› 5wdl

X-ray diffraction
2.62Å resolution

A processive dipeptidyl aminopeptidase secreted from an established commensal bacterium P. distasonis

Released:
DOI: 10.2210/pdb5wdl/pdb
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PDB entry 5wdl coloured by chain, front view.
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Source organism: Parabacteroides distasonis ATCC 8503
Primary publication:
A Commensal Dipeptidyl Aminopeptidase with Specificity for N-Terminal Glycine Degrades Human-Produced Antimicrobial Peptides in Vitro.
Xu JH, Jiang Z, Solania A, Chatterjee S, Suzuki B, Lietz CB, Hook VYH, O'Donoghue AJ, Wolan DW
ACS Chem Biol 13 2513-2521 (2018)
PMID: 30085657

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107944 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Aminopeptidase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 401 amino acids
Theoretical weight: 45.9 KDa
Source organism: Parabacteroides distasonis ATCC 8503
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: A6LE66 (Residues: 23-405; Coverage: 100%)
Gene name: BDI_2249
Sequence domains: Peptidase C1-like family
Structure domains: Cysteine proteinases

Ligands and Environments

2 bound ligands:
Ligand R33 6 x R33
Ligand K 12 x K
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P212121
Unit cell:
a: 104.841Å b: 140.299Å c: 221.087Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.171 0.212
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

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Citations

2 review citations

Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health.
Ezeji et al. (2021)
1 more

1 mention without citation

A Commensal Dipeptidyl Aminopeptidase with Specificity for N-Terminal Glycine Degrades Human-Produced Antimicrobial Peptides in Vitro.
Xu et al. (2018)

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