http://www.ebi.ac.uk/pdbsum/5jug PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jug ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The enzymatic cleavage of beta-1,4-mannans is achieved by endo-beta-1,4-mannanases, enzymes involved in germination of seeds and microbial hemicellulose degradation, and which have increasing industrial and consumer product applications. beta-Mannanases occur in a range of families of the CAZy sequence-based glycoside hydrolase (GH) classification scheme including families 5, 26, and 113. In this work we reveal that beta-mannanases of the newly described GH family 134 differ from other mannanase families in both their mechanism and tertiary structure. A representative GH family 134 endo-beta-1,4-mannanase from a Streptomyces sp. displays a fold closely related to that of hen egg white lysozyme but acts with inversion of stereochemistry. A Michaelis complex with mannopentaose, and a product complex with mannotriose, reveal ligands with pyranose rings distorted in an unusual inverted chair conformation. Ab initio quantum mechanics/molecular mechanics metadynamics quantified the energetically accessible ring conformations and provided evidence in support of a 1C4 --> 3H4double dagger --> 3S1 conformational itinerary along the reaction coordinate. This work, in concert with that on GH family 124 cellulases, reveals how the lysozyme fold can be co-opted to catalyze the hydrolysis of different polysaccharides in a mechanistically distinct manner.
		+
		+	A beta-Mannanase with a Lysozyme-like Fold and a Novel Molecular Catalytic Mechanism.,Jin Y, Petricevic M, John A, Raich L, Jenkins H, Portela De Souza L, Cuskin F, Gilbert HJ, Rovira C, Goddard-Borger ED, Williams SJ, Davies GJ ACS Cent Sci. 2016 Dec 28;2(12):896-903. doi: 10.1021/acscentsci.6b00232. Epub, 2016 Nov 8. PMID:28058278<ref>PMID:28058278</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5jug" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 03:28, 10 December 2016

OCA — Sat, 10 Dec 2016 03:28:13 GMT

←Older revision		Revision as of 03:28, 10 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jug is ~~ON HOLD~~	+	==Structure of an inactive (E45Q) variant of a beta-1,4-mannanase, SsGH134, in complex with Man5==
-		+	<StructureSection load='5jug' size='340' side='right' caption='[[5jug]], [[Resolution\|resolution]] 0.96Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5jug]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JUG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JUG 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannan_endo-1,4-beta-mannosidase Mannan endo-1,4-beta-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.78 3.2.1.78] </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=5jug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jug OCA], [http://pdbe.org/5jug PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jug RCSB], [http://www.ebi.ac.uk/pdbsum/5jug PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jug ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Mannan endo-1,4-beta-mannosidase]]
		+	[[Category: Davies, G J]]
		+	[[Category: Goddard-Borger, E D]]
		+	[[Category: Jin, Y]]
		+	[[Category: Petricevic, M]]
		+	[[Category: Williams, S J]]
		+	[[Category: 4-mannanase]]
		+	[[Category: Beta-1]]
		+	[[Category: Carbohydrate degrading]]
		+	[[Category: Glycosyl hydrolase]]
		+	[[Category: Hydrolase]]

OCA: Protected "5jug" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 13:50:59 GMT

Protected "5jug" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:50, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5jug is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Jun 2016 13:50:57 GMT

New page: '''Unreleased structure''' The entry 5jug is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5jug is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]