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Biochimica Et Biophysica Acta Jan 2012Visualization of three-dimensional structures is essential to the transmission of information to the general reader and the comparison of related structures. Therefore,... (Review)
Review
Visualization of three-dimensional structures is essential to the transmission of information to the general reader and the comparison of related structures. Therefore, it would be useful to provide a common framework. Based on the work of Schechter and Berger, and the finding that most peptidases bind their substrates in extended conformation, we suggest a "standard orientation" for the overall description of metallopeptidases (MPs) as done before for peptidases of other classes. This entails a frontal view of the horizontally-aligned active-site cleft. A substrate is bound N- to C-terminally from left (on the non-primed side of the cleft) to right (on the primed side), and the catalytic metal ion resides at the cleft bottom at roughly half width. This view enables us to see that most metalloendopeptidases are bifurcated into an upper and a lower sub-domain by the cleft, whose back is framed by a nearly horizontal "active-site helix." The latter comprises a short zinc-binding consensus sequence, either HEXXH or HXXEH, which provides two histidines to bind the single catalytic metal and the general-base/acid glutamate required for catalysis. In addition, an oblique "backing helix" is observed behind the active-site helix, and a mixed β-sheet of at least three strands is positioned in the upper sub-domain paralleling the cleft. The lowermost "upper-rim" strand of the sheet runs antiparallel to the substrate bound in the cleft and therefore contributes both to delimitating the cleft top and to binding of the substrate main-chain on its non-primed side through β-ribbon-like interactions. In contrast, in metalloexopeptidases, which chop off N- or C-terminal residues only, extensive binding on both sides of the cleft is not required and a different overall scaffold is generally observed. This consists of an αβα-sandwich, which is reminiscent of, but clearly distinct from, the archetypal α/β-hydrolase fold. Metalloexopeptidases have their active sites at the C-terminal end of a central, eight-stranded twisted β-sheet, and can contain one or two catalytic metal ions. As the zinc-binding site and the residues engaged in substrate binding and catalysis are mainly provided by loops connecting the β-sheet strands and the helices on either side, the respective standard orientations vary with respect to the position of the sheets. The standard orientation of eight prototypic MP structures is presented and discussed. This article is part of a Special Issue entitled: Proteolysis 50 years after the discovery of lysosome.
Topics: Animals; Cell Polarity; Humans; Metalloproteases; Models, Biological; Models, Molecular; Phylogeny; Protein Conformation; Reference Standards; Structure-Activity Relationship
PubMed: 21558023
DOI: 10.1016/j.bbapap.2011.04.014 -
The Journal of Biological Chemistry May 2009
Review
Topics: Animals; Aspartic Acid Endopeptidases; Cell Membrane; Humans; Metalloproteases; Peptide Hydrolases; Serine Endopeptidases
PubMed: 19189971
DOI: 10.1074/jbc.R800039200 -
Neuron Feb 2003Two families of metalloproteases, the matrix metalloproteases (MMPs) and the A Disintegrin and Metalloproteases (ADAMs), have recently been implicated in the formation... (Review)
Review
Two families of metalloproteases, the matrix metalloproteases (MMPs) and the A Disintegrin and Metalloproteases (ADAMs), have recently been implicated in the formation of neural connections in the developing central nervous system. Invertebrate and vertebrate axons fail to extend and/or make pathfinding errors when metalloprotease function is inhibited or absent. Culture studies suggest that this requirement for metalloprotease activity results from their ability to cleave ligands, or their receptors, so as to activate or inhibit specific axon extension or guidance signaling pathways.
Topics: Amyloid Precursor Protein Secretases; Animals; Aspartic Acid Endopeptidases; Axons; Drosophila; Endopeptidases; Growth Cones; Ligands; Matrix Metalloproteinases; Metalloendopeptidases; Mice; Nerve Tissue Proteins; Receptors, Immunologic; Signal Transduction; Superior Colliculi; Visual Pathways; Roundabout Proteins
PubMed: 12597854
DOI: 10.1016/s0896-6273(03)00089-8 -
Current Pharmaceutical Design 2014Degradation of the extracellular matrix is an important feature of embryonic development, morphogenesis, angiogenesis, tissue repair and remodeling. It is precisely... (Review)
Review
Degradation of the extracellular matrix is an important feature of embryonic development, morphogenesis, angiogenesis, tissue repair and remodeling. It is precisely regulated under physiological conditions, but when dysregulated it becomes a cause of many diseases, including atherosclerosis, osteoarthritis, diabetic vascular complications, and neurodegeneration. Various types of proteinases are implicated in extracellular matrix degradation, but the major enzymes are considered to be metalloproteinases such as matrix metalloproteinases (MMPs) and disintegrin and metalloproteinase domain (ADAMs) that include ADAMs with a thrombospondin domain (ADAMTS). This review discusses involvement of the major metalloproteinases in some age-related chronic diseases, and examines what is currently known about the beneficial effects of their inhibitors, used as new therapeutic strategies for treating or preventing the development and progression of these diseases.
