› 8br1

X-ray diffraction
2.04Å resolution

ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, bound to Latrunculin-B-ATP-Mg-actin, and 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE and 2 Mg ions

Released:
DOI: 10.2210/pdb8br1/pdb
PDB entry 8br1 coloured by chain, front view.
PDB entry 8br1 coloured by chain, side view.
PDB entry 8br1 coloured by chain, top view.
Source organisms:
Primary publication:
Functional and structural insights into the multi-step activation and catalytic mechanism of bacterial ExoY nucleotidyl cyclase toxins bound to actin-profilin.
Teixeira-Nunes M, Retailleau P, Raoux-Barbot D, Comisso M, Missinou AA, Velours C, Plancqueel S, Ladant D, Mechold U, Renault L
OpenAccess logo PLoS Pathog 19 e1011654 (2023)
PMID: 37747912

Function and Biology Details

Reaction catalysed: 
ATP = 3',5'-cyclic AMP + diphosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-269704 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Actin, alpha skeletal muscle Chains: A, C
Molecule details ›
Chains: A, C
Length: 375 amino acids
Theoretical weight: 41.86 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: P68135 (Residues: 3-377; Coverage: 100%)
Gene names: ACTA, ACTA1
Sequence domains: Actin
Peptidase C80 domain-containing protein Chains: B, D
Molecule details ›
Chains: B, D
Length: 413 amino acids
Theoretical weight: 46.25 KDa
Source organism: Vibrio nigripulchritudo
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A9P1NJI6 (Residues: 3455-3863; Coverage: 8%)
Gene name: VIBNI_0210
Sequence domains: Anthrax toxin LF subunit

Ligands and Environments

7 bound ligands:
Ligand LAB 2 x LAB
Ligand ATP 2 x ATP
Ligand MG 6 x MG
Ligand 3AT 2 x 3AT
Ligand SO4 2 x SO4
Ligand GOL 1 x GOL
Ligand PEO 1 x PEO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P21
Unit cell:
a: 76.116Å b: 132.443Å c: 96.396Å
α: 90° β: 110.57° γ: 90°
R-values:
R R work R free
0.192 0.19 0.222
Expression system: Escherichia coli

Quick links

Citations

1 mention without citation

Functional and structural insights into the multi-step activation and catalytic mechanism of bacterial ExoY nucleotidyl cyclase toxins bound to actin-profilin.
Teixeira Nunes et al. (2023)