6kpl - Revision history

OCA at 06:09, 10 October 2019

OCA — Thu, 10 Oct 2019 06:09:30 GMT

←Older revision		Revision as of 06:09, 10 October 2019
Line 3:		Line 3:
	<StructureSection load='6kpl' size='340' side='right'caption='[[6kpl]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='6kpl' size='340' side='right'caption='[[6kpl]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kpl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KPL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KPL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kpl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cormm Cormm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KPL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KPL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCM_08020 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=983644 CORMM])</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=6kpl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kpl OCA], [http://pdbe.org/6kpl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kpl RCSB], [http://www.ebi.ac.uk/pdbsum/6kpl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kpl 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=6kpl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kpl OCA], [http://pdbe.org/6kpl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kpl RCSB], [http://www.ebi.ac.uk/pdbsum/6kpl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kpl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	Endo-beta-N-acetylglucosaminidase (ENGase) ~~catalyzes hydrolysis~~ of N-~~linked oligosaccharides~~. Although ~~many~~ ENGases have been ~~characterized from various organisms~~, ~~so far no~~ fucose-~~containing oligosaccharides-specific ENGase has been identified in any organism~~. ~~Here~~, we ~~screened soil samples, using dansyl chloride (Dns)~~-~~labeled sialylglycan~~ (~~Dns~~-SG) ~~as a substrate~~, and discovered a strain that exhibits ENGase activity in the culture supernatant; this strain, named here as strain HMA12, was identified as a Sphingobacterium species by 16S ribosomal RNA gene analysis. By draft genome sequencing, five candidate ENGase encoding genes were identified in the genome of this strain. Recombinant proteins, purified from Escherichia coli expressing candidate genes ORF1152, ORF1188, ORF3046 and ORF3750 exhibited fucose-containing ~~oligosaccharides-specific ENGase activity. These ENGases exhibited optimum activities~~ at ~~very acidic pHs (between pH 2~~.3-2.5). ~~BLAST searches using sequences of these candidate genes identified two fungal homologs of ORF1188, one~~ in ~~Beauveria bassiana and~~ the ~~other in Cordyceps militaris~~. ~~Recombinant ORF1188, Beauveria~~ and ~~Cordyceps ENGases released~~ the fucose-containing ~~oligosaccharides residues from~~ rituximab (~~immunoglobulin G~~) ~~but not the high~~-~~mannose~~-~~containing oligosaccharides residues from RNase B~~, a ~~result that~~ not ~~only confirmed~~ the ~~substrate specificity~~ of ~~these novel ENGases but also suggested that natural glycoproteins could be their substrates~~.	+	N-linked glycans play important roles in various cellular and immunological events. Endo-beta-N-acetylglucosaminidase (ENGase) can release or transglycosylate N-glycans and is a promising tool for the chemoenzymatic synthesis of glycoproteins with homogenously modified glycans. The ability of ENGases to act on core-fucosylated glycans is a key factor determining their therapeutic utility because mammalian N-glycans are frequently alpha-1,6-fucosylated. Although the biochemistries and structures of various ENGases have been studied extensively, the structural basis for the recognition of the core fucose and the asparagine-linked GlcNAc is unclear. Herein, we determined the crystal structures of a core fucose-specific ENGase from the caterpillar fungus Cordyceps militaris (Endo-CoM), which belongs to glycoside hydrolase family 18. Structures complexed with fucose-containing ligands were determined at 1.75-2.35 A resolutions. The fucose moiety linked to GlcNAc is extensively recognized by protein residues in a round-shaped pocket, while the asparagine moiety linked to the GlcNAc is exposed to the solvent. The N-glycan-binding cleft of Endo-CoM is Y-shaped and that several lysine and arginine residues are present at its terminal regions. These structural features were consistent with the activity of Endo-CoM on fucose-containing glycans on rituximab (IgG) and its preference for a sialobiantennary substrate. Comparisons with other ENGases provided structural insights into their core fucose tolerance and specificity. In particular, Endo-F3, a known core fucose-specific ENGase, has a similar fucose-binding pocket, but the surrounding residues are not shared with Endo-CoM. Our study provides a foothold for protein engineering to develop enzymatic tools for the preparation of more effective therapeutic antibodies.

