› 3tfh

X-ray diffraction
2.1Å resolution

DMSP-dependent demethylase from P. ubique - apo

Released:
DOI: 10.2210/pdb3tfh/pdb
PDB entry 3tfh coloured by chain, front view.
PDB entry 3tfh coloured by chain, side view.
PDB entry 3tfh coloured by chain, top view.
Source organism: Candidatus Pelagibacter ubique HTCC1062
Primary publication:
Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelagabacter ubique.
Schuller DJ, Reisch CR, Moran MA, Whitman WB, Lanzilotta WN
Protein Sci 21 289-98 (2012)
PMID: 22162093

Function and Biology Details

Reaction catalysed: 
S,S-dimethyl-beta-propiothetin + tetrahydrofolate = 3-(methylthio)propanoate + 5-methyltetrahydrofolate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175510 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dimethylsulfonioproprionate demethylase DmdA Chains: A, B
Molecule details ›
Chains: A, B
Length: 369 amino acids
Theoretical weight: 41.89 KDa
Source organism: Candidatus Pelagibacter ubique HTCC1062
Expression system: Escherichia coli
UniProt:
  • Canonical: Q4FP21 (Residues: 1-369; Coverage: 100%)
Gene names: SAR11_0246, dmdA
Sequence domains:
Structure domains: Probable tRNA modification gtpase trme; domain 1

Ligands and Environments

2 bound ligands:
Ligand GOL 2 x GOL
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 53.656Å b: 121.727Å c: 59.648Å
α: 90° β: 101.01° γ: 90°
R-values:
R R work R free
0.168 0.166 0.231
Expression system: Escherichia coli

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Citations

3 review citations

Sarcosine as a potential prostate cancer biomarker--a review.
Cernei et al. (2013)
2 more

2 mentions without citation

Functional annotation of orthologs in metagenomes: a case study of genes for the transformation of oceanic dimethylsulfoniopropionate.
González et al. (2019)
1 more