2F4O

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 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.4 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.Biol.Chem. 281: 13751-13761

  • DOI: 10.1074/jbc.M600137200
  • Primary Citation of Related Structures:  

  • 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 ...

    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 11794-5115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
peptide N-glycanase
A
295Mus musculusMutation(s): 0 
Gene Names: Ngly1
EC: 3.5.1.52
Find proteins for Q9JI78 (Mus musculus)
Go to UniProtKB:  Q9JI78
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
XP-C repair complementing complex 58 kDa protein
B
61Mus musculusMutation(s): 0 
Gene Names: Rad23b (Mhr23b)
Find proteins for P54728 (Mus musculus)
Go to UniProtKB:  P54728
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PHQ-VAL-ALA-ASP-CF0
I
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000338
Query on PRD_000338
IN-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamidePeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 96.958α = 90.00
b = 52.097β = 113.50
c = 80.848γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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