› 4q3d

X-ray diffraction
2.2Å resolution

PylD cocrystallized with L-Ornithine-Nd-D-ornithine and NAD+

Released:
DOI: 10.2210/pdb4q3d/pdb
PDB entry 4q3d coloured by chain, front view.
PDB entry 4q3d coloured by chain, side view.
PDB entry 4q3d 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

7 bound ligands:
Ligand NAD 4 x NAD
Ligand NA 4 x NA
Ligand MG 4 x MG
Ligand 2YH 4 x 2YH
Ligand PEG 2 x PEG
Ligand GOL 2 x GOL
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21212
Unit cell:
a: 86.93Å b: 259.32Å c: 48.82Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.177 0.237
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

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