PDBsum entry 1x3w

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
320 a.a. *
57 a.a. *
SUC ×3
Waters ×17
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of a peptide:n-glycanase-rad23 complex
Structure: Peptide:n-glycanase. Chain: a. Fragment: residues 8-342. Engineered: yes. Uv excision repair protein rad23. Chain: b. Fragment: xpc binding domain. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PQS)
3.00Å     R-factor:   0.245     R-free:   0.274
Authors: J.-H.Lee,J.M.Choi,C.Lee,K.J.Yi,Y.Cho
Key ref:
J.H.Lee et al. (2005). Structure of a peptide:N-glycanase-Rad23 complex: insight into the deglycosylation for denatured glycoproteins. Proc Natl Acad Sci U S A, 102, 9144-9149. PubMed id: 15964983 DOI: 10.1073/pnas.0502082102
11-May-05     Release date:   14-Jun-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q02890  (PNG1_YEAST) -  Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
363 a.a.
320 a.a.
Protein chain
Pfam   ArchSchema ?
P32628  (RAD23_YEAST) -  UV excision repair protein RAD23
398 a.a.
57 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain A: E.C.  - Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of an N(4)-(acetyl-beta-D-glucosaminyl)asparagine residue in which the N-acetyl-D-glucosamine residue may be further glycosylated, to yield a (substituted) N-acetyl-beta-D- glucosaminylamine and the peptide containing an aspartic residue.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   3 terms 
  Biological process     protein deglycosylation   4 terms 
  Biochemical function     hydrolase activity     4 terms  


DOI no: 10.1073/pnas.0502082102 Proc Natl Acad Sci U S A 102:9144-9149 (2005)
PubMed id: 15964983  
Structure of a peptide:N-glycanase-Rad23 complex: insight into the deglycosylation for denatured glycoproteins.
J.H.Lee, J.M.Choi, C.Lee, K.J.Yi, Y.Cho.
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.
  Selected figure(s)  
Figure 1.
Fig. 1. Schematic representation of the yPNGase-yRad23 complex, providing two different views of the yPNGase-yRad23 complex structure. yPNGase is shown in blue and yRad23 is in yellow. yPNGase comprises three domains, an N-terminal Rad23-binding, a core, and a Zn-binding domain. Three sucrose molecules (green) are located in the deep cleft. A Zn atom (red) is coordinated by Cys-129, -132, -165, and -168 in yPNGase.
Figure 4.
Fig. 4. Active site of yPNGase and the surface representation of the yPNGase-yRad23XBD complex. (A) Interactions between yPNGase and the inhibitor (Left) or sucrose molecules (Center and Right). A sucrose molecule in site 1 of yPNGase (Center) is replaced by an inhibitor, Z-VAD-fmk, but the other two sucrose molecules in sites 2 and 3 remained in the same position upon inhibitor binding (Right). H-bonds are represented by dashed lines. O, N, and S atoms are shown in red, blue, and orange, respectively. Residues that replaced in mutational analyses are marked with red circles. (B) The molecular surfaces of yPNGase and yRad23XBD are colored in white and yellow, respectively. The surface of the yPNGase residues that is >80% conserved in four yPNGase orthologues (Fig. 2) is colored in purple. A catalytic triad is shown in yellow. Axes indicate the close-up views for the inhibitor and sugar-binding sites.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23151626 S.S.Bhaskaran, and C.E.Stebbins (2012).
Structure of the catalytic domain of the Salmonella virulence factor SseI.
  Acta Crystallogr D Biol Crystallogr, 68, 1613-1621.
PDB codes: 4g29 4g2b
19819901 M.A.Hossain, R.Nakano, K.Nakamura, and Y.Kimura (2010).
Molecular identification and characterization of an acidic peptide:N-glycanase from tomato (Lycopersicum esculentum) fruits.
  J Biochem, 147, 157-165.  
19940117 S.Maerz, Y.Funakoshi, Y.Negishi, T.Suzuki, and S.Seiler (2010).
The Neurospora peptide:N-glycanase ortholog PNG1 is essential for cell polarity despite its lack of enzymatic activity.
  J Biol Chem, 285, 2326-2332.  
