› 2dcm

X-ray diffraction
2.9Å resolution

The Crystal Structure of S603A Mutated Prolyl Tripeptidyl Aminopeptidase Complexed with Substrate

Released:
DOI: 10.2210/pdb2dcm/pdb
PDB entry 2dcm coloured by chain, front view.
PDB entry 2dcm coloured by chain, side view.
PDB entry 2dcm coloured by chain, top view.
Source organism: Porphyromonas gingivalis W83
Primary publication:
Crystal structure and mechanism of tripeptidyl activity of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis.
Ito K, Nakajima Y, Xu Y, Yamada N, Onohara Y, Ito T, Matsubara F, Kabashima T, Nakayama K, Yoshimoto T
J Mol Biol 362 228-40 (2006)
PMID: 16914159

Function and Biology Details

Reaction catalysed: 
Hydrolysis of Xaa-Xaa-Pro-|-Yaa- releasing the N-terminal tripeptide of a peptide with Pro as the third residue (position P1) and where Yaa is not proline
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181748 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Prolyl tripeptidyl peptidase Chain: A
Molecule details ›
Chain: A
Length: 706 amino acids
Theoretical weight: 79.59 KDa
Source organism: Porphyromonas gingivalis W83
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7MUW6 (Residues: 39-732; Coverage: 98%)
Gene names: PG_1361, ptpA
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand GA0 1 x GA0
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P6322
Unit cell:
a: 149.453Å b: 149.453Å c: 159.644Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.206 0.206 0.263
Expression system: Escherichia coli

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Citations

3 review citations

Exopeptidases and gingipains in Porphyromonas gingivalis as prerequisites for its amino acid metabolism.
Nemoto et al. (2016)
2 more

6 mentions without citation

The expanding diversity of serine hydrolases.
Botos et al. (2007)
5 more