1pnf: Difference between revisions
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==PNGASE F COMPLEX WITH DI-N-ACETYLCHITOBIOSE== | ==PNGASE F COMPLEX WITH DI-N-ACETYLCHITOBIOSE== | ||
<StructureSection load='1pnf' size='340' side='right' caption='[[1pnf]], [[Resolution|resolution]] 2.00Å' scene=''> | <StructureSection load='1pnf' size='340' side='right'caption='[[1pnf]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1pnf]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[1pnf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Elizabethkingia_meningoseptica Elizabethkingia meningoseptica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PNF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PNF FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pnf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pnf OCA], [https://pdbe.org/1pnf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pnf RCSB], [https://www.ebi.ac.uk/pdbsum/1pnf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pnf ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/PNGF_ELIMR PNGF_ELIMR] Cleaves an entire glycan from a glycoprotein. Requires that the glycosylated asparagine moiety (reaction 1) be substituted on its amino (R1) and carboxyl (R2) terminus with a polypeptide chain. | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 1pnf" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 1pnf" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Peptide N-glycanase|Peptide N-glycanase]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Elizabethkingia meningoseptica]] | [[Category: Elizabethkingia meningoseptica]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Kuhn P]] | ||
[[Category: | [[Category: Van Roey P]] | ||
Latest revision as of 11:46, 11 October 2023
PNGASE F COMPLEX WITH DI-N-ACETYLCHITOBIOSEPNGASE F COMPLEX WITH DI-N-ACETYLCHITOBIOSE
Structural highlights
FunctionPNGF_ELIMR Cleaves an entire glycan from a glycoprotein. Requires that the glycosylated asparagine moiety (reaction 1) be substituted on its amino (R1) and carboxyl (R2) terminus with a polypeptide chain. Publication Abstract from PubMedCrystallographic analysis and site-directed mutagenesis have been used to identify the catalytic and oligosaccharide recognition residues of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F (PNGase F), an amidohydrolase that removes intact asparagine-linked oligosaccharide chains from glycoproteins and glycopeptides. Mutagenesis has shown that three acidic residues, Asp-60, Glu-206, and Glu-118, that are located in a cleft at the interface between the two domains of the protein are essential for activity. The D60N mutant has no detectable activity, while E206Q and E118Q have less than 0.01 and 0.1% of the wild-type activity, respectively. Crystallographic analysis, at 2.0-A resolution, of the complex of the wild-type enzyme with the product, N,N'-diacetylchitobiose, shows that Asp-60 is in direct contact with the substrate at the cleavage site, while Glu-206 makes contact through a bridging water molecule. This indicates that Asp-60 is the primary catalytic residue, while Glu-206 probably is important for stabilization of reaction intermediates. Glu-118 forms a hydrogen bond with O6 of the second N-acetylglucosamine residue of the substrate and the low activity of the E118Q mutant results from its reduced ability to bind the oligosaccharide. This analysis also suggests that the mechanism of action of PNGase F differs from those of L-asparaginase and glycosylasparaginase, which involve a threonine residue as the nucleophile. Active site and oligosaccharide recognition residues of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F.,Kuhn P, Guan C, Cui T, Tarentino AL, Plummer TH Jr, Van Roey P J Biol Chem. 1995 Dec 8;270(49):29493-7. PMID:7493989[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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