Summary
PDB 2DQ6 deposited: 2006-05-22 modified: 2009-02-24
Title Crystal Structure of Aminopeptidase N from Escherichia coli
Authors Ito, K., Ito, T., Matsubara, F., Nakajima, Y., Nakashima, K., Onohara, Y., Takeo, M., Yoshimoto, T.
Method X-RAY DIFFRACTION
Structure factors resolution 1.5 rfactor 0.181 rfree 0.191
DPI 0.18 theoretical min: 0.07
Related PDB Entries 2DQM
Citations

Aminopeptidase N from Escherichia coli is a broad specificity zinc exopeptidase belonging to aminopeptidase clan MA, family M1. The structures of the ligand-free form and the enzyme-bestatin complex were determined at 1.5- and 1.6-A resolution, respectively. The enzyme is composed of four domains: an N-terminal beta-domain (Met(1)-Asp(193)), a catalytic domain (Phe(194)-Gly(444)), a middle beta-domain (Thr(445)-Trp(546)), and a C-terminal alpha-domain (Ser(547)-Ala(870)). The structure of the catalytic domain exhibits similarity to thermolysin, and a metal-binding motif (HEXXHX(18)E) is found in the domain. The zinc ion is coordinated by His(297), His(301), Glu(320), and a water molecule. The groove on the catalytic domain that contains the active site is covered by the C-terminal alpha-domain, and a large cavity is formed inside the protein. However, there exists a small hole at the center of the C-terminal alpha-domain. The N terminus of bestatin is recognized by Glu(121) and Glu(264), which are located in the N-terminal and catalytic domains, respectively. Glu(298) and Tyr(381), located near the zinc ion, are considered to be involved in peptide cleavage. A difference revealed between the ligand-free form and the enzyme-bestatin complex indicated that Met(260) functions as a cushion to accept substrates with different N-terminal residue sizes, resulting in the broad substrate specificity of this enzyme.

J.Biol.Chem. 2006 Nov; 281(44):33664-33676 doi:10.1074/jbc.M605203200

Cross References
Database source Identifier Description
PubMed 16885166 JBCHA3
Biomolecule Structure Assembly Serial Assembly Type Conformational State Chains Ligands Atoms
2DQ6/0 2DQ6 0 monomer 0 1 2 7118