› 3s7t

X-ray diffraction
2.81Å resolution

Crystal structure of SeMet B. licheniformis CDPS YvmC-Blic

Released:
DOI: 10.2210/pdb3s7t/pdb
PDB entry 3s7t coloured by chain, front view.
PDB entry 3s7t coloured by chain, side view.
PDB entry 3s7t coloured by chain, top view.
Source organism: Bacillus licheniformis DSM 13 = ATCC 14580
Primary publication:
Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog.
Bonnefond L, Arai T, Sakaguchi Y, Suzuki T, Ishitani R, Nureki O
Proc Natl Acad Sci U S A 108 3912-7 (2011)
PMID: 21325056

Function and Biology Details

Reaction catalysed: 
2 L-leucyl-tRNA(Leu) = 2 tRNA(Leu) + cyclo(L-leucyl-L-leucyl)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179203 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cyclo(L-leucyl-L-leucyl) synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 257 amino acids
Theoretical weight: 30.08 KDa
Source organism: Bacillus licheniformis DSM 13 = ATCC 14580
Expression system: Escherichia coli
UniProt:
  • Canonical: Q65EX3 (Residues: 1-249; Coverage: 100%)
Gene names: BL00817, BLi03566, yvmC
Sequence domains: Cyclodipeptide synthase
Structure domains: Cyclodipeptide synthase

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 18 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: C2
Unit cell:
a: 150.172Å b: 54.713Å c: 101.556Å
α: 90° β: 130.05° γ: 90°
R-values:
R R work R free
0.187 0.182 0.232
Expression system: Escherichia coli

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Citations

13 review citations

The nonribosomal synthesis of diketopiperazines in tRNA-dependent cyclodipeptide synthase pathways.
Belin et al. (2012)
12 more