2HPO image
Deposition Date 2006-07-17
Release Date 2006-08-15
Last Version Date 2024-02-14
Entry Detail
PDB ID:
2HPO
Keywords:
Title:
Structure of Aminopeptidase N from E. coli Suggests a Compartmentalized, Gated Active Site
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.65 Å
R-Value Free:
0.18
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 31 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Aminopeptidase N
Gene (Uniprot):pepN
Chain IDs:A
Chain Length:891
Number of Molecules:1
Biological Source:Escherichia coli K12
Primary Citation
Structure of aminopeptidase N from Escherichia coli suggests a compartmentalized, gated active site.
Proc.Natl.Acad.Sci.Usa 103 13339 13344 (2006)
PMID: 16938892 DOI: 10.1073/pnas.0606167103

Abstact

Aminopeptidase N from Escherichia coli is a major metalloprotease that participates in the controlled hydrolysis of peptides in the proteolytic pathway. Determination of the 870-aa structure reveals that it has four domains similar to the tricorn-interacting factor F3. The thermolysin-like active site is enclosed within a large cavity with a volume of 2,200 A(3), which is inaccessible to substrates except for a small opening of approximately 8-10 A. The substrate-based inhibitor bestatin binds to the protein with minimal changes, suggesting that this is the active form of the enzyme. The previously described structure of F3 had three distinct conformations that were described as "closed," "intermediate," and "open." The structure of aminopeptidase N from E. coli, however, is substantially more closed than any of these. Taken together, the results suggest that these proteases, which are involved in intracellular peptide degradation, prevent inadvertent hydrolysis of inappropriate substrates by enclosing the active site within a large cavity. There is also some evidence that the open form of the enzyme, which admits substrates, remains inactive until it adopts the closed form.

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