› 3dp9

X-ray diffraction
2.3Å resolution

Crystal structure of Vibrio cholerae 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with butylthio-DADMe-Immucillin A

Released:
DOI: 10.2210/pdb3dp9/pdb
PDB entry 3dp9 coloured by chain, front view.
PDB entry 3dp9 coloured by chain, side view.
PDB entry 3dp9 coloured by chain, top view.
Source organism: Vibrio cholerae
Primary publication:
Transition state analogs of 5'-methylthioadenosine nucleosidase disrupt quorum sensing.
Gutierrez JA, Crowder T, Rinaldo-Matthis A, Ho MC, Almo SC, Schramm VL
Nat Chem Biol 5 251-7 (2009)
PMID: 19270684

Function and Biology Details

Reaction catalysed: 
5'-deoxyadenosine + H(2)O = 5-deoxy-D-ribose + adenine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192006 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase Chains: A, C
Molecule details ›
Chains: A, C
Length: 231 amino acids
Theoretical weight: 24.55 KDa
Source organism: Vibrio cholerae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9KPI8 (Residues: 1-231; Coverage: 100%)
Gene names: VC_2379, mtnN
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

2 bound ligands:
Ligand BIG 2 x BIG
Ligand IOD 1 x IOD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21
Unit cell:
a: 67.738Å b: 54.332Å c: 69.786Å
α: 90° β: 115.35° γ: 90°
R-values:
R R work R free
0.203 0.2 0.264
Expression system: Escherichia coli

Quick links

Citations

32 review citations

Quorum sensing signal-response systems in Gram-negative bacteria.
Papenfort et al. (2016)
31 more

7 mentions without citation

Enzymatic Transition States and Drug Design.
Schramm VL. (2018)
6 more