1WM1

Crystal Structure of Prolyl Aminopeptidase, Complex with Pro-TBODA

Summary for 1WM1

• Entry DOI: 10.2210/pdb1wm1/pdb
• Related: 1QTR
• Descriptor: Proline iminopeptidase, (5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)[(2R)-PYRROLIDIN-2-YL]METHANONE (3 entities in total)
• Functional Keywords: proline iminopeptidase, complex with inhibitor, hydrolase
• Biological source: Serratia marcescens
• Cellular location: Cytoplasm: O32449
• Total number of polymer chains: 1
• Total formula weight: 36353.87

Authors

Nakajima, Y.,Inoue, T.,Ito, K.,Tozaka, T.,Hatakeyama, S.,Tanaka, N.,Nakamura, K.T.,Yoshimoto, T. (deposition date: 2004-07-01, release date: 2004-07-20, Last modification date: 2024-03-13)

Primary citation

Inoue, T.,Ito, K.,Tozaka, T.,Hatakeyama, S.,Tanaka, N.,Nakamura, K.T.,Yoshimoto, T.
Novel inhibitor for prolyl aminopeptidase from Serratia marcescens and studies on the mechanism of substrate recognition of the enzyme using the inhibitor
ARCH.BIOCHEM.BIOPHYS., 416:147-154, 2003

PubMed Abstract: Prolyl aminopeptidase from Serratia marcescens hydrolyzed x-beta-naphthylamides (x=prolyl, alanyl, sarcosinyl, L-alpha-aminobutylyl, and norvalyl), which suggested that the enzyme has a pocket for a five-member ring. Based on the substrate specificity, novel inhibitors of Pro, Ala, and Sar having 2-tert-butyl-[1,3,4]oxadiazole (TBODA) were synthesized. The K(i) value of Pro-TBODA, Ala-TBODA, and Sar-TBODA was 0.5 microM, 1.6 microM, and 12mM, respectively. The crystal structure of enzyme-Pro-TBODA complex was determined. Pro-TBODA was located at the active site. Four electrostatic interactions were located between the enzyme and the amino group of Pro inhibitors (Glu204:0E1-N:Inh, Glu204:0E2-N:Inh, Glu232:0E1-N:Inh, and Gly46:O-N:Inh), and the residue of the inhibitors was inserted into the hydrophobic pocket composed of Phe139, Leu141, Leu146, Tyr149, Tyr150, and Phe236. The roles of Phe139, Tyr149, and Phe236 in the hydrophobic pocket and Glu204 and Glu232 in the electrostatic interactions were confirmed by site-directed mutagenesis, which indicated that the molecular recognition of proline is achieved through four electrostatic interactions and an insertion in the hydrophobic pocket of the enzyme.

PubMed: 12893291
DOI: 10.1016/S0003-9861(03)00293-5

Experimental method

X-RAY DIFFRACTION (2.1 Å)