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New page: left|200px<br /><applet load="1pnf" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pnf, resolution 2.00Å" /> '''PNGASE F COMPLEX WIT...
 
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[[Image:1pnf.gif|left|200px]]<br /><applet load="1pnf" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1pnf, resolution 2.00&Aring;" />
'''PNGASE F COMPLEX WITH DI-N-ACETYLCHITOBIOSE'''<br />


==Overview==
==PNGASE F COMPLEX WITH DI-N-ACETYLCHITOBIOSE==
Crystallographic 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.
<StructureSection load='1pnf' size='340' side='right'caption='[[1pnf]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</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'>[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>
== 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;">
== Publication Abstract from PubMed ==
Crystallographic 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.


==About this Structure==
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<ref>PMID:7493989</ref>
1PNF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Elizabethkingia_meningoseptica Elizabethkingia meningoseptica] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine_amidase Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.52 3.5.1.52] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PNF OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7493989 7493989]
</div>
<div class="pdbe-citations 1pnf" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Peptide N-glycanase|Peptide N-glycanase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Elizabethkingia meningoseptica]]
[[Category: Elizabethkingia meningoseptica]]
[[Category: Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Kuhn P]]
[[Category: Kuhn, P.]]
[[Category: Van Roey P]]
[[Category: Roey, P.Van.]]
[[Category: SO4]]
[[Category: hydrolase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:56:43 2007''

Latest revision as of 08:46, 11 October 2023

PNGASE F COMPLEX WITH DI-N-ACETYLCHITOBIOSE

1pnf, resolution 2.00Å

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