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Annales de Biologie Clinique 2004Proteolysis plays an central role in key metabolic pathways and cellular adaptation to environmental changes. It modulates the activity of regulatory peptides and... (Review)
Review
Proteolysis plays an central role in key metabolic pathways and cellular adaptation to environmental changes. It modulates the activity of regulatory peptides and eliminates misfolded or damaged proteins such as those generated by stress exposure. In eucaryotic cells ATP- dependent proteolysis is carried out by the 26S proteasome whose substrates are identified by ubiquitin tags. Conversely, bacteria possess several tagging systems and different ATP- dependent proteases. Bacterial ATP-dependent proteases carry distinct chaperone-ATPase and peptidase activities, either on the same molecule or on separate subunits. Although unrelated, all ATP-dependent proteases function according to a similar multistep scheme, from the docking of a substrate by the ATPase region to its proteolysis by the peptidase. Major bacterial ATP- dependent proteases include FtsH, Lon, HslUV and the Clp proteases. Clp proteases are multimeric complexes assembled into a structure centered on the proteolytic component ClpP. They are essential for quick adaptation to stress and regulate important developmental processes. Clp-mediated proteolysis is also required for disease progression and virulence of several bacterial pathogens, favoring survival in the host or modulating the activity of genuine virulence factors.
Topics: ATP-Dependent Proteases; Adenosine Triphosphatases; Bacteria; Endopeptidase Clp; Heat-Shock Proteins; Serine Endopeptidases
PubMed: 15047485
DOI: No ID Found -
Journal of Bacteriology Feb 1992
Review
Topics: ATP-Dependent Proteases; Animals; Bacterial Proteins; Binding Sites; Carrier Proteins; Endopeptidase Clp; Escherichia coli Proteins; Fungal Proteins; Heat-Shock Proteins; Humans; Protein Sorting Signals; Serine Endopeptidases
PubMed: 1735703
DOI: 10.1128/jb.174.4.1081-1085.1992 -
Cell May 2009The dynamic and reversible process of ubiquitin modification controls various cellular activities. Ubiquitin exists as monomers, unanchored chains, or protein-conjugated...
The dynamic and reversible process of ubiquitin modification controls various cellular activities. Ubiquitin exists as monomers, unanchored chains, or protein-conjugated forms, but the regulation of these interconversions remains largely unknown. Here, we identified a protein designated Rfu1 (regulator of free ubiquitin chains 1), which regulates intracellular concentrations of monomeric ubiquitins and free ubiquitin chains in Saccharomyces cerevisiae. Rfu1 functions as an inhibitor of Doa4, a deubiquitinating enzyme. Rapid loss of free ubiquitