› 5u0t

X-ray diffraction
2.11Å resolution

Crystal structure of a methyltransferase involved in the biosynthesis of gentamicin in complex with (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-3-(methylamino)-alpha-D-glucopyranosyl]oxy}-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside

Released:
DOI: 10.2210/pdb5u0t/pdb
PDB entry 5u0t coloured by chain, front view.
PDB entry 5u0t coloured by chain, side view.
PDB entry 5u0t coloured by chain, top view.
Source organism: Micromonospora echinospora
Primary publication:
Structural Basis of the Selectivity of GenN, an Aminoglycoside N-Methyltransferase Involved in Gentamicin Biosynthesis.
Bury PDS, Huang F, Li S, Sun Y, Leadlay PF, Dias MVB
ACS Chem Biol 12 2779-2787 (2017)
PMID: 28876898

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-173726 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Methyltransferase small domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 341 amino acids
Theoretical weight: 37.4 KDa
Source organism: Micromonospora echinospora
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q2MG72 (Residues: 1-321; Coverage: 100%)
Gene name: genN
Sequence domains: Methyltransferase small domain

Ligands and Environments

3 bound ligands:
Ligand SAH 1 x SAH
Ligand 7QM 1 x 7QM
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: LNLS BEAMLINE W01B-MX2
Spacegroup: P212121
Unit cell:
a: 50.815Å b: 69.886Å c: 84.7Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.157 0.154 0.22
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 citation in other articles

Structure and dynamics of gold nanoparticles decorated with chitosan-gentamicin conjugates: ReaxFF molecular dynamics simulations to disclose drug delivery.
Monti et al. (2019)
3 more