-	~~Characterization~~ of ~~novel~~ endo-beta-N-~~acetylglucosaminidases~~ from ~~Sphingobacterium species, Beauveria bassiana and~~ Cordyceps militaris ~~that specifically hydrolyze fucose-containing oligosaccharides and human IgG~~.,Huang Y, ~~Higuchi Y~~, Kinoshita T, ~~Mitani A~~, ~~Eshima~~ Y, Takegawa K ~~Sci Rep~~. ~~2018 Jan 10;8(1)~~:~~246~~. doi: 10.~~1038~~/~~s41598-017-17467-y~~. PMID:~~29321565~~<ref>PMID:~~29321565~~</ref>	+	Structural basis for the specific cleavage of core-fucosylated N-glycans by endo-beta-N-acetylglucosaminidase from the fungus Cordyceps militaris.,Seki H, Huang Y, Arakawa T, Yamada C, Kinoshita T, Iwamoto S, Higuchi Y, Takegawa K, Fushinobu S J Biol Chem. 2019 Sep 23. pii: RA119.010842. doi: 10.1074/jbc.RA119.010842. PMID:31548313<ref>PMID:31548313</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cormm]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Arakawa, T]]		[[Category: Arakawa, T]]

OCA at 10:24, 2 October 2019

OCA — Wed, 02 Oct 2019 10:24:58 GMT

←Older revision		Revision as of 10:24, 2 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6kpl is ~~ON HOLD~~	+	==Crystal Structure of endo-beta-N-acetylglucosaminidase from Cordyceps militaris in apo form==
		+	<StructureSection load='6kpl' size='340' side='right'caption='[[6kpl]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6kpl]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KPL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KPL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=6kpl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kpl OCA], [http://pdbe.org/6kpl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kpl RCSB], [http://www.ebi.ac.uk/pdbsum/6kpl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kpl ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Endo-beta-N-acetylglucosaminidase (ENGase) catalyzes hydrolysis of N-linked oligosaccharides. Although many ENGases have been characterized from various organisms, so far no fucose-containing oligosaccharides-specific ENGase has been identified in any organism. Here, we screened soil samples, using dansyl chloride (Dns)-labeled sialylglycan (Dns-SG) as a substrate, and discovered a strain that exhibits ENGase activity in the culture supernatant; this strain, named here as strain HMA12, was identified as a Sphingobacterium species by 16S ribosomal RNA gene analysis. By draft genome sequencing, five candidate ENGase encoding genes were identified in the genome of this strain. Recombinant proteins, purified from Escherichia coli expressing candidate genes ORF1152, ORF1188, ORF3046 and ORF3750 exhibited fucose-containing oligosaccharides-specific ENGase activity. These ENGases exhibited optimum activities at very acidic pHs (between pH 2.3-2.5). BLAST searches using sequences of these candidate genes identified two fungal homologs of ORF1188, one in Beauveria bassiana and the other in Cordyceps militaris. Recombinant ORF1188, Beauveria and Cordyceps ENGases released the fucose-containing oligosaccharides residues from rituximab (immunoglobulin G) but not the high-mannose-containing oligosaccharides residues from RNase B, a result that not only confirmed the substrate specificity of these novel ENGases but also suggested that natural glycoproteins could be their substrates.

-	~~Authors~~:	+	Characterization of novel endo-beta-N-acetylglucosaminidases from Sphingobacterium species, Beauveria bassiana and Cordyceps militaris that specifically hydrolyze fucose-containing oligosaccharides and human IgG.,Huang Y, Higuchi Y, Kinoshita T, Mitani A, Eshima Y, Takegawa K Sci Rep. 2018 Jan 10;8(1):246. doi: 10.1038/s41598-017-17467-y. PMID:29321565<ref>PMID:29321565</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6kpl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Arakawa, T]]
		+	[[Category: Fushinobu, S]]
		+	[[Category: Seki, H]]
		+	[[Category: Takegawa, K]]
		+	[[Category: Yamada, C]]
		+	[[Category: Hydrolase]]
		+	[[Category: Tim barrel]]

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

OCA — Wed, 21 Aug 2019 04:06:29 GMT

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

←Older revision

Revision as of 04:06, 21 August 2019

OCA: New page: '''Unreleased structure''' The entry 6kpl is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 21 Aug 2019 04:06:27 GMT

New page: '''Unreleased structure''' The entry 6kpl is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6kpl is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]