› 4ffp

X-ray diffraction
2Å resolution

PylC in complex with L-lysine-Ne-D-ornithine (cocrystallized with L-lysine and D-ornithine)

Released:
DOI: 10.2210/pdb4ffp/pdb
PDB entry 4ffp coloured by chain, front view.
PDB entry 4ffp coloured by chain, side view.
PDB entry 4ffp coloured by chain, top view.
Source organism: Methanosarcina barkeri str. Fusaro
Primary publication:
Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5Å resolution.
Quitterer F, List A, Beck P, Bacher A, Groll M
J Mol Biol 424 270-82 (2012)
PMID: 22985965

Function and Biology Details

Reaction catalysed: 
ATP + (3R)-3-methyl-D-ornithine + L-lysine = ADP + phosphate + N(6)-((3R)-3-methyl-D-ornithinyl)-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175175 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-methyl-D-ornithine--L-lysine ligase Chain: A
Molecule details ›
Chain: A
Length: 363 amino acids
Theoretical weight: 40.86 KDa
Source organism: Methanosarcina barkeri str. Fusaro
Expression system: Escherichia coli
UniProt:
  • Canonical: Q46E79 (Residues: 1-363; Coverage: 100%)
Gene names: Mbar_A0837, pylC
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand 0TF 1 x 0TF
Ligand ADP 2 x ADP
Ligand PO4 1 x PO4
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P43212
Unit cell:
a: 61.26Å b: 61.26Å c: 172.08Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.154 0.151 0.181
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Radical S-adenosylmethionine enzymes.
Broderick et al. (2014)
4 more

1 mention without citation

Improved pyrrolysine biosynthesis through phage assisted non-continuous directed evolution of the complete pathway.
Ho et al. (2021)