› 4q6g

X-ray diffraction
2.25Å resolution

Crystal Structure of the C-terminal domain of AcKRS-1 bound with N-acetyl-lysine and ADPNP

Released:
DOI: 10.2210/pdb4q6g/pdb
PDB entry 4q6g coloured by chain, front view.
PDB entry 4q6g coloured by chain, side view.
PDB entry 4q6g coloured by chain, top view.
Source organism: Methanosarcina mazei Go1
Primary publication:
Polyspecific pyrrolysyl-tRNA synthetases from directed evolution.
Guo LT, Wang YS, Nakamura A, Eiler D, Kavran JM, Wong M, Kiessling LL, Steitz TA, O'Donoghue P, Söll D
Proc Natl Acad Sci U S A 111 16724-9 (2014)
PMID: 25385624

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185815 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyrrolysine--tRNA ligase Chain: A
Molecule details ›
Chain: A
Length: 267 amino acids
Theoretical weight: 30.81 KDa
Source organism: Methanosarcina mazei Go1
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)
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ANP 1 x ANP
Ligand EDO 6 x EDO
Ligand ALY 1 x ALY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P64
Unit cell:
a: 105.031Å b: 105.031Å c: 70.731Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.187 0.186 0.214
Expression system: Escherichia coli

Quick links

Citations

20 review citations

Playing with the Molecules of Life.
Young et al. (2018)
19 more

5 mentions without citation

Polyspecific pyrrolysyl-tRNA synthetases from directed evolution.
Guo et al. (2014)
4 more