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(2006). Crystal structure and mechanism of tripeptidyl activity of prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis. J Mol Biol. 362, 228240.  Umezawa, Y., Yokoyama, K., Kikuchi, Y., Date, M., Ito, K., Yoshimoto, T., Matsui, H. (2004). Novel prolyl tri/tetra-peptidyl aminopeptidase from Streptomyces mobaraensis: substrate specificity and enzyme gene cloning. J. Biochem. 136, 293300.
 Fujimura, S., Ueda, O., Shibata, Y., Hirai, K. (2003). Isolation and properties of a tripeptidyl peptidase from a periodontal pathogen Prevotella nigrescens. FEMS Microbiol Lett. 219, 305309.  Xu, Y., Nakajima, Y., Ito, K., Zheng, H., Oyama, H., Heiser, U., Hoffmann, T., Gartner, U-G., Demuth, H.-U., Yoshimoto, T. (2008). Novel inhibitor for prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis and details of substrate-recognition mechanism. J. Mol. Biol. 375, 708719.
Yoshitaka Nakajima Department of Lifescience, Setsunani University Faculty of Science and Technology, Neyagawa, 572-8508, Japan. Email: [email protected]
Kiyoshi Ito Department of Biotechnology, Nagasaki University School of Pharmaceutical Sciences, Nagasaki, 8528521, Japan. Email: [email protected]
Tadashi Yoshimoto Department of Lifescience, Setsunani University Faculty of Science and Technology, Neyagawa, 572-8508, Japan. Email: [email protected]
© 2013 Elsevier Ltd. All rights reserved. DOI: http://dx.doi.org/10.1016/B978-0-12-382219-2.00744-4
Handbook of Proteolytic Enzymes, 3rd Edn ISBN: 978-0-12-382219-2
Dipeptidyl-peptidase IV DATABANKS MEROPS name: dipeptidyl-peptidase IV (eukaryote) MEROPS classification: clan SC, family S9, subfamily S9B, peptidase S09.003 IUBMB: EC 18.104.22.168 (BRENDA) Tertiary structure: Available Species distribution: subphylum Vertebrata Reference sequence from: Homo sapiens (UniProt: P27487) MEROPS name: dipeptidyl-peptidase IV (bacteria) MEROPS classification: clan SC, family S9, subfamily S9B, peptidase S09.013 Species distribution: superkingdom Bacteria sequence from: Chryseobacterium Reference meningosepticum
Name and History Dipeptidyl-peptidase IV (DPP IV) is a serine exopeptidase that cleaves Xaa-Pro dipeptides from the N-terminus of oligo- and polypeptides. It was first reported as glycylproline naphthylamidase by Hopsu-Havu & Glenner , and has
been named dipeptidyl aminopeptidase IV or postproline dipeptidyl peptidase IV in early work . The enzyme was found to be abundant in kidney, small intestine, submaxillary gland and liver, from which it has been purified in a soluble form released by autolysis of microsomes . Immunocytochemical studies revealed that the enzyme is localized in an apical domain of the plasma membrane in polarized epithelial cells , accounting for its enrichment in the above mentioned tissues. The entire sequence of the enzyme molecule was first determined by cloning and sequencing the cDNA for rat DPP IV , allowing structural comparison with other proteins [9,10]. Both CD26, a surface marker involved in transduction of mitogenic signals in thymocytes and T lymphocytes , and rat liver plasma membrane glycoprotein gp110 were found to be identical to DPP IV .
Activity and Specificity DPP IV is specific for a proline residue at the penultimate position, and hydrolyzes on the carboxyl side of this residue (Xaa-ProkXbb-). The Pro residue can be substituted
Clan SC S9 | 745. Dipeptidyl-peptidase IV
by an Ala or a hydroxyproline, although the rates of hydrolysis for these substrates are much lower than that for the corresponding substrate containing Pro. The identity of the N-terminal residue of the substrate is not important for the enzyme activity  although it must have a free amino group. DPP IV cannot hydrolyze substrates with Pro  or hydroxyproline in the third position (P10 ) . DPP IV shows quite similar substrate specificity to the unrelated Xaa-Pro dipeptidyl-peptidase of lactococci (Chapter 757) . Assay of activity can be done with Gly-ProkNHPhNO2 by measuring released p-nitroaniline photometrically . This synthetic substrate is available from Sigma and Peptide Institute. One unit of activity is defined as the amount of activity which is capable of cleaving 1 µmol of substrate min21 at 37 C. DPP IV requires neither metals nor any cofactors for its activity. The pH optimum is about 7.8. DPP IV shows pH stability over a wide range (pH 510), is thermostable (up to 72 C), and is remarkably resistant to denaturation with 8 M urea [2,16]. DPP IV is very sensitive to DFP, but much less sensitive to other well-known serine protease inhibitors such as diethyl p-nitrophenylphosphate and PMSF . Ala-(or Pro)-boroPro dipeptide  and aminoacylpyrrolidine-2nitriles  are specific and potent inhibitors of DPP IV, but are not yet commercially available. Heavy metals such as zinc, cadmium, mercury and lead inhibit the enzyme activity remarkably . Recently, DPP IV has become a target for the design of drugs, and this has driven the discovery of novel inhibitors. Amongst these are NVP-DPP728 (1-(2-[(5-cyanopyridin-2-yl)amino]ethylamino)acetyl-2-cyano-S-pyrrolidine monohydrochloride salt) [20,21], Lys[Z(NO2)]thiazolidine and Lys[Z(NO2)] pyrrolidide , P32/98  and FE999011 . It has also been found that proteins with the N-terminal sequence Xaa-Xaa-Pro inhibit DPP IV . In the last decade, peptide-derived slow-tight binding inhibitors such as NVP-LAF237 (vildagliptin), MK-0431 (sitagliptin) and SYR-322 (alogliptin) have been used for preclinical and clinical studies for potential treatment of type 2 diabetes [26,27].
