2F4O | pdb_00002f4o

The Mouse PNGase-HR23 Complex Reveals a Complete Remodulation of the Protein-Protein Interface Compared to its Yeast Orthologs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 
    0.293 (Depositor), 0.375 (DCC) 
  • R-Value Work: 
    0.220 (Depositor) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.6 of the entry. See complete history

Literature

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

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

(2006) J Biological Chem 281: 13751-13761

  • DOI: https://doi.org/10.1074/jbc.M600137200
  • Primary Citation Related Structures: 
    2F4M, 2F4O

  • PubMed 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.


  • Organizational Affiliation
    • Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794.

Macromolecule Content 

  • Total Structure Weight: 42.69 kDa 
  • Atom Count: 2,966 
  • Modeled Residue Count: 356 
  • Deposited Residue Count: 361 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
peptide N-glycanase295Mus musculusMutation(s): 0 
EC: 3.5.1.52
UniProt
Find proteins for Q9JI78 (Mus musculus)
Explore Q9JI78 
Go to UniProtKB:  Q9JI78
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JI78
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
XP-C repair complementing complex 58 kDa protein61Mus musculusMutation(s): 0 
Gene Names: Rad23bMhr23b
EC: 1.14.11
UniProt
Find proteins for P54728 (Mus musculus)
Explore P54728 
Go to UniProtKB:  P54728
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54728
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PHQ-VAL-ALA-ASP-CF0C [auth I]5N/AMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free:  0.293 (Depositor), 0.375 (DCC) 
  • R-Value Work:  0.220 (Depositor) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.958α = 90
b = 52.097β = 113.5
c = 80.848γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2017-10-18
    Changes: Refinement description
  • Version 1.5: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2024-11-13
    Changes: Structure summary