› 5wxi

X-ray diffraction
2Å resolution

EarP bound with dTDP-rhamnose (soaked)

Released:
DOI: 10.2210/pdb5wxi/pdb
PDB entry 5wxi coloured by chain, front view.
PDB entry 5wxi coloured by chain, side view.
PDB entry 5wxi coloured by chain, top view.
Source organism: Neisseria meningitidis H44/76
Primary publication:
Structural basis of protein arginine rhamnosylation by glycosyltransferase EarP.
Sengoku T, Suzuki T, Dohmae N, Watanabe C, Honma T, Hikida Y, Yamaguchi Y, Takahashi H, Yokoyama S, Yanagisawa T
Nat Chem Biol 14 368-374 (2018)
PMID: 29440735

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123024 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Protein-arginine rhamnosyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 382 amino acids
Theoretical weight: 44.22 KDa
Source organism: Neisseria meningitidis H44/76
Expression system: Escherichia coli
UniProt:
  • Canonical: E6MVV9 (Residues: 1-382; Coverage: 100%)
Gene names: NMH_0797, earP
Sequence domains: Elongation-Factor P (EF-P) rhamnosyltransferase EarP

Ligands and Environments

4 bound ligands:
Ligand TRH 2 x TRH
Ligand BME 6 x BME
Ligand SO4 7 x SO4
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P21212
Unit cell:
a: 97.578Å b: 195.388Å c: 46.366Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.172 0.213
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Bacteria-Catalyzed Arginine Glycosylation in Pathogens and Host.
Pan et al. (2020)
8 other articles

1 mention without citation

Translation factor accelerating peptide bond formation on the ribosome: EF-P and eIF5A as entropic catalysts and a potential drug targets.
Mudryi et al. (2023)