› 6icq

X-ray diffraction
1.9Å resolution

Pseudomonas putida CBB5 NdmA QL mutant with theobromine

Released:
DOI: 10.2210/pdb6icq/pdb
PDB entry 6icq coloured by chain, front view.
PDB entry 6icq coloured by chain, side view.
PDB entry 6icq coloured by chain, top view.
Source organism: Pseudomonas putida
Primary publication:
Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex.
Kim JH, Kim BH, Brooks S, Kang SY, Summers RM, Song HK
J Mol Biol 431 3647-3661 (2019)
PMID: 31412262

Function and Biology Details

Reaction catalysed: 
Caffeine + O(2) + NAD(P)H = theobromine + NAD(P)(+) + H(2)O + formaldehyde
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124960 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Methylxanthine N1-demethylase NdmA Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 369 amino acids
Theoretical weight: 42.36 KDa
Source organism: Pseudomonas putida
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: H9N289 (Residues: 1-351; Coverage: 100%)
Gene name: ndmA
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand FES 3 x FES
Ligand FE 3 x FE
Ligand 37T 3 x 37T
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 5C (4A)
Spacegroup: P3221
Unit cell:
a: 135.946Å b: 135.946Å c: 155.637Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.17 0.17 0.196
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Engineering Rieske oxygenase activity one piece at a time.
Brimberry et al. (2023)
1 more