› 7rsm

X-ray diffraction
2.15Å resolution

Crystal structure of pyrrolysyl-tRNA synthetase (N346D/C348S/Y384F) in complex with o-Chlorophenylalanine and AMP-PNP

Released:
DOI: 10.2210/pdb7rsm/pdb
PDB entry 7rsm coloured by chain, front view.
PDB entry 7rsm coloured by chain, side view.
PDB entry 7rsm coloured by chain, top view.
Source organism: Methanosarcina mazei
Primary publication:
A Designed, Highly Efficient Pyrrolysyl-tRNA Synthetase Mutant Binds o-Chlorophenylalanine Using Two Halogen Bonds.
Vatansever EC, Yang KS, Geng ZZ, Qiao Y, Li P, Xu S, Liu WR
J Mol Biol 434 167534 (2022)
PMID: 35278475

Function and Biology Details

Reaction catalysed: 
ATP + L-pyrrolysine + tRNA(Pyl) = AMP + diphosphate + L-pyrrolysyl-tRNA(Pyl)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185817 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyrrolysine--tRNA ligase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 267 amino acids
Theoretical weight: 30.85 KDa
Source organism: Methanosarcina mazei
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8PWY1 (Residues: 188-454; Coverage: 59%)
Gene names: MM_1445, pylS
Sequence domains: tRNA synthetases class II core domain (F)

Ligands and Environments

2 bound ligands:
Ligand ANP 4 x ANP
Ligand 2L5 4 x 2L5
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P21
Unit cell:
a: 66.7Å b: 135.2Å c: 72.24Å
α: 90° β: 112.54° γ: 90°
R-values:
R R work R free
0.25 0.247 0.309
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Engineering of enzymes using non-natural amino acids.
Li et al. (2022)
1 more

1 mention without citation

A Designed, Highly Efficient Pyrrolysyl-tRNA Synthetase Mutant Binds o-Chlorophenylalanine Using Two Halogen Bonds.
Vatansever et al. (2022)