4BJR

Crystal structure of the complex between Prokaryotic Ubiquitin-like Protein Pup and its Ligase PafA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Complex between Prokaryotic Ubiquitin-Like Protein Pup and its Ligase Pafa.

Barandun, J.Delley, C.L.Ban, N.Weber-Ban, E.

(2013) J.Am.Chem.Soc. 135: 6794

  • DOI: 10.1021/ja4024012

  • PubMed Abstract: 
  • Prokaryotic ubiquitin-like protein (Pup) is covalently attached to target proteins by the ligase PafA, tagging substrates for proteasomal degradation. The crystal structure of Pup in complex with PafA, reported here, reveals that a long groove wrappi ...

    Prokaryotic ubiquitin-like protein (Pup) is covalently attached to target proteins by the ligase PafA, tagging substrates for proteasomal degradation. The crystal structure of Pup in complex with PafA, reported here, reveals that a long groove wrapping around the enzyme serves as a docking site for Pup. Upon binding, the C-terminal region of the intrinsically disordered Pup becomes ordered to form two helices connected by a linker, positioning the C-terminal glutamate in the active site of PafA.


    Organizational Affiliation

    Institute of Molecular Biology & Biophysics, ETH Zürich, Zürich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUP--PROTEIN LIGASE, PROKARYOTIC UBIQUITIN-LIKE PROTEIN PUP
A, B
517Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)Mutation(s): 1 
Gene Names: pafA, pup
EC: 6.3.1.19
Find proteins for Q8NQE1 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025))
Go to UniProtKB:  Q8NQE1
Find proteins for Q8NQE0 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025))
Go to UniProtKB:  Q8NQE0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.840α = 90.00
b = 84.020β = 90.00
c = 215.110γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-05-15
    Type: Structure summary
  • Version 1.2: 2013-05-22
    Type: Database references