› 7z5z

X-ray diffraction
1.49Å resolution

CRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMXVV NON-RIBOSOMAL AMINO ACID TRANSFERASE IN COMPLEX WITH A PEPTIDYL-XNA CONJUGATE

Released:
DOI: 10.2210/pdb7z5z/pdb
PDB entry 7z5z coloured by chain, front view.
PDB entry 7z5z coloured by chain, side view.
PDB entry 7z5z coloured by chain, top view.
Source organisms:
Primary publication:
Amino-acyl tXNA as inhibitors or amino acid donors in peptide synthesis.
Rietmeyer L, Li De La Sierra-Gallay I, Schepers G, Dorchêne D, Iannazzo L, Patin D, Touzé T, van Tilbeurgh H, Herdewijn P, Ethève-Quelquejeu M, Fonvielle M
OpenAccess logo Nucleic Acids Res (2022)
PMID: 36350642

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-512411 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA 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
UDP-MurNAc-pentapeptide Chain: C
Molecule details ›
Chain: C
Length: 5 amino acids
Theoretical weight: 464 Da
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*AP*CP*C)-R(P*(A9Z))-3') Chain: B
Molecule details ›
Chain: B
Length: 4 nucleotides
Theoretical weight: 1.25 KDa

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 A9Z 1 x A9Z
Ligand FGA 1 x FGA
Ligand DAL 2 x DAL

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 2
Spacegroup: P21
Unit cell:
a: 42.19Å b: 101.49Å c: 46.26Å
α: 90° β: 102.51° γ: 90°
R-values:
R R work R free
0.196 0.195 0.224
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Synthesis of Peptidyl-tRNA Mimics for Structural Biology Applications.
Polikanov et al. (2023)

1 mention without citation

Amino-acyl tXNA as inhibitors or amino acid donors in peptide synthesis.
Rietmeyer et al. (2022)