PDBsum entry: 1x3z

Hydrolase/hydrolase inhibitor

PDB id: 1x3z

Contents

Protein chains

320 a.a. *

57 a.a. *

Ligands

VAL-ALA-ASP-CF0

SUC ×2

Metals

_ZN

Waters ×29

* Residue conservation analysis

PDB id:

1x3z

Name:

Hydrolase/hydrolase inhibitor

Title:

Structure of a peptide:n-glycanase-rad23 complex

Structure:

Peptide: n-glycanase. Chain: a. Engineered: yes. Uv excision repair protein rad23. Chain: b. Fragment: xpc binding domain. Engineered: yes. Peptide phq-val-ala-asp-cf0. Chain: i.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: the peptide was chemically synthesized

Biol. unit:

Hexamer (from PQS)

Resolution:

2.80Å R-factor: 0.237 R-free: 0.270

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

Date:

11-May-05 Release date: 14-Jun-05

Protein chain

Q02890  (PNG1_YEAST) -  Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase

Seq: 363 a.a.

Struc: 320 a.a.

Protein chain

P32628  (RAD23_YEAST) -  UV excision repair protein RAD23

Seq: 398 a.a.

Struc: 57 a.a.

Enzyme reactions

• Enzyme class: Chain A: E.C.3.5.1.52 - Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase.
• 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 

• Cellular component: cytoplasm (4 terms)
• Biological process: protein deglycosylation (4 terms)
• Biochemical function: protein binding (5 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.

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.

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 the author.