› 4rzy

X-ray diffraction
1.95Å resolution

Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase RlDddP in complex with MES

Released:
DOI: 10.2210/pdb4rzy/pdb
PDB entry 4rzy coloured by chain, front view.
PDB entry 4rzy coloured by chain, side view.
PDB entry 4rzy coloured by chain, top view.
Source organism: Ruegeria lacuscaerulensis ITI-1157
Primary publication:
Structural and molecular basis for the novel catalytic mechanism and evolution of DddP, an abundant peptidase-like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold.
Wang P, Chen XL, Li CY, Gao X, Zhu DY, Xie BB, Qin QL, Zhang XY, Su HN, Zhou BC, Xun LY, Zhang YZ
Mol Microbiol 98 289-301 (2015)
PMID: 26154071

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-165182 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidase M24 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 447 amino acids
Theoretical weight: 50.46 KDa
Source organism: Ruegeria lacuscaerulensis ITI-1157
Expression system: Escherichia coli
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand FE 8 x FE
Ligand MES 4 x MES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P32
Unit cell:
a: 175.301Å b: 175.301Å c: 109.689Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.164 0.163 0.188
Expression system: Escherichia coli

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Citations

1 review citation

Evolution of Dimethylsulfoniopropionate Metabolism in Marine Phytoplankton and Bacteria.
Bullock et al. (2017)
13 other articles