contains glycosylation sites (mostly in the N-terminal half), a cysteine-rich region (C-terminal half) and the catalytic active site. The presence of eight potential N-linked glycosylation sites accounts for the difference in molecular mass between the predicted polypeptide (88 kDa) and the mature form (109 kDa). In the native state, DPP IV is present on the cell surface as a noncovalently linked homodimer . In the rat enzyme, the active-site Ser631 residue was identified by chemical modification and mutagenesis , and is in the sequence Gly-Trp-Ser-Tyr-Gly, which corresponds to the consensus motif Gly-Xaa-Ser-Xaa-Gly proposed for the active site of serine proteases generally . It is of interest to note that a single substitution of either Gly residue in the motif results in retention of the newly synthesized enzyme in the endoplasmic reticulum, and rapid degradation [29,30], suggesting that both residues are also essential for correct folding of the molecule and its transport to the cell surface. Other essential residues required for the catalytic triad of the rat enzyme are Asp709 and His741 . The sequential order of the catalytic triad residues (Ser/Asp/His) in DPP IV from all species is characteristic of clan SC (see Chapters 742752). A soluble form of DPP IV that occurs in human serum was characterized and found to be a proteolytic derivative cleaved on the amino side of Ser39 so as to detach the enzyme from its N-terminal membrane-insertion domain . A crystal structure of DPP IV was analyzed by using purified ectodomains of recombinant human DPP IV expressed in Pichica pasteria and the insect cell Sf9 or natively prepared porcine DPP IV [33,34]. The structure shows a homodimer or tetramer in the crystal form, in agreement with the data obtained by biochemical analysis. One site substitution introduced at His750 was found to disrupt dimer formation and cause no enzyme activity, demonstrating that the dimer formation is essential for full activity of the enzyme .
DPP IV is widely distributed in a variety of species and tissues, from which it has been prepared with various degrees of purity. Since it is most abundant in kidney, small intestine, submaxillary gland and placenta [3,6,7,26] and relatively enriched in liver , the enzyme has been purified to homogeneity from these tissues. The intact membrane form is usually prepared by solubilizing the enzyme with Triton X-100, while a soluble form is obtained by autolysis of microsomes incubated at low pH or by digestion of membranes with papain  which cleaves a site adjacent to the transmembrane domain and releases the enzyme with a
The entire amino acid sequences of DPP IV for human, rat and mouse have been determined by cDNA cloning and sequencing. Rat DPP IV contains 767 amino acids with a calculated molecular mass of 88 107 Da . It is a type II membrane protein whose N-terminal hydrophobic sequence represents an uncleavable signal peptide that also functions as a membrane-anchoring domain. Thus, DPP IV has a short cytoplasmic tail (six residues), a transmembrane domain (23 residues) and a long extracellular domain (738 residues). The extracellular domain
slightly smaller molecular mass . DPP IV was transiently expressed in COS-1 cells , and stably transfected CHO cells , mouse fibroblast Lm  and Jurkat cells  have been established. Human DPP IV has been expressed in insect Sf9 cells with a yield of about 10 mg per liter of culture .
