› 4bjr

X-ray diffraction
2.8Å resolution

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

Released:
DOI: 10.2210/pdb4bjr/pdb
PDB entry 4bjr coloured by chain, front view.
PDB entry 4bjr coloured by chain, side view.
PDB entry 4bjr coloured by chain, top view.
Source organism: Corynebacterium glutamicum ATCC 13032
Primary publication:
Crystal structure of the complex between prokaryotic ubiquitin-like protein and its ligase PafA.
Barandun J, Delley CL, Ban N, Weber-Ban E
J Am Chem Soc 135 6794-7 (2013)
PMID: 23601177

Function and Biology Details

Reaction catalysed: 
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N(6)-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185634 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Prokaryotic ubiquitin-like protein Pup; Pup--protein ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 517 amino acids
Theoretical weight: 57.51 KDa
Source organism: Corynebacterium glutamicum ATCC 13032
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8NQE1 (Residues: 2-482; Coverage: 100%)
  • Canonical: Q8NQE0 (Residues: 38-64; Coverage: 42%)
Gene names: Cgl1494, Cgl1495, cg1688, cg1689, pafA, pup
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand ATP 2 x ATP
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 63.84Å b: 84.02Å c: 215.11Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.213 0.248
Expression system: Escherichia coli BL21(DE3)

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Citations

6 review citations

Bacterial Proteasomes.
Jastrab et al. (2015)
5 more

6 mentions without citation

Prokaryotic ubiquitin-like protein modification.
Maupin-Furlow JA. (2014)
5 more