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Dipeptidyl Peptidases: From Structure to Function
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Dipeptidyl Peptidases: From Structure to Function

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: 20 February 2025 | Viewed by 3026

Special Issue Editor

Dr. Mihaela Matovina

E-Mail Website
Guest Editor
Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
Interests: dipeptidyl peptidases

Special Issue Information

Dear Colleagues, 

Dipeptidyl peptidases (DPPs) belong to a family of peptidases that consists of 8 members in mamals, DPP1 (cathepsin C), DPP2 (DPP7), DPP3, DPP4, DPP6, DPP8, DPP9 and DPP10. It is a diverse family consisting of the proteins with the enzymatic activity that cleave dipeptides from the amino-termini of oligopeptides or polypeptides, and catalitically inactive proteins (DPP6 and DPP10). Enzymatically active members belong to different groups of peptidases, based on the mechanism of catalysis. DPP1 is a cystein peptidase, DPP2, 4, 8 and 9 are serine peptidases, while DPP3 is a metallopeptidase. The most thorougly investigated protein of the family is DPP4, which is mainly located on membranes, but it is also found in a circulationg form. It is involved in glucose-metabolism and is a therapeutic target in diabetes, but it is also a differentiation marker in T-lymphocytes, where it is called CD26. The only metallopeptides in the family, DPP3, which was first identified in the 1960s has regained interest in the last decade after the discovery of its role in the oxidative stress response regulation, and its identification as a potential biomaker or even therapeutic target of cardiogenic shock. Other proteins from the family have important roles in immune system, however, their patophysiological roles are still largely obscure, and are the targets of ongoing investigations.

Dr. Mihaela Matovina
Guest Editor

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Keywords

  • dipeptidyl peptidase
  • protein structure
  • inhibitors
  • protein-protein interactions
  • cell signaling
  • oxidative stress
  • cancer
  • immune control

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Published Papers (2 papers)

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Research

19 pages, 5767 KiB  
Article
Identification of SH2 Domain-Containing Protein 3C as a Novel, Putative Interactor of Dipeptidyl Peptidase 3
by Mihaela Matovina, Ana Tomašić Paić, Sanja Tomić, Hrvoje Brkić, Lucija Horvat, Lea Barbarić, Vedrana Filić, Marija Pinterić, Snježana Jurić and Akmaral Kussayeva
Int. J. Mol. Sci. 2023, 24(18), 14178; https://doi.org/10.3390/ijms241814178 - 16 Sep 2023
Viewed by 1339
Abstract
Dipeptidyl peptidase 3 (DPP3) is a zinc-dependent exopeptidase with broad specificity for four to eight amino acid residue substrates. It has a role in the regulation of oxidative stress response NRF2–KEAP1 pathway through the interaction with KEAP1. We have conducted stable isotope labeling [...] Read more.
Dipeptidyl peptidase 3 (DPP3) is a zinc-dependent exopeptidase with broad specificity for four to eight amino acid residue substrates. It has a role in the regulation of oxidative stress response NRF2–KEAP1 pathway through the interaction with KEAP1. We have conducted stable isotope labeling by amino acids in a cell culture coupled to mass spectrometry (SILAC-MS) interactome analysis of TRex HEK293T cells using DPP3 as bait and identified SH2 Domain-Containing Protein 3C (SH2D3C) as prey. SH2D3C is one of three members of a family of proteins that contain both the SH2 domain and a domain similar to guanine nucleotide exchange factor domains of Ras family GTPases (Ras GEF-like domain), named novel SH2-containing proteins (NSP). NSPs, including SH2D3C (NSP3), are adaptor proteins involved in the regulation of adhesion, migration, tissue organization, and immune response. We have shown that SH2D3C binds to DPP3 through its C-terminal Ras GEF-like domain, detected the colocalization of the proteins in living cells, and confirmed direct interaction in the cytosol and membrane ruffles. Computational analysis also confirmed the binding of the C-terminal domain of SH2D3C to DPP3, but the exact model could not be discerned. This is the first indication that DPP3 and SH2D3C are interacting partners, and further studies to elucidate the physiological significance of this interaction are on the way. Full article
(This article belongs to the Special Issue Dipeptidyl Peptidases: From Structure to Function)
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23 pages, 5150 KiB  
Article
Identification of an Additional Metal-Binding Site in Human Dipeptidyl Peptidase III
by Antonia Matić, Filip Šupljika, Hrvoje Brkić, Jasna Jurasović, Zrinka Karačić and Sanja Tomić
Int. J. Mol. Sci. 2023, 24(16), 12747; https://doi.org/10.3390/ijms241612747 - 13 Aug 2023
Viewed by 1215
Abstract
Dipeptidyl peptidase III (DPP III, EC 3.4.14.4) is a monozinc metalloexopeptidase that hydrolyzes dipeptides from the N-terminus of peptides consisting of three or more amino acids. Recently, DPP III has attracted great interest from scientists, and numerous studies have been conducted showing that [...] Read more.
Dipeptidyl peptidase III (DPP III, EC 3.4.14.4) is a monozinc metalloexopeptidase that hydrolyzes dipeptides from the N-terminus of peptides consisting of three or more amino acids. Recently, DPP III has attracted great interest from scientists, and numerous studies have been conducted showing that it is involved in the regulation of various physiological processes. Since it is the only metalloenzyme among the dipeptidyl peptidases, we considered it important to study the process of binding and exchange of physiologically relevant metal dications in DPP III. Using fluorimetry, we measured the Kd values for the binding of Zn2+, Cu2+, and Co2+ to the catalytic site, and using isothermal titration calorimetry (ITC), we measured the Kd values for the binding of these metals to an additional binding site. The structure of the catalytic metal’s binding site is known from previous studies, and in this work, the affinities for this site were calculated for Zn2+, Cu2+, Co2+, and Mn2+ using the QM approach. The structures of the additional binding sites for the Zn2+ and Cu2+ were also identified, and MD simulations showed that two Cu2+ ions bound to the catalytic and inhibitory sites exchanged less frequently than the Zn2+ ions bound to these sites. Full article
(This article belongs to the Special Issue Dipeptidyl Peptidases: From Structure to Function)
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