Biological Aspects The gene structure of human DPP IV was elucidated by Abbott and coworkers . The human DPP IV gene located at 2q24.3 spans approximately 70 kbp and contains 26 exons. The nucleotides that encode the active-site sequence (Gly-Xaa-Ser-Xaa-Gly) are split between two exons. This clearly distinguishes the genomic organization of DPP IV from that of the classical serine proteases . The promoter region contains an unmethylated CpG island with several Sp1-binding sites and no consensus TATA box, which are characteristics of promoters found in housekeeping genes. In spite of these sequence features, the DPP IV promoter shows widely varying transcriptional activity that mirrors the enzyme activities in several cells . These characteristics of the promoter may play a role in the ubiquitous expression of the DPP IV transcript at different levels: high expression in kidney, small intestine and placenta, moderate expression in lung, spleen and liver, and a low level of expression in heart, pancreas and brain [40,42]. DPP IV has been proposed to serve a number of different functions [43,44]. In kidney brush border membranes, the enzyme may be involved in a transport system specific for dipeptides and tripeptides . DPP IV levels in rat small intestine can be increased by feeding a gelatin (high proline) diet . These results suggest that DPP IV is one of the peptidases important in the digestion and assimilation of prolyl peptides. Studies of cell adhesion have suggested an involvement of DPP IV in interaction of cells with the extracellular matrix, especially with collagens . Based on experiments with monoclonal antibodies that inhibit the binding of DPP IV to collagen matrix, it is proposed that a putative binding site of the enzyme against collagens is the cysteine-rich domain distinct from the catalytic domain . In the immune system, DPP IV (CD26) is considered to be an activation factor on the surface of human T lymphocytes, and to play a key role in the regulation of proliferation and differentiation of the lymphocytes , including production of lymphokines ). Studies with specific inhibitors of the enzyme suggest that DPP IV contributes to T-cell activation through its dipeptidyl-peptidase activity . However, experiments in which the putative catalytic Ser residue of DPP IV was mutated to Ala, eliminating catalytic activity, suggested that the peptidase activity plays an important, but not absolute role in the enhancement of interleukin 2 (IL-2) production by Jurkat cells .
Clan SC S9 | 745. Dipeptidyl-peptidase IV
DPP IV is found to be identical to a protein that was known as ‘adenosine deaminase complexing protein’ . Human adenosine deaminase, but not the mouse homolog, binds to DPP IV, and a cluster of charged amino acid residues seems to be responsible . The kinetics of hydrolysis of a number of bioactive peptides in vitro were described by Lambeir et al. . DPP IV also inactivates a number of biologically active peptides in vivo. These include the incretin hormones glucagon-like peptide-1 and glucose-dependent insulinotropic polypeptide. DPP IV inhibition with NVP-DPP728 prevents the Nterminal degradation of the endogenous incretins in vivo, resulting in increased plasma concentrations of the intact, biologically active peptides with insulinotropic activity . Inhibitors such as NVP-DPP728 and FE 999011 show promise as leads to drugs in various models of diabetes and related disturbances of glucose metabolism [24,54,55]. DPP IV also removes dipeptides sequentially from the N-termini of glucagon  and procalcitonin .
Distinguishing Features The cellular localization and enzymatic properties of DPP IV are quite different from those of other dipeptidylpeptidases (dipeptidyl-peptidases I, II and III) found in mammalian tissues [57,58]. Dipeptidyl-peptidase I (Chapter 448) and dipeptidyl-peptidase II (Chapter 759) are localized in lysosomes and require acidic pH (5.06.0) for maximal activity, while dipeptidyl-peptidase III (Chapter 285) is a cytosolic enzyme with an optimum pH near 9. Dipeptidyl-peptidase II hydrolyzes substrates with Pro or Ala in the penultimate position as does DPP IV, but neither dipeptidyl-peptidase I nor dipeptidyl-peptidase III can cleave the Xaa-Pro dipeptide from substrates. Dipeptidylpeptidase I is a cysteine peptidase, DPP II and DPP IV are serine peptidases, and DPP III is a metallopeptidase. Polyclonal antisera to rat liver [8,42] and pig kidney  DPP IV have been produced in rabbits. Monoclonal anti-human DPP IV (Coulter, Eurogenetics), polyclonal anti-human DPP IV (Transformation Research) and polyclonal anti-pig DPP IV antibodies (Serva) are commercially available.
Further Reading A full description of the purification and assay methods for liver DPP IV has been provided by Ikehara et al. , and biological and clinical aspects of DPP IV have been reviewed by several investigators .
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 Ansorge, S., Bank, U., Heinburg, A., Helmuth, M., Koch, G., Tadje, J., Lendeckel, U., Wolke, C., Neubert, K., Faust, J., Fuchs, P., Reinhold, D., Tager, M. (2009). Recent insights into the
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Yoshio Misumi Department of Cell Biology, Fukuoka University School of Medicine, Jonan-ku, Fukuoka 814-0181, Japan. Email: [email protected]
Yukio Ikehara Fukuoka University (Professor emeritus), Sawara-ku, Fukuoka 814-0171, Japan. Email: [email protected]
Handbook of Proteolytic Enzymes, 3rd Edn ISBN: 978-0-12-382219-2
© 2013 Elsevier Ltd. All rights reserved. DOI: http://dx.doi.org/10.1016/B978-0-12-382219-2.00745-6