› 3n5i

X-ray diffraction
1.8Å resolution

Crystal structure of the precursor (S250A mutant) of the N-terminal beta-aminopeptidase BapA

Released:
DOI: 10.2210/pdb3n5i/pdb
PDB entry 3n5i coloured by chain, front view.
PDB entry 3n5i coloured by chain, side view.
PDB entry 3n5i coloured by chain, top view.
Source organism: Sphingosinicella xenopeptidilytica
Primary publication:
Autoproteolytic and catalytic mechanisms for the β-aminopeptidase BapA--a member of the Ntn hydrolase family.
Merz T, Heck T, Geueke B, Mittl PR, Briand C, Seebach D, Kohler HP, Grütter MG
Structure 20 1850-60 (2012)
PMID: 22980995

Function and Biology Details

Reaction catalysed: 
Cleaves N-terminal beta-homoamino acids from peptides composed of 2 to 6 amino acids
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176035 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-peptidyl aminopeptidase BapA Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 373 amino acids
Theoretical weight: 38.62 KDa
Source organism: Sphingosinicella xenopeptidilytica
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q52VH2 (Residues: 30-402; Coverage: 100%)
Gene name: bapA
Sequence domains: Peptidase family S58
Structure domains: L-amino peptidase D-ALA esterase/amidase

Ligands and Environments

2 bound ligands:
Ligand GOL 4 x GOL
Ligand SO4 5 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 99.7Å b: 113.7Å c: 126Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.155 0.154 0.18
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Visible-Light Microscopic Discovery of Up to 150 μm Long Helical Amyloid Fibrils Built of the Dodecapeptide H-(Val-Ala-Leu)4 -OH and of Decapeptides Derived from Insulin.
Świontek et al. (2016)
1 more

1 mention without citation

Preparation and Characterization of an Ancient Aminopeptidase Obtained from Ancestral Sequence Reconstruction for L-Carnosine Synthesis.
Liu et al. (2022)