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.
Structure factors resolution 1.5 rfactor 0.181 rfree 0.191
DPI 0.18 theoretical min: 0.07
Related PDB Entries 2DQM

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