› 6aqr

X-ray diffraction
2.1Å resolution

SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73 bound to monoubiquitin

Released:
DOI: 10.2210/pdb6aqr/pdb
PDB entry 6aqr coloured by chain, front view.
PDB entry 6aqr coloured by chain, side view.
PDB entry 6aqr coloured by chain, top view.
Source organisms:
Primary publication:
Active site alanine mutations convert deubiquitinases into high-affinity ubiquitin-binding proteins.
Morrow ME, Morgan MT, Clerici M, Growkova K, Yan M, Komander D, Sixma TK, Simicek M, Wolberger C
EMBO Rep 19 (2018)
PMID: 30150323

Function and Biology Details

Reaction catalysed: 
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-143355 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Ubiquitin carboxyl-terminal hydrolase 8 Chain: A
Molecule details ›
Chain: A
Length: 476 amino acids
Theoretical weight: 54 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P50102 (Residues: 1-471; Coverage: 100%)
Gene names: UBP8, YM9959.05, YMR223W
Sequence domains:
Structure domains:
Transcription and mRNA export factor SUS1 Chain: B
Molecule details ›
Chain: B
Length: 96 amino acids
Theoretical weight: 11.09 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6WNK7 (Residues: 1-96; Coverage: 100%)
Gene names: SUS1, YBR111W-A
Sequence domains: Transcription factor e(y)2
Structure domains: Serum Albumin; Chain A, Domain 1
SAGA-associated factor 11 Chain: C
Molecule details ›
Chain: C
Length: 99 amino acids
Theoretical weight: 11.3 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q03067 (Residues: 1-99; Coverage: 100%)
Gene names: SGF11, YPL047W
Sequence domains:
Ubiquitin Chain: D
Molecule details ›
Chain: D
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
SAGA-associated factor 73 Chain: E
Molecule details ›
Chain: E
Length: 96 amino acids
Theoretical weight: 10.82 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P53165 (Residues: 1-96; Coverage: 15%)
Gene names: SGF73, YGL066W
Sequence domains: Zinc finger domain

Ligands and Environments

1 bound ligand:
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P212121
Unit cell:
a: 78.755Å b: 103.177Å c: 112.846Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.201 0.249
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Breaking the chains: deubiquitylating enzyme specificity begets function.
Clague et al. (2019)
1 more

2 mentions without citation

Active site alanine mutations convert deubiquitinases into high-affinity ubiquitin-binding proteins.
Morrow et al. (2018)
1 more