› 3s04

X-ray diffraction
2.44Å resolution

Crystal structure of Escherichia coli type I signal peptidase in complex with an Arylomycin Lipoglycopeptide Antibiotic

Released:
DOI: 10.2210/pdb3s04/pdb
PDB entry 3s04 coloured by chain, front view.
PDB entry 3s04 coloured by chain, side view.
PDB entry 3s04 coloured by chain, top view.
Source organisms:
Primary publication:
Synthesis and characterization of the arylomycin lipoglycopeptide antibiotics and the crystallographic analysis of their complex with signal peptidase.
Liu J, Luo C, Smith PA, Chin JK, Page MG, Paetzel M, Romesberg FE
J Am Chem Soc 133 17869-77 (2011)
PMID: 21999324

Function and Biology Details

Reaction catalysed: 
Cleavage of hydrophobic, N-terminal signal or leader sequences from secreted and periplasmic proteins.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-133587 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Signal peptidase I Chains: A, B
Molecule details ›
Chains: A, B
Length: 250 amino acids
Theoretical weight: 28.08 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00803 (Residues: 75-324; Coverage: 77%)
Gene names: JW2552, b2568, lepB
Sequence domains: Signal peptidase, peptidase S26
Structure domains:
Glyco-Arylomycin Chains: I, J
Molecule details ›
Chains: I, J
Length: 6 amino acids
Theoretical weight: 661 Da
Source organism: Streptomyces sp.

Ligands and Environments

2 bound ligands:
Ligand 02U 2 x 02U
Ligand RAM 2 x RAM
2 modified residues:
Ligand DSE 2 x DSE
Ligand DAL 2 x DAL

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P43212
Unit cell:
a: 72.01Å b: 72.01Å c: 262.57Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.246 0.245 0.265
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

12 review citations

Prospects for new antibiotics: a molecule-centered perspective.
Walsh et al. (2014)
11 more

3 mentions without citation

The Sec System: Protein Export in Escherichia coli.
Crane et al. (2017)
2 more