5z4t - Revision history

OCA at 08:45, 22 November 2023

2023-11-22T08:45:21Z

←Older revision		Revision as of 08:45, 22 November 2023
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	==Complex structure - AxMan113A-M3==		==Complex structure - AxMan113A-M3==
-	<StructureSection load='5z4t' size='340' side='right' caption='[[5z4t]], [[Resolution\|resolution]] 1.68Å' scene=''>	+	<StructureSection load='5z4t' size='340' side='right'caption='[[5z4t]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z4t]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ampxn Ampxn~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z4T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Z4T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z4t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amphibacillus_xylanus_NBRC_15112 Amphibacillus xylanus NBRC 15112]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z4T 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]] 1.68Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~AXY_22370 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=698758 AMPXN])~~</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=PRD_900115:4beta-beta-mannobiose'>PRD_900115</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=5z4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z4t OCA], [~~http~~://pdbe.org/5z4t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5z4t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5z4t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5z4t 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=5z4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z4t OCA], [https://pdbe.org/5z4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z4t RCSB], [https://www.ebi.ac.uk/pdbsum/5z4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z4t ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/K0J0N5_AMPXN K0J0N5_AMPXN]
	<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: ~~Ampxn~~]]	+	[[Category: Amphibacillus xylanus NBRC 15112]]
-	[[Category: Huang, P]]	+	[[Category: Large Structures]]
-	[[Category: Jiang~~, Z Q~~]]	+	[[Category: Huang P]]
-	[[Category: Ma~~, J W~~]]	+	[[Category: Jiang ZQ]]
-	[[Category: Yang~~, S Q~~]]	+	[[Category: Ma JW]]
-	[[Category: You, X]]	+	[[Category: Yang SQ]]
-	~~[[Category: Complex]]~~	+	[[Category: You X]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 22:04, 9 August 2018

2018-08-09T22:04:49Z

←Older revision		Revision as of 22:04, 9 August 2018
Line 3:		Line 3:
	<StructureSection load='5z4t' size='340' side='right' caption='[[5z4t]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='5z4t' size='340' side='right' caption='[[5z4t]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z4t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z4T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z4t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ampxn Ampxn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z4T 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">AXY_22370 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=698758 AMPXN])</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=5z4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z4t OCA], [http://pdbe.org/5z4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z4t RCSB], [http://www.ebi.ac.uk/pdbsum/5z4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z4t 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=5z4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z4t OCA], [http://pdbe.org/5z4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z4t RCSB], [http://www.ebi.ac.uk/pdbsum/5z4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z4t ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ampxn]]
	[[Category: Huang, P]]		[[Category: Huang, P]]
	[[Category: Jiang, Z Q]]		[[Category: Jiang, Z Q]]

OCA at 05:44, 20 June 2018

2018-06-20T05:44:39Z

←Older revision		Revision as of 05:44, 20 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5z4t is ~~ON HOLD until Paper~~ Publication	+	==Complex structure - AxMan113A-M3==
		+	<StructureSection load='5z4t' size='340' side='right' caption='[[5z4t]], [[Resolution\|resolution]] 1.68Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5z4t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z4T 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>
		+	<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=5z4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z4t OCA], [http://pdbe.org/5z4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z4t RCSB], [http://www.ebi.ac.uk/pdbsum/5z4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z4t ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	beta-1,4-Mannanase degrades beta-1,4-mannan polymers into manno-oligosaccharides with a low degree of polymerization. To date, only one glycoside hydrolase (GH) family 113 beta-1,4-mannanase, from Alicyclobacillus acidocaldarius (AaManA) has been structurally characterized, and no complex structure of enzyme-manno-oligosaccharides from this family has been reported. Here, crystal structures of a GH family 113 beta-1,4-mannanase from Amphibacillus xylanus (AxMan113A) and its complexes with mannobiose, mannotriose, mannopentaose and mannahexaose were solved. AxMan113A had a stronger affinity for -1 and +1 mannoses, which explains why the enzyme can hydrolyze mannobiose. At least six subsites (-4 to +2) exist in the groove, but mannose units preferentially occupied subsites -4 to -1 owing to steric hindrance formed by Lys238 and Trp239. Based on the structural information and bioinformatics, rational design was implemented to enhance hydrolysis activity. Enzyme activity of AxMan113A mutants V139C, N237W, K238A and W239Y was improved by 93.7%, 63.4%, 112.9% and 36.4%, respectively, compared to the wild type. In addition, previously unreported surface binding sites were observed. Site-directed mutagenesis studies and kinetic data indicated that key residues near the surface sites play important roles in substrate binding and recognition. These first GH family 113 beta-1,4-mannanase-manno-oligosaccharide complex structures may be useful in further studying the catalytic mechanism of GH family 113 members, and provide novel insight into protein engineering of GHs to improve their hydrolysis activity.

