PDBsum entry 2ecf

Hydrolase

PDB id: 2ecf

Contents

Protein chain

700 a.a. *

Waters ×66

* Residue conservation analysis

PDB id:

2ecf

Name:

Hydrolase

Title:

Crystal structure of dipeptidyl aminopeptidase iv from stenotrophomonas maltophilia

Structure:

Dipeptidyl peptidase iv. Chain: a. Synonym: dipeptidyl aminopeptidase iv. Engineered: yes

Source:

Stenotrophomonas maltophilia. Organism_taxid: 40324. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.80Å R-factor: 0.185 R-free: 0.240

Authors:

Y.Nakajima,K.Ito,T.Yoshimoto

Key ref:

Y.Nakajima et al. (2008). Dipeptidyl aminopeptidase IV from Stenotrophomonas maltophilia exhibits activity against a substrate containing a 4-hydroxyproline residue. J Bacteriol, 190, 7819-7829. PubMed id: 18820015

Date:

13-Feb-07 Release date: 26-Feb-08

Protein chain

P95782  (P95782_STEMA) -  Dipeptidyl peptidase IV from Stenotrophomonas maltophilia

Seq: 741 a.a.

Struc: 700 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.14.5 - dipeptidyl-peptidase Iv.
• Reaction: Release of an N-terminal dipeptide, Xaa-Xbb-|-Xcc, from a polypeptide, preferentially when Xbb is Pro, provided Xcc is neither Pro nor hydroxyproline.

J Bacteriol 190:7819-7829 (2008)

PubMed id: 18820015

Dipeptidyl aminopeptidase IV from Stenotrophomonas maltophilia exhibits activity against a substrate containing a 4-hydroxyproline residue.

Y.Nakajima, K.Ito, T.Toshima, T.Egawa, H.Zheng, H.Oyama, Y.F.Wu, E.Takahashi, K.Kyono, T.Yoshimoto.

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.