› 4ffo

X-ray diffraction
2Å resolution

PylC in complex with phosphorylated D-ornithine

Released:
DOI: 10.2210/pdb4ffo/pdb
PDB entry 4ffo coloured by chain, front view.
PDB entry 4ffo coloured by chain, side view.
PDB entry 4ffo 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 0TK 1 x 0TK
Ligand ADP 1 x ADP
Ligand MG 2 x MG
Ligand ATP 1 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P43212
Unit cell:
a: 61.43Å b: 61.43Å c: 172.02Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.162 0.16 0.2
Expression system: Escherichia coli

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Citations

5 review citations

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