1x3w | pdb_00001x3w
Structure of a peptide:N-glycanase-Rad23 complex
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Overview
In eukaryotes, misfolded proteins must be distinguished from correctly, folded proteins during folding and transport processes by quality control, systems. Yeast peptide:N-glycanase (yPNGase) specifically deglycosylates, the denatured form of N-linked glycoproteins in the cytoplasm and assists, proteasome-mediated glycoprotein degradation by forming a complex with 26S, proteasome through DNA repair protein, yRad23. Here, we describe the, crystal structures of a yPNGase and XPC-binding domain of yRad23, (yRad23XBD, residues 238-309) complex and of a yPNGase-yRad23XBD complex, bound to a caspase inhibitor, Z-VAD-fmk. yPNGase is formed with three, domains, a core domain containing a Cys-His-Asp triad, a Zn-binding, domain, and a Rad23-binding domain. Both N- and C-terminal helices of, yPNGase interact with yRad23 through extensive hydrophobic interactions., The active site of yPNGase is located in a deep cleft that is formed with, residues conserved in all PNGase members, and three sugar molecules are, bound to this cleft. Complex structures in conjunction with mutational, analyses revealed that the walls of the cleft block access to the active, site of yPNGase by native glycoprotein, whereas the cleft is sufficiently, wide to accommodate denatured glycoprotein, thus explaining the, specificity of PNGase for denatured substrates.
About this Structure
1X3W is a Protein complex structure of sequences from Saccharomyces cerevisiae with SUC and ZN as ligands. Active as Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase, with EC number 3.5.1.52 Full crystallographic information is available from OCA.
Reference
Structure of a peptide:N-glycanase-Rad23 complex: insight into the deglycosylation for denatured glycoproteins., Lee JH, Choi JM, Lee C, Yi KJ, Cho Y, Proc Natl Acad Sci U S A. 2005 Jun 28;102(26):9144-9. Epub 2005 Jun 17. PMID:15964983
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