2ECF

Crystal Structure of Dipeptidyl Aminopeptidase IV from Stenotrophomonas maltophilia

Summary for 2ECF

• Entry DOI: 10.2210/pdb2ecf/pdb
• Descriptor: Dipeptidyl peptidase IV (2 entities in total)
• Functional Keywords: prolyl oligopeptidase family, peptidase family s9, dipeptidyl peptidase iv, hydrolase
• Biological source: Stenotrophomonas maltophilia
• Total number of polymer chains: 1
• Total formula weight: 82180.33

Authors

Nakajima, Y.,Ito, K.,Yoshimoto, T. (deposition date: 2007-02-13, release date: 2008-02-26, Last modification date: 2024-11-20)

Primary citation

Nakajima, Y.,Ito, K.,Toshima, T.,Egawa, T.,Zheng, H.,Oyama, H.,Wu, Y.-F.,Takahashi, E.,Kyono, K.,Yoshimoto, T.
Dipeptidyl aminopeptidase IV from Stenotrophomonas maltophilia exhibits activity against a substrate containing a 4-hydroxyproline residue
J.Bacteriol., 190:7819-7829, 2008

PubMed Abstract: The crystal structure of dipeptidyl aminopeptidase IV from Stenotrophomonas maltophilia was determined at 2.8-A resolution by the multiple isomorphous replacement method, using platinum and selenomethionine derivatives. The crystals belong to space group P4(3)2(1)2, with unit cell parameters a = b = 105.9 A and c = 161.9 A. Dipeptidyl aminopeptidase IV is a homodimer, and the subunit structure is composed of two domains, namely, N-terminal beta-propeller and C-terminal catalytic domains. At the active site, a hydrophobic pocket to accommodate a proline residue of the substrate is conserved as well as those of mammalian enzymes. Stenotrophomonas dipeptidyl aminopeptidase IV exhibited activity toward a substrate containing a 4-hydroxyproline residue at the second position from the N terminus. In the Stenotrophomonas enzyme, one of the residues composing the hydrophobic pocket at the active site is changed to Asn611 from the corresponding residue of Tyr631 in the porcine enzyme, which showed very low activity against the substrate containing 4-hydroxyproline. The N611Y mutant enzyme was generated by site-directed mutagenesis. The activity of this mutant enzyme toward a substrate containing 4-hydroxyproline decreased to 30.6% of that of the wild-type enzyme. Accordingly, it was considered that Asn611 would be one of the major factors involved in the recognition of substrates containing 4-hydroxyproline.

PubMed: 18820015
DOI: 10.1128/JB.02010-07

Experimental method

X-RAY DIFFRACTION (2.8 Å)