Topics: Age Factors; Animals; Disease Progression; Extracellular Matrix; Humans; Matrix Metalloproteinase Inhibitors; Matrix Metalloproteinases; Metalloproteases
PubMed: 24079771
DOI: 10.2174/13816128113196660701 -
Communications Biology Jan 2024Mitochondrial function plays an important role in the maintenance of male fertility. However, the mechanisms underlying mitochondrial defect-related infertility remain...
Mitochondrial function plays an important role in the maintenance of male fertility. However, the mechanisms underlying mitochondrial defect-related infertility remain mostly unclear. Here we show that a deficiency of PARL (Parl), a mitochondrial protease, causes complete arrest of spermatogenesis during meiosis I. PARL deficiency led to severe downregulation of proteins of respiratory chain complex IV in testes that did not occur in other tested organs, causing a deficit in complex IV activity and ATP production. Furthermore, Parl testes showed an almost complete loss of HSD17B3, a protein of the sER responsible for the last step in testosterone synthesis. While testosterone production appeared to be restored by overexpression of HSD17B12, loss of the canonical testosterone synthesis led to an upregulation of luteinizing hormone (LH) and of LH-regulated responses. These results suggest an important impact of the downstream regulation of mitochondrial defects that manifest in a cell-type-specific manner and extend beyond mitochondria.
Topics: Humans; Male; Endopeptidases; Mitochondria; Peptide Hydrolases; Spermatogenesis; Testosterone; Mitochondrial Proteins; Metalloproteases
PubMed: 38182793
DOI: 10.1038/s42003-023-05703-3 -
Structure (London, England : 1993) Jul 2021Zinc metalloprotease 1 (Zmp1), a Mycobacterium tuberculosis 75 kDa secreted enzyme, mediates key stages of tuberculosis disease progression. The biological activity of...
Zinc metalloprotease 1 (Zmp1), a Mycobacterium tuberculosis 75 kDa secreted enzyme, mediates key stages of tuberculosis disease progression. The biological activity of Zmp1 presumably stems from its ability to degrade bacterium- and/or host-derived peptides. The crystal structures of Zmp1 and related M13 metalloproteases, such as neprilysin and endothelin-converting enzyme-1 were determined only in the closed conformation, which cannot capture substrates or release proteolytic products. Thus, the mechanisms of substrate binding and selectivity remain elusive. Here we report two open-state cryo-EM structures of Zmp1, revealed by our SAXS analysis to be the dominant states in solution. Our structural analyses reveal how ligand binding induces a conformational switch in four linker regions to drive the rigid body motion of the D1 and D2 domains, which form the sizable catalytic chamber. Furthermore, they offer insights into the catalytic cycle and mechanism of substrate recognition of M13 metalloproteases for future therapeutic innovations.
Topics: Bacterial Proteins; Cryoelectron Microscopy; Ligands; Metalloproteases; Models, Molecular; Mycobacterium tuberculosis; Protein Binding; Protein Conformation; Protein Domains; Scattering, Small Angle; X-Ray Diffraction
PubMed: 33378640
DOI: 10.1016/j.str.2020.12.002 -
Scientific Reports Feb 2021Deinococcus bacteria are extremely resistant to radiation and other DNA damage- and oxidative stress-generating conditions. An efficient SOS-independent response...
Deinococcus bacteria are extremely resistant to radiation and other DNA damage- and oxidative stress-generating conditions. An efficient SOS-independent response mechanism inducing expression of several DNA repair genes is essential for this resistance, and is controlled by metalloprotease IrrE that cleaves and inactivates transcriptional repressor DdrO. Here, we identify the molecular signaling mechanism that triggers DdrO cleavage. We show that reactive oxygen species (ROS) stimulate the zinc-dependent metalloprotease activity of IrrE in Deinococcus. Sudden exposure of Deinococcus to zinc excess also rapidly induces DdrO cleavage, but is not accompanied by ROS production and DNA damage. Further, oxidative treatment leads to an increase of intracellular free zinc, indicating that IrrE activity is very likely stimulated directly by elevated levels of available zinc ions. We conclude that radiation and oxidative stress induce changes in redox homeostasis that result in IrrE activation by zinc in Deinococcus. We propose that a part of the zinc pool coordinated with cysteine thiolates is released due to their oxidation. Predicted regulation systems involving IrrE- and DdrO-like proteins are present in many bacteria, including pathogens, suggesting that such a redox signaling pathway including zinc as a second messenger is widespread and participates in various stress responses.
Topics: DNA Damage; DNA Replication; Deinococcus; Gene Expression Regulation, Bacterial; Metalloproteases; Models, Biological; Mutagenesis; Oxidation-Reduction; Oxidative Stress; Radiation Tolerance; Radiation, Ionizing; Signal Transduction; Zinc
PubMed: 33633226
DOI: 10.1038/s41598-021-84026-x -
International Journal of Molecular... Aug 2022Leishmanolysin, also known as major promastigote protease (PSP) or gp63, is the most abundant surface glycoprotein of spp., and has been extensively studied and...