20479940 Y.Funakoshi, Y.Negishi, J.P.Gergen, J.Seino, K.Ishii, W.J.Lennarz, I.Matsuo, Y.Ito, N.Taniguchi, and T.Suzuki (2010).
Evidence for an essential deglycosylation-independent activity of PNGase in Drosophila melanogaster.
  PLoS One, 5, e10545.  
18695987 A.Miyazaki, I.Matsuo, S.Hagihara, A.Kakegawa, T.Suzuki, and Y.Ito (2009).
Systematic synthesis and inhibitory activity of haloacetamidyl oligosaccharide derivatives toward cytoplasmic peptide:N-glycanase.
  Glycoconj J, 26, 133-140.  
18854368 G.Zhao, G.Li, X.Zhou, I.Matsuo, Y.Ito, T.Suzuki, W.J.Lennarz, and H.Schindelin (2009).
Structural and mutational studies on the importance of oligosaccharide binding for the activity of yeast PNGase.
  Glycobiology, 19, 118-125.
PDB code: 3esw
19497384 L.Madsen, M.Seeger, C.A.Semple, and R.Hartmann-Petersen (2009).
New ATPase regulators--p97 goes to the PUB.
  Int J Biochem Cell Biol, 41, 2380-2388.  
20016784 S.Wang, F.Xin, X.Liu, Y.Wang, Z.An, Q.Qi, and P.G.Wang (2009).
N-terminal deletion of Peptide:N-glycanase results in enhanced deglycosylation activity.
  PLoS One, 4, e8335.  
17666024 A.Diepold, G.Li, W.J.Lennarz, T.Nürnberger, and F.Brunner (2007).
The Arabidopsis AtPNG1 gene encodes a peptide: N-glycanase.
  Plant J, 52, 94.  
17496150 G.Zhao, X.Zhou, L.Wang, G.Li, H.Schindelin, and W.J.Lennarz (2007).
Studies on peptide:N-glycanase-p97 interaction suggest that p97 phosphorylation modulates endoplasmic reticulum-associated degradation.
  Proc Natl Acad Sci U S A, 104, 8785-8790.
PDB codes: 2hpj 2hpl
17971999 M.D.Witte, C.V.Descals, Lavoir, B.I.Florea, G.A.van der Marel, and H.S.Overkleeft (2007).
Bodipy-VAD-Fmk, a useful tool to study yeast peptide N-glycanase activity.
  Org Biomol Chem, 5, 3690-3697.  
17950635 T.Suzuki (2007).
Cytoplasmic peptide:N-glycanase and catabolic pathway for free N-glycans in the cytosol.
  Semin Cell Dev Biol, 18, 762-769.  
17427805 Z.L.Nimchuk, E.J.Fisher, D.Desveaux, J.H.Chang, and J.L.Dangl (2007).
The HopX (AvrPphE) family of Pseudomonas syringae type III effectors require a catalytic triad and a novel N-terminal domain for function.
  Mol Plant Microbe Interact, 20, 346-357.  
17154534 C.G.Bunick, M.R.Miller, B.E.Fuller, E.Fanning, and W.J.Chazin (2006).
Biochemical and structural domain analysis of xeroderma pigmentosum complementation group C protein.
  Biochemistry, 45, 14965-14979.  
16401726 I.Kim, J.Ahn, C.Liu, K.Tanabe, J.Apodaca, T.Suzuki, and H.Rao (2006).
The Png1-Rad23 complex regulates glycoprotein turnover.
  J Cell Biol, 172, 211-219.  
17088551 X.Zhou, G.Zhao, J.J.Truglio, L.Wang, G.Li, W.J.Lennarz, and H.Schindelin (2006).
Structural and biochemical studies of the C-terminal domain of mouse peptide-N-glycanase identify it as a mannose-binding module.
  Proc Natl Acad Sci U S A, 103, 17214-17219.
PDB codes: 2g9f 2g9g 2i74
16249333 G.Li, X.Zhou, G.Zhao, H.Schindelin, and W.J.Lennarz (2005).
Multiple modes of interaction of the deglycosylation enzyme, mouse peptide N-glycanase, with the proteasome.
  Proc Natl Acad Sci U S A, 102, 15809-15814.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.