› 4re6

X-ray diffraction
2.55Å resolution

Acylaminoacyl peptidase complexed with a chloromethylketone inhibitor

Released:
DOI: 10.2210/pdb4re6/pdb
PDB entry 4re6 coloured by chain, front view.
PDB entry 4re6 coloured by chain, side view.
PDB entry 4re6 coloured by chain, top view.
Source organism: Aeropyrum pernix K1
Primary publication:
Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality.
Menyhárd DK, Orgován Z, Szeltner Z, Szamosi I, Harmat V
Acta Crystallogr D Biol Crystallogr 71 461-72 (2015)
PMID: 25760596

Function and Biology Details

Reaction catalysed: 
Cleavage of an N-acetyl or N-formyl amino acid from the N-terminus of a polypeptide.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-195456 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Acylamino-acid-releasing enzyme Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 582 amino acids
Theoretical weight: 63.11 KDa
Source organism: Aeropyrum pernix K1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9YBQ2 (Residues: 1-582; Coverage: 100%)
Gene name: APE_1547.1
Sequence domains: Prolyl oligopeptidase family
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand Y3A 2 x Y3A
Ligand CL 6 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P1
Unit cell:
a: 71.58Å b: 97.3Å c: 99.16Å
α: 105.15° β: 103.96° γ: 100.26°
R-values:
R R work R free
0.214 0.212 0.26
Expression system: Escherichia coli

Quick links

Citations

6 citation in other articles

The acid-base-nucleophile catalytic triad in ABH-fold enzymes is coordinated by a set of structural elements.
Denesyuk et al. (2020)
5 more