› 4u0m

X-ray diffraction
2.3Å resolution

Structure of the Vibrio cholerae di-nucleotide cyclase (DncV) mutant D193N in complex with ATP, GTP and 5MTHFGLU2

Released:
DOI: 10.2210/pdb4u0m/pdb
PDB entry 4u0m coloured by chain, front view.
PDB entry 4u0m coloured by chain, side view.
PDB entry 4u0m coloured by chain, top view.
Source organism: Vibrio cholerae O1 biovar El Tor str. N16961
Primary publication:
Structural biochemistry of a Vibrio cholerae dinucleotide cyclase reveals cyclase activity regulation by folates.
Zhu D, Wang L, Shang G, Liu X, Zhu J, Lu D, Wang L, Kan B, Zhang JR, Xiang Y
Mol Cell 55 931-937 (2014)
PMID: 25201413

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192139 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cyclic GMP-AMP synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 427 amino acids
Theoretical weight: 48.82 KDa
Source organism: Vibrio cholerae O1 biovar El Tor str. N16961
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9KVG7 (Residues: 1-419; Coverage: 96%)
Gene names: VC_0179, dncV
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand GTP 2 x GTP
Ligand ATP 2 x ATP
Ligand MG 2 x MG
Ligand TLL 1 x TLL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 69.898Å b: 59.86Å c: 104.185Å
α: 90° β: 95.55° γ: 90°
R-values:
R R work R free
0.202 0.199 0.253
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Cyclic GMP-AMP as an Endogenous Second Messenger in Innate Immune Signaling by Cytosolic DNA.
Kato et al. (2017)
13 more

1 mention without citation

The World of Cyclic Dinucleotides in Bacterial Behavior.
Aline Dias da et al. (2020)