6kpm: Difference between revisions
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The | ==Crystal Structure of endo-beta-N-acetylglucosaminidase from Cordyceps militaris in complex with L-fucose== | ||
<StructureSection load='6kpm' size='340' side='right'caption='[[6kpm]], [[Resolution|resolution]] 1.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6kpm]] 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=6KPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KPM FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <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=6kpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kpm OCA], [http://pdbe.org/6kpm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kpm RCSB], [http://www.ebi.ac.uk/pdbsum/6kpm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kpm ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6kpm" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Cormm]] | |||
[[Category: Large Structures]] | |||
[[Category: Arakawa, T]] | |||
[[Category: Fushinobu, S]] | |||
[[Category: Seki, H]] | |||
[[Category: Takegawa, K]] | |||
[[Category: Yamada, C]] | |||
[[Category: Hydrolase]] | |||
[[Category: Tim barrel]] | |||
