› 6ryo

X-ray diffraction
1.92Å resolution

Bacterial membrane enzyme structure by the in meso method at 1.9 A resolution

Released:
DOI: 10.2210/pdb6ryo/pdb
PDB entry 6ryo coloured by chain, front view.
PDB entry 6ryo coloured by chain, side view.
PDB entry 6ryo coloured by chain, top view.
Source organisms:
Primary publication:
Structures of lipoprotein signal peptidase II from Staphylococcus aureus complexed with antibiotics globomycin and myxovirescin.
Olatunji S, Yu X, Bailey J, Huang CY, Zapotoczna M, Bowen K, Remškar M, Müller R, Scanlan EM, Geoghegan JA, Olieric V, Caffrey M
Nat Commun 11 140 (2020)
PMID: 31919415

Function and Biology Details

Reaction catalysed: 
Release of signal peptides from bacterial membrane prolipoproteins including murein prolipoprotein. Hydrolyzes -Xaa-Yaa-Zaa-|-(S,diacylglyceryl)Cys-, in which Xaa is hydrophobic (preferably Leu), and Yaa (Ala or Ser) and Zaa (Gly or Ala) have small, neutral sidechains.
Biochemical function:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-167424 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lipoprotein signal peptidase Chain: A
Molecule details ›
Chain: A
Length: 187 amino acids
Theoretical weight: 21.23 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6GHN9 (Residues: 1-163; Coverage: 100%)
Gene names: SAR1172, lsp, lspA
Sequence domains: Signal peptidase (SPase) II
Globomycin Chain: B
Molecule details ›
Chain: B
Length: 5 amino acids
Theoretical weight: 674 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand OLC 6 x OLC
Ligand GOL 5 x GOL
Ligand 7PE 10 x 7PE
Ligand ZN 1 x ZN
3 modified residues:
Ligand MLE 1 x MLE
Ligand IIL 1 x IIL
Ligand ALO 1 x ALO

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P3221
Unit cell:
a: 52.258Å b: 52.258Å c: 135.882Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.252 0.25 0.276
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Bacterial Signal Peptides- Navigating the Journey of Proteins.
Kaushik et al. (2022)
1 more

4 mentions without citation

Bacterial Lipoprotein Posttranslational Modifications. New Insights and Opportunities for Antibiotic and Vaccine Development.
Smithers et al. (2021)
3 more