› 4ii9

X-ray diffraction
1.66Å resolution

Crystal structure of Weissella viridescens FemXVv non-ribosomal amino acid transferase in complex with a peptidyl-RNA conjugate

Released:
DOI: 10.2210/pdb4ii9/pdb
PDB entry 4ii9 coloured by chain, front view.
PDB entry 4ii9 coloured by chain, side view.
PDB entry 4ii9 coloured by chain, top view.
Source organism: Weissella viridescens
Primary publication:
The structure of FemX(Wv) in complex with a peptidyl-RNA conjugate: mechanism of aminoacyl transfer from Ala-tRNA(Ala) to peptidoglycan precursors.
Fonvielle M, Li de La Sierra-Gallay I, El-Sagheer AH, Lecerf M, Patin D, Mellal D, Mayer C, Blanot D, Gale N, Brown T, van Tilbeurgh H, Ethève-Quelquejeu M, Arthur M
Angew Chem Int Ed Engl 52 7278-81 (2013)
PMID: 23744707

Function and Biology Details

Reaction catalysed: 
L-alanyl-tRNA(Ala) + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-L-lysyl-D-alanyl-D-alanine = tRNA(Ala) + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-N(6)-(L-alanyl)-L-lysyl-D-alanyl-D-alanine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-164575 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (3 distinct):
UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase Chain: A
Molecule details ›
Chain: A
Length: 343 amino acids
Theoretical weight: 39.21 KDa
Source organism: Weissella viridescens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9EY50 (Residues: 1-336; Coverage: 100%)
Gene name: femX
Sequence domains: FemAB family
Structure domains: Aminopeptidase
5-mer peptide Chain: B
Molecule details ›
Chain: B
Length: 5 amino acids
Theoretical weight: 464 Da
Source organism: Weissella viridescens
Expression system: Not provided
RNA (5'-R(P*CP*CP*(A9Z))-3') Chain: C
Molecule details ›
Chain: C
Length: 3 nucleotides
Theoretical weight: 974 Da
Source organism: Weissella viridescens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand GOL 1 x GOL
Ligand UDP 1 x UDP
Ligand MUB 1 x MUB
3 modified residues:
Ligand FGA 1 x FGA
Ligand DAL 2 x DAL
Ligand A9Z 1 x A9Z

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P21
Unit cell:
a: 42.13Å b: 101.77Å c: 46.32Å
α: 90° β: 102.6° γ: 90°
R-values:
R R work R free
0.178 0.175 0.209
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Bacterial GCN5-Related N-Acetyltransferases: From Resistance to Regulation.
Favrot et al. (2016)
6 more

7 mentions without citation

Structure and Functional Diversity of GCN5-Related N-Acetyltransferases (GNAT).
Salah Ud-Din et al. (2016)
6 more