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Dipeptidyl Peptidases: From Structure to Function

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Dr. Mihaela Matovina

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Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
Interests: dipeptidyl peptidases

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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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19 pages, 5767 KiB

Open AccessArticle

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 793

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 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

Open AccessArticle

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 803

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 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 K_d values for the binding of Zn²⁺, Cu²⁺, and Co²⁺ to the catalytic site, and using isothermal titration calorimetry (ITC), we measured the K_d 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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