-	~~Authors: Jiang~~, ~~Z.Q~~., You, X., ~~Yang~~, S.Q., ~~Huang~~, ~~P., Ma~~, J.W.	+	Structural insights into the catalytic mechanism of a novel glycoside hydrolase family 113 beta-1,4-mannanase from Amphibacillus xylanus.,You X, Qin Z, Yan Q, Yang S, Li Y, Jiang Z J Biol Chem. 2018 Jun 5. pii: RA118.002363. doi: 10.1074/jbc.RA118.002363. PMID:29871927<ref>PMID:29871927</ref>

-	~~Description: Complex structure~~ -~~AxMan113A~~-M3	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Jiang, Z.Q]]~~	+	<div class="pdbe-citations 5z4t" style="background-color:#fffaf0;"></div>
-	~~[[Category: You, X]]~~	+	== References ==
-	~~[[Category: Ma, J.W]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Huang, P]]		[[Category: Huang, P]]
-	[[Category: Yang, S.Q]]	+	[[Category: Jiang, Z Q]]
		+	[[Category: Ma, J W]]
		+	[[Category: Yang, S Q]]
		+	[[Category: You, X]]
		+	[[Category: Complex]]
		+	[[Category: Hydrolase]]

OCA at 04:39, 31 January 2018

2018-01-31T04:39:34Z

←Older revision		Revision as of 04:39, 31 January 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z4t is ON HOLD	+	The entry 5z4t is ON HOLD until Paper Publication

	Authors: Jiang, Z.Q., You, X., Yang, S.Q., Huang, P., Ma, J.W.		Authors: Jiang, Z.Q., You, X., Yang, S.Q., Huang, P., Ma, J.W.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Jiang, Z.Q]]		[[Category: Jiang, Z.Q]]
-	[[Category: Huang, P]]
-	[[Category: Yang, S.Q]]
	[[Category: You, X]]		[[Category: You, X]]
	[[Category: Ma, J.W]]		[[Category: Ma, J.W]]
		+	[[Category: Huang, P]]
		+	[[Category: Yang, S.Q]]

OCA: Protected "5z4t" [edit=sysop:move=sysop]

2018-01-24T17:11:09Z

Protected "5z4t" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:11, 24 January 2018

OCA: New page: '''Unreleased structure''' The entry 5z4t is ON HOLD Authors: Jiang, Z.Q., You, X., Yang, S.Q., Huang, P., Ma, J.W. Description: Complex structure -AxMan113A-M3 [[Category: Unreleased ...

2018-01-24T17:11:08Z

New page: '''Unreleased structure''' The entry 5z4t is ON HOLD Authors: Jiang, Z.Q., You, X., Yang, S.Q., Huang, P., Ma, J.W. Description: Complex structure -AxMan113A-M3 [[Category: Unreleased ...

New page

'''Unreleased structure'''

The entry 5z4t is ON HOLD

Authors: Jiang, Z.Q., You, X., Yang, S.Q., Huang, P., Ma, J.W.

Description: Complex structure -AxMan113A-M3
[[Category: Unreleased Structures]]
[[Category: Jiang, Z.Q]]
[[Category: Huang, P]]
[[Category: Yang, S.Q]]
[[Category: You, X]]
[[Category: Ma, J.W]]