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PDBsum entry 2f4m

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protein metals Protein-protein interface(s) links
Hydrolase PDB id
2f4m
Jmol
Contents
Protein chains
295 a.a. *
61 a.a. *
Metals
_CL
_ZN
Waters ×255
* Residue conservation analysis
PDB id:
2f4m
Name: Hydrolase
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. Uv excision repair protein rad23 homolog b. Chain: b. Fragment: xpcb domain, residues 273-332. Synonym: mhr23b, xp-c repair complementing complex 58 kda p p58.
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rad23b, mhr23b.
Biol. unit: Dimer (from PQS)
Resolution:
1.85Å     R-factor:   0.189     R-free:   0.239
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9JI78  (NGLY1_MOUSE) -  Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
Seq:
Struc:
 
Seq:
Struc:
651 a.a.
295 a.a.*
Protein chain
Pfam   ArchSchema ?
P54728  (RD23B_MOUSE) -  UV excision repair protein RAD23 homolog B
Seq:
Struc:
416 a.a.
61 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 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.
[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!
  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 an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
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.  
18200608 O.Okhrimenko, and I.Jelesarov (2008).
A survey of the year 2006 literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 21, 1.  
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
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.  
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
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 code is shown on the right.