PDBsum entry: 2f4o

Hydrolase/hydrolase inhibitor

PDB id: 2f4o

Contents

Protein chains

290 a.a. *

61 a.a. *

Ligands

PHQ-VAL-ALA-ASP-CF0

Metals

_CL

_ZN ×2

Waters ×18

* Residue conservation analysis

PDB id:

2f4o

Name:

Hydrolase/hydrolase inhibitor

Title:

The mouse pngase-hr23 complex reveals a complete remodulatio protein-protein interface compared to its yeast orthologs

Structure:

Peptide n-glycanase. Chain: a. Fragment: catalytic domain, residues 164-450. Engineered: yes. Xp-c repair complementing complex 58 kda protein. Chain: b. Fragment: xpcb domain, residues 273-332. Synonym: mhr23b, uv excision repair protein rad23 homolog b engineered: yes.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rad23b, mhr23b. Synthetic: yes

Biol. unit:

Trimer (from PQS)

Resolution:

2.26Å R-factor: 0.220 R-free: 0.293

Authors:

G.Zhao,X.Zhou,L.Wang,C.Kisker,W.J.Lennarz,H.Schindelin

Key ref:

G.Zhao et al. (2006). Structure of the mouse peptide N-glycanase-HR23 complex suggests co-evolution of the endoplasmic reticulum-associated degradation and DNA repair pathways. J Biol Chem, 281, 13751-13761. PubMed id: 16500903 DOI: 10.1074/jbc.M600137200

Date:

23-Nov-05 Release date: 07-Mar-06

Protein chain

Q9JI78  (NGLY1_MOUSE) -  Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase

Seq: 651 a.a.

Struc: 290 a.a.*

Protein chain

P54728  (RD23B_MOUSE) -  UV excision repair protein RAD23 homolog B

Seq: 416 a.a.

Struc: 61 a.a.*

* PDB and UniProt seqs differ at 7 residue positions (black crosses)

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 

• Biological process: nucleotide-excision repair (2 terms)
• Biochemical function: damaged DNA binding (1 term)

DOI no: 10.1074/jbc.M600137200

J Biol Chem 281:13751-13761 (2006)

PubMed id: 16500903

Structure of the mouse peptide N-glycanase-HR23 complex suggests co-evolution of the endoplasmic reticulum-associated degradation and DNA repair pathways.

G.Zhao, X.Zhou, L.Wang, G.Li, C.Kisker, W.J.Lennarz, H.Schindelin.

ABSTRACT

Peptide N-glycanase removes N-linked oligosaccharides from misfolded glycoproteins as part of the endoplasmic reticulum-associated degradation pathway. This process involves the formation of a tight complex of peptide N-glycanase with Rad23 in yeast and the orthologous HR23 proteins in mammals. In addition to its function in endoplasmic reticulum-associated degradation, HR23 is also involved in DNA repair, where it plays an important role in damage recognition in complex with the xeroderma pigmentosum group C protein. To characterize the dual role of HR23, we have determined the high resolution crystal structure of the mouse peptide N-glycanase catalytic core in complex with the xeroderma pigmentosum group C binding domain from HR23B. Peptide N-glycanase features a large cleft between its catalytic cysteine protease core and zinc binding domain. Opposite the zinc binding domain is the HR23B-interacting region, and surprisingly, the complex interface is fundamentally different from the orthologous yeast peptide N-glycanase-Rad23 complex. Different regions on both proteins are involved in complex formation, revealing an amazing degree of divergence in the interaction between two highly homologous proteins. Furthermore, the mouse peptide N-glycanase-HR23B complex mimics the interaction between xeroderma pigmentosum group C and HR23B, thereby providing a first structural model of how the two proteins interact within the nucleotide excision repair cascade in higher eukaryotes. The different interaction interfaces of the xeroderma pigmentosum group C binding domains in yeast and mammals suggest a co-evolution of the endoplasmic reticulum-associated degradation and DNA repair pathways.

Selected figure(s)

Figure 2.
FIGURE 2. Overall structure of the complex. A, ribbon diagram with the mPNGase transglutaminase-like core in dark blue, the zinc binding domain in cyan, and the XPCB domain in yellow. The bound zinc ion is shown as a red sphere. Secondary structure elements, N and C termini, and the residues adjacent to the disordered loop have been labeled at least once on either panel. B, surface representation of the inhibitor-bound complex in the same orientation and color-coded as in the left panel of A, with the inhibitor in an all-bonds representation. C, close-up view into the active site and catalytic triad showing the detailed interactions between the inhibitor and contacting residues of mPNGase (all labeled in single-letter code). Hydrogen bonds and ionic interactions are shown as red dashed lines. A SIGMAA-weighted 2F[o] - F[c] electron density map of the inhibitor is shown at a contour level of one times the r.m.s. deviation in blue. The N-terminal carbobenzyloxy group of the inhibitor is labeled with a Z.

Figure 5.
FIGURE 5. PNGase-XPCB domain interface. A, close-up view of the interface between the mPNGase core domain (dark blue) and the XPCB domain (yellow). Residues involved in hydrophobic interactions are shown in green, and those involved in hydrogen bonds are in magenta, whereas the hydrogen bonds are shown as red dotted lines. The interacting -helices of the mPNGase core domain, H11 and H12, and adjacent helices in mPNGase as well as all helices of the XPCB domain are labeled. B, the mouse complex. Surface representation of the XPCB domain color-coded as in A. Shown is a ribbon diagram of the mPNGase core with helices H11 and H12 of the core domain in dark blue and the remainder of the core rendered partially transparent. The first and last residues of PNGase are indicated. C, the yeast complex with PNGase in the same relative orientation as in B. PNGase (ribbon diagram) and the XPCB domain of Rad23 (surface representation) are displayed as described in B, with the exception that in this case helices H1 and H12 of PNGase are shown in blue.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 13751-13761) copyright 2006.

Figures were selected by the author.