› 4q3a

X-ray diffraction
2.2Å resolution

PylD cocrystallized with L-Lysine-Ne-3S-methyl-L-ornithine and NAD+

Released:
DOI: 10.2210/pdb4q3a/pdb
PDB entry 4q3a coloured by chain, front view.
PDB entry 4q3a coloured by chain, side view.
PDB entry 4q3a coloured by chain, top view.
Source organism: Methanosarcina barkeri str. Fusaro
Primary publication:
The formation of pyrroline and tetrahydropyridine rings in amino acids catalyzed by pyrrolysine synthase (PylD).
Quitterer F, Beck P, Bacher A, Groll M
Angew Chem Int Ed Engl 53 8150-3 (2014)
PMID: 24916332

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-175176 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyrrolysine synthase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 260 amino acids
Theoretical weight: 27.96 KDa
Source organism: Methanosarcina barkeri str. Fusaro
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q46E80 (Residues: 5-263; Coverage: 99%)
Gene names: Mbar_A0835, pylD
Sequence domains: Pyrrolysine biosynthesis protein PylD, N-terminal domain
Structure domains:

Ligands and Environments

8 bound ligands:
Ligand NAI 4 x NAI
Ligand NA 4 x NA
Ligand MG 4 x MG
Ligand 2YC 4 x 2YC
Ligand GOL 14 x GOL
Ligand PEG 3 x PEG
Ligand EDO 13 x EDO
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21212
Unit cell:
a: 87.49Å b: 259.85Å c: 48.66Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.169 0.204
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Pyrrolysine Amber Stop-Codon Suppression: Development and Applications.
Brabham et al. (2017)