› 2bas

X-ray diffraction
2.61Å resolution

Crystal Structure of the Bacillus subtilis YkuI Protein, with an EAL Domain.

Released:
DOI: 10.2210/pdb2bas/pdb
PDB entry 2bas coloured by chain, front view.
PDB entry 2bas coloured by chain, side view.
PDB entry 2bas 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 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: 51.27 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

1 bound ligand:
Ligand BME 1 x BME
1 modified residue:
Ligand MSE 22 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P212121
Unit cell:
a: 46.335Å b: 125.271Å c: 167.962Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.203 0.287
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

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

8 mentions without citation

Sensing the messenger: the diverse ways that bacteria signal through c-di-GMP.
Krasteva et al. (2012)
7 more