4RE5 image
Entry Detail
PDB ID:
4RE5
Title:
Acylaminoacyl peptidase complexed with a chloromethylketone inhibitor
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2014-09-22
Release Date:
2015-01-28
Method Details:
Experimental Method:
Resolution:
1.90 Å
R-Value Free:
0.21
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Acylamino-acid-releasing enzyme
Chain IDs:A, B
Chain Length:582
Number of Molecules:2
Biological Source:Aeropyrum pernix
Peptide-like Molecules
PRD_001053
Primary Citation
Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality.
Acta Crystallogr.,Sect.D 71 461 472 (2015)
PMID: 25760596 DOI: 10.1107/S1399004714026819

Abstact

Acylaminoacyl peptidase (AAP) is an oligopeptidase that only cleaves short peptides or protein segments. In the case of AAP from Aeropyrum pernix (ApAAP), previous studies have led to a model in which the clamshell-like opening and closing of the enzyme provides the means of substrate-size selection. The closed form of the enzyme is catalytically active, while opening deactivates the catalytic triad. The crystallographic results presented here show that the open form of ApAAP is indeed functionally disabled. The obtained crystal structures also reveal that the closed form is penetrable to small ligands: inhibitor added to the pre-formed crystal was able to reach the active site of the rigidified protein, which is only possible through the narrow channel of the propeller domain. Molecular-dynamics simulations investigating the structure of the complexes formed with longer peptide substrates showed that their binding within the large crevice of the closed form of ApAAP leaves the enzyme structure unperturbed; however, their accessing the binding site seems more probable when assisted by opening of the enzyme. Thus, the open form of ApAAP corresponds to a scavenger of possible substrates, the actual cleavage of which only takes place if the enzyme is able to re-close.

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Primary Citation of related structures