Leishmanolysin, also known as major promastigote protease (PSP) or gp63, is the most abundant surface glycoprotein of spp., and has been extensively studied and recognized as the main parasite virulence factor. Characterized as a metalloprotease, gp63 can be powerfully inactivated in the presence of a metal chelator. In this study, we first used the structural parameters of a 7-hydroxycoumarin derivative, L1 compound, to evaluate the theoretical-computational experiments against gp63, comparing it with an available metal chelator already described. The methodology followed was (i) analysis of the three-dimensional structure of gp63 as well as its active site, and searching the literature and molecular databases for possible inhibitors; (ii) molecular docking simulations and investigation of the interactions in the generated protein-ligand complexes; and (iii) the individual energy of the gp63 amino acids that interacted most with the ligands of interest was quantified by ab initio calculations using Molecular Fraction with Conjugated Caps (MFCC). MFCC still allowed the final quantum balance calculations of the protein interaction to be obtained with each inhibitor candidate binder. L1 obtained the best energy quantum balance result with -2 eV, followed by DETC (-1.4 eV), doxycycline (-1.3 eV), and 4-terpineol (-0.6 eV), and showed evidence of covalent binding in the enzyme active site. In vitro experiments confirmed L1 as highly effective against parasites. The compound also exhibited a low cytotoxicity profile against mammalian RAW and 3T3 cells lines, presenting a selective index of 149.19 and 380.64 µM, respectively. L1 induced promastigote forms' death by necrosis and the ultrastructural analysis revealed disruption in membrane integrity. Furthermore, leakage of the contents and destruction of the parasite were confirmed by Spectroscopy Dispersion analysis. These results together suggested L1 has a potential effect against the etiologic agent of diffuse leishmaniasis, and the only one that currently does not have a satisfactory treatment.
Topics: Animals; Chelating Agents; Leishmania; Mammals; Metalloendopeptidases; Metalloproteases; Mice; Molecular Docking Simulation; Phagocytosis
PubMed: 35955687
DOI: 10.3390/ijms23158553 -
Clinical and Translational Science Oct 2009The pathophysiology of various types of thrombotic microangiopathies is coming progressively into focus. Therapeutic advances are likely to follow at a quickening pace.... (Review)
Review
The pathophysiology of various types of thrombotic microangiopathies is coming progressively into focus. Therapeutic advances are likely to follow at a quickening pace. This discussion focuses on thrombotic thrombocytopenic purpura (TTP), the hemolytic-uremic syndrome (HUS), thrombotic microangiopathies associated with transplantation-immunosuppression or anti-angiogenesis therapy, and the preeclampsia/hemolysis-elevated liver enzymes and low platelets syndrome (HELLP).
Topics: ADAM Proteins; ADAMTS13 Protein; Angiogenesis Inhibitors; Antineoplastic Agents; Hemolytic-Uremic Syndrome; Humans; Immunosuppressive Agents; Metalloproteases; Models, Biological; Platelet Adhesiveness; Protein Structure, Tertiary; Purpura, Thrombotic Thrombocytopenic; Thrombotic Microangiopathies; von Willebrand Factor
PubMed: 20443921
DOI: 10.1111/j.1752-8062.2009.00142.x -
Journal of Experimental Botany Apr 2021The ATP-dependent metalloprotease FtsH12 (filamentation temperature sensitive protein H 12) has been suggested to participate in a heteromeric motor complex, driving...
The ATP-dependent metalloprotease FtsH12 (filamentation temperature sensitive protein H 12) has been suggested to participate in a heteromeric motor complex, driving protein translocation into the chloroplast. FtsH12 was immuno-detected in proplastids, seedlings, leaves, and roots. Expression of Myc-tagged FtsH12 under its native promotor allowed identification of FtsHi1, 2, 4, and 5, and plastidic NAD-malate dehydrogenase, five of the six interaction partners in the suggested import motor complex. Arabidopsis thaliana mutant seedlings with reduced FTSH12 abundance exhibited pale cotyledons and small, deformed chloroplasts with altered thylakoid structure. Mature plants retained these chloroplast defects, resulting in slightly variegated leaves and lower chlorophyll content. Label-free proteomics revealed strong changes in the proteome composition of FTSH12 knock-down seedlings, reflecting impaired plastid development. The composition of the translocon on the inner chloroplast membrane (TIC) protein import complex was altered, with coordinated reduction of the FtsH12-FtsHi complex subunits and accumulation of the 1 MDa TIC complex subunits TIC56, TIC214 and TIC22-III. FTSH12 overexpressor lines showed no obvious phenotype, but still displayed distinct differences in their proteome. N-terminome analyses further demonstrated normal proteolytic maturation of plastid-imported proteins irrespective of FTSH12 abundance. Together, our data suggest that FtsH12 has highest impact during seedling development; its abundance alters the plastid import machinery and impairs chloroplast development.
Topics: ATP-Dependent Proteases; Arabidopsis; Arabidopsis Proteins; Chloroplast Proteins; Chloroplasts; Membrane Proteins; Metalloproteases; Mutation
PubMed: 33216923
DOI: 10.1093/jxb/eraa550