PDBsum entry 1tk3

Hydrolase

PDB id: 1tk3

Contents

Protein chain

726 a.a. *

Ligands

NAG-NAG-FUC ×3

NAG-NAG ×4

NAG-NDG-MAN

NAG-NAG-BMA ×2

NAG-NDG

NAG ×3

Waters ×1211

* Residue conservation analysis

PDB id:

1tk3

Name:

Hydrolase

Title:

Crystal structure of human apo dipeptidyl peptidase iv/cd26

Structure:

Dipeptidyl peptidase iv. Chain: a, b. Fragment: extracellular domain. Synonym: dpp iv, t-cell activation antigen cd26, tp103, adenosine deaminase complexing protein-2, adabp. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: dpp4, adcp2, cd26. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: high5.

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.229 R-free: 0.272

Authors:

J.R.Bjelke,J.Christensen,S.Branner,N.Wagtmann,C.Olsen,A.B.Kanstrup, H.B.Rasmussen

Key ref:

J.R.Bjelke et al. (2004). Tyrosine 547 constitutes an essential part of the catalytic mechanism of dipeptidyl peptidase IV. J Biol Chem, 279, 34691-34697. PubMed id: 15175333 DOI: 10.1074/jbc.M405400200

Date:

08-Jun-04 Release date: 06-Jul-04

Protein chains

P27487  (DPP4_HUMAN) -  Dipeptidyl peptidase 4 from Homo sapiens

Seq: 766 a.a.

Struc: 726 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.

DOI no: 10.1074/jbc.M405400200

J Biol Chem 279:34691-34697 (2004)

PubMed id: 15175333

Tyrosine 547 constitutes an essential part of the catalytic mechanism of dipeptidyl peptidase IV.

J.R.Bjelke, J.Christensen, S.Branner, N.Wagtmann, C.Olsen, A.B.Kanstrup, H.B.Rasmussen.

ABSTRACT

Human dipeptidyl peptidase IV (DPP-IV) is a ubiquitously expressed type II transmembrane serine protease. It cleaves the penultimate positioned prolyl bonds at the N terminus of physiologically important peptides such as the incretin hormones glucagon-like peptide 1 and glucose-dependent insulinotropic peptide. In this study, we have characterized different active site mutants. The Y547F mutant as well as the catalytic triad mutants S630A, D708A, and H740L showed less than 1% wild type activity. X-ray crystal structure analysis of the Y547F mutant revealed no overall changes compared with wild type apoDPP-IV, except the ablation of the hydroxyl group of Tyr(547) and a water molecule positioned in close proximity to Tyr(547). To elucidate further the reaction mechanism, we determined the crystal structure of DPP-IV in complex with diisopropyl fluorophosphate, mimicking the tetrahedral intermediate. The kinetic and structural findings of the tyrosine residue are discussed in relation to the catalytic mechanism of DPP-IV and to the inhibitory mechanism of the 2-cyanopyrrolidine class of potent DPP-IV inhibitors, proposing an explanation for the specificity of this class of inhibitors for the S9b family among serine proteases.

Selected figure(s)

Figure 1.
FIG. 1. The structure of one monomer of DPP-IV in complex with ValPyr and close-up of the active site. The -propeller and the / hydrolase domains are shown in purple and brown, respectively. Residues in close proximity of the ValPyr inhibitor are shown with interatomic distances. See text for details.

Figure 4.
FIG. 4. Close-up of active site residues. The initial F[o] - F[c] electron density maps are overlaid the apoDPP-IV (A), Y547F mutant (B), and complex DFP·DPP-IV (C, slightly different view, relative to A and B) contoured at 2 (cyan), 3 (red), 5 (purple, only contoured in the apo structure), and 8 (blue, only contoured in the DFP structure). The initial 2F[o] - F[c] electron density map is overlaid the complex DFP·DPP-IV contoured at 1 (gray). Structural inspections of the active site of the Y547F mutant reveals a missing water molecule, clearly seen in the wild type apo structure (i.e. hydrogen bonds between Tyr547-OH, Ser630-OH, and Tyr631-NH are indicated). The mutated residue (Phe^547) is positioned exactly as the tyrosine residue. The water molecule designated Wat258 and Wat421 in the apo and the Y547F mutant structure, respectively, is moved 0.5 Å away from the 547 residue and 0.3 Å (2.9 versus 3.2 Å) closer to the neighboring Tyr666-OH (not shown) in the mutant structure. The complex between DFP and DPP-IV showed that the organophosphorous inhibitor was covalently bound to Ser630, mimicking the tetrahedral intermediate.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 34691-34697) copyright 2004.

Figures were selected by an automated process.