5xtj - Revision history

OCA at 10:20, 27 March 2024

2024-03-27T10:20:21Z

← Older revision		Revision as of 10:20, 27 March 2024
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	<StructureSection load='5xtj' size='340' side='right'caption='[[5xtj]], [[Resolution\|resolution]] 2.22Å' scene=''>		<StructureSection load='5xtj' size='340' side='right'caption='[[5xtj]], [[Resolution\|resolution]] 2.22Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5xtj]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rhizd Rhizd~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XTJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XTJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5xtj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhizopus_microsporus Rhizopus microsporus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XTJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XTJ FirstGlance]. <br>
	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~RMCBS344292_04886 (~~[~~http://www.ncbi.nlm.nih~~.~~gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5~~&~~id=58291 RHIZD])~~</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]] 2.22Å</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=5xtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xtj OCA], [~~http~~://pdbe.org/5xtj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xtj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xtj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xtj 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=5xtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xtj OCA], [https://pdbe.org/5xtj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xtj RCSB], [https://www.ebi.ac.uk/pdbsum/5xtj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xtj ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~		== Function ==
	== ~~Publication Abstract from PubMed~~ ==		[https://www.uniprot.org/uniprot/A0A2U8ZTY7_RHIZD A0A2U8ZTY7_RHIZD]
	Mannan is one of the major constituent groups of hemicellulose, which is a renewable resource from higher plants. beta-Mannanases are enzymes capable of degrading lignocellulosic biomass. Here, an endo-beta-mannanase from Rhizopus microsporus (RmMan134A) was cloned and expressed. The recombinant RmMan134A showed maximal activity at pH5.0 and 50 degrees C, and exhibited high specific activity towards locust bean gum (2337U/mg). To gain insight into the substrate-binding mechanism of RmMan134A, four complex structures (RmMan134A-M3, RmMan134A-M4, RmMan134A-M5 and RmMan134A-M6) were further solved. These structures showed that there were at least seven subsites (-3 to +4) in the catalytic groove of RmMan134A. Mannose in the -1 subsite hydrogen bonded with His113 and Tyr131, revealing a unique conformation. Lys48 and Val159 formed steric hindrance, which impedes to bond with galactose branches. In addition, the various binding modes of RmMan134A-M5 indicated that subsites -2 to +2 are indispensable during the hydrolytic process. The structure of RmMan134A-M4 showed that mannotetrose only binds at subsites +1 to +4, and RmMan134A could therefore not hydrolyze mannan oligosaccharides with degree of polymerization </=4. Through rational design, the specific activity and optimal conditions of RmMan134A were significantly improved. The purpose of this paper is to investigate the structure and function of fungal GH family 134 beta-1,4-mannanases, and substrate-binding mechanism of GH family 134 members.

	Structural and biochemical insights into the substrate-binding mechanism of a novel glycoside hydrolase family 134 beta-mannanase.,You X, Qin Z, Li YX, Yan QJ, Li B, Jiang ZQ Biochim Biophys Acta Gen Subj. 2018 Jun;1862(6):1376-1388. doi:~~, 10.1016~~/~~j.bbagen.2018.03.016. Epub 2018 Mar 14. PMID:29550433<ref>PMID:29550433</ref>~~

	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 5xtj" style="background-color:#fffaf0;"><~~/~~div>~~
	~~== References ==~~
	~~<references~~/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Rhizd~~]]		[[Category: Rhizopus microsporus]]
	[[Category: Huang, P]]		[[Category: Huang P]]
	[[Category: Jiang~~, Z Q~~]]		[[Category: Jiang ZQ]]
	[[Category: You, X]]		[[Category: You X]]
	~~[[Category: Hydrolase]]~~
	~~[[Category: Native protein~~]]

OCA at 06:13, 10 July 2019

2019-07-10T06:13:49Z

← Older revision		Revision as of 06:13, 10 July 2019
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	==Mannanase(RmMan134A)==		==Mannanase(RmMan134A)==
	<StructureSection load='5xtj' size='340' side='right' caption='[[5xtj]], [[Resolution\|resolution]] 2.22Å' scene=''>		<StructureSection load='5xtj' size='340' side='right'caption='[[5xtj]], [[Resolution\|resolution]] 2.22Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5xtj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XTJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XTJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5xtj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhizd Rhizd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XTJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XTJ FirstGlance]. <br>
	</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=5xtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xtj OCA], [http://pdbe.org/5xtj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xtj RCSB], [http://www.ebi.ac.uk/pdbsum/5xtj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xtj ProSAT]</span></td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RMCBS344292_04886 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=58291 RHIZD])</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=5xtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xtj OCA], [http://pdbe.org/5xtj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xtj RCSB], [http://www.ebi.ac.uk/pdbsum/5xtj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xtj ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Mannan is one of the major constituent groups of hemicellulose, which is a renewable resource from higher plants. beta-Mannanases are enzymes capable of degrading lignocellulosic biomass. Here, an endo-beta-mannanase from Rhizopus microsporus (RmMan134A) was cloned and expressed. The recombinant RmMan134A showed maximal activity at pH5.0 and 50 degrees C, and exhibited high specific activity towards locust bean gum (2337U/mg). To gain insight into the substrate-binding mechanism of RmMan134A, four complex structures (RmMan134A-M3, RmMan134A-M4, RmMan134A-M5 and RmMan134A-M6) were further solved. These structures showed that there were at least seven subsites (-3 to +4) in the catalytic groove of RmMan134A. Mannose in the -1 subsite hydrogen bonded with His113 and Tyr131, revealing a unique conformation. Lys48 and Val159 formed steric hindrance, which impedes to bond with galactose branches. In addition, the various binding modes of RmMan134A-M5 indicated that subsites -2 to +2 are indispensable during the hydrolytic process. The structure of RmMan134A-M4 showed that mannotetrose only binds at subsites +1 to +4, and RmMan134A could therefore not hydrolyze mannan oligosaccharides with degree of polymerization </=4. Through rational design, the specific activity and optimal conditions of RmMan134A were significantly improved. The purpose of this paper is to investigate the structure and function of fungal GH family 134 beta-1,4-mannanases, and substrate-binding mechanism of GH family 134 members.

			Structural and biochemical insights into the substrate-binding mechanism of a novel glycoside hydrolase family 134 beta-mannanase.,You X, Qin Z, Li YX, Yan QJ, Li B, Jiang ZQ Biochim Biophys Acta Gen Subj. 2018 Jun;1862(6):1376-1388. doi:, 10.1016/j.bbagen.2018.03.016. Epub 2018 Mar 14. PMID:29550433<ref>PMID:29550433</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 5xtj" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
			[[Category: Rhizd]]
	[[Category: Huang, P]]		[[Category: Huang, P]]
	[[Category: Jiang, Z Q]]		[[Category: Jiang, Z Q]]

OCA at 05:29, 27 June 2018

2018-06-27T05:29:50Z

← Older revision		Revision as of 05:29, 27 June 2018
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 5xtj is ~~ON HOLD until Paper Publication~~		==Mannanase(RmMan134A)==
			<StructureSection load='5xtj' size='340' side='right' caption='[[5xtj]], [[Resolution\|resolution]] 2.22Å' scene=''>
	~~Authors~~: ~~Jiang~~, Z.Q., ~~You~~, X., ~~Huang~~, P.		== Structural highlights ==
			<table><tr><td colspan='2'>[[5xtj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XTJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XTJ FirstGlance]. <br>
	~~Description~~: ~~A mannanase(RmMan134A)~~		</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=5xtj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xtj OCA], [http://pdbe.org/5xtj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xtj RCSB], [http://www.ebi.ac.uk/pdbsum/5xtj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xtj ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Huang, P]]
			[[Category: Jiang, Z Q]]
	[[Category: You, X]]		[[Category: You, X]]
	[[Category: ~~Jiang, Z.Q~~]]		[[Category: Hydrolase]]
	[[Category: ~~Huang, P~~]]		[[Category: Native protein]]

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

2017-09-27T15:45:44Z

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

← Older revision	Revision as of 15:45, 27 September 2017
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5xtj is ON HOLD until Paper Publication Authors: Jiang, Z.Q., You, X., Huang, P. Description: A mannanase(RmMan134A) [[Category: Unreleased Structu...

2017-09-27T15:45:43Z

New page: '''Unreleased structure''' The entry 5xtj is ON HOLD until Paper Publication Authors: Jiang, Z.Q., You, X., Huang, P. Description: A mannanase(RmMan134A) [[Category: Unreleased Structu...

New page

'''Unreleased structure'''

The entry 5xtj is ON HOLD until Paper Publication

Authors: Jiang, Z.Q., You, X., Huang, P.

Description: A mannanase(RmMan134A)
[[Category: Unreleased Structures]]
[[Category: You, X]]
[[Category: Jiang, Z.Q]]
[[Category: Huang, P]]