2CM0 | pdb_00002cm0

The PUB domain functions as a p97 binding module in human peptide N-glycanase.

• PDB DOI: https://doi.org/10.2210/pdb2CM0/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-05-03 Released: 2006-06-28 
• Deposition Author(s): Allen, M.D., Buchberger, A., Bycroft, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.223 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

The Pub Domain Functions as a P97 Binding Module in Human Peptide N-Glycanase.

Allen, M.D., Buchberger, A., Bycroft, M.

(2006) J Biological Chem 281: 25502

• PubMed: 16807242 
• DOI: https://doi.org/10.1074/jbc.M601173200
• Primary Citation Related Structures: 
  2CCQ, 2CM0


• PubMed Abstract: 
  

  The AAA ATPase p97 is a ubiquitin-selective molecular machine involved in multiple cellular processes, including protein degradation through the ubiquitin-proteasome system and homotypic membrane fusion. Specific p97 functions are mediated by a variety of cofactors, among them peptide N-glycanase, an enzyme that removes glycans from misfolded glycoproteins. Here we report the three-dimensional structure of the aminoterminal PUB domain of human peptide N-glycanase. We demonstrate that the PUB domain is a novel p97 binding module interacting with the D1 and/or D2 ATPase domains of p97 and identify an evolutionary conserved surface patch required for p97 binding. Furthermore, we show that the PUB and UBX domains do not bind to p97 in a mutually exclusive manner. Our results suggest that PUB domain-containing proteins constitute a widespread family of diverse p97 cofactors.

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Organizational Affiliation: 
• Centre for Protein Engineering, Medical Research Council, Hills Road, Cambridge CB2 2QH, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 11.1 kDa 
• Atom Count: 876 
• Modeled Residue Count: 99 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE N-GLYCANASE HOMOLOG	A	99	Homo sapiens	Mutation(s): 3  EC: 3.5.1.52
UniProt & NIH Common Fund Data Resources
Find proteins for Q96IV0 (Homo sapiens) Explore Q96IV0  Go to UniProtKB:  Q96IV0
PHAROS:  Q96IV0 GTEx:  ENSG00000151092

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
BME	C [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.223 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.987	α = 90
b = 73.987	β = 90
c = 32.994	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-28 
Deposition Author(s): Allen, M.D., Buchberger, A., Bycroft, M.

Revision History  

• Version 1.0: 2006-06-28
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-24
  Changes: Source and taxonomy
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description