1X3Z

Structure of a peptide:N-glycanase-Rad23 complex

Summary for 1X3Z

• Entry DOI: 10.2210/pdb1x3z/pdb
• Related: 1X3W
• Related PRD ID: PRD_000338 PRD_900003
• Descriptor: peptide: N-glycanase, UV excision repair protein RAD23, peptide PHQ-Val-Ala-Asp-CF0, ... (6 entities in total)
• Functional Keywords: hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Total number of polymer chains: 3
• Total formula weight: 48092.86

Authors

Lee, J.-H.,Choi, J.M.,Lee, C.,Yi, K.J.,Cho, Y. (deposition date: 2005-05-11, release date: 2005-06-14, Last modification date: 2024-10-09)

Primary citation

Lee, J.H.,Choi, J.M.,Lee, C.,Yi, K.J.,Cho, Y.
Structure of a peptide:N-glycanase-Rad23 complex: insight into the deglycosylation for denatured glycoproteins.
Proc.Natl.Acad.Sci.Usa, 102:9144-9149, 2005

PubMed Abstract: 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.

PubMed: 15964983
DOI: 10.1073/pnas.0502082102

Experimental method

X-RAY DIFFRACTION (2.8 Å)