› 2w27

X-ray diffraction
2.8Å resolution

CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS YKUI PROTEIN, WITH AN EAL DOMAIN, IN COMPLEX WITH SUBSTRATE C-DI-GMP AND CALCIUM

Released:
DOI: 10.2210/pdb2w27/pdb
PDB entry 2w27 coloured by chain, front view.
PDB entry 2w27 coloured by chain, side view.
PDB entry 2w27 coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Crystal structures of YkuI and its complex with second messenger cyclic Di-GMP suggest catalytic mechanism of phosphodiester bond cleavage by EAL domains.
Minasov G, Padavattan S, Shuvalova L, Brunzelle JS, Miller DJ, Baslé A, Massa C, Collart FR, Schirmer T, Anderson WF
J Biol Chem 284 13174-84 (2009)
PMID: 19244251

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128644 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Uncharacterized EAL-domain containing protein YkuI Chains: A, B
Molecule details ›
Chains: A, B
Length: 431 amino acids
Theoretical weight: 50.75 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O35014 (Residues: 1-407; Coverage: 100%)
Gene names: BSU14090, ykuI
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand 5GP 4 x 5GP
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 46.167Å b: 124.521Å c: 168.751Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.226 0.275
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 review citations

Structural and mechanistic determinants of c-di-GMP signalling.
Schirmer et al. (2009)
7 more

10 mentions without citation

Cyclic di-GMP: the first 25 years of a universal bacterial second messenger.
Römling et al. (2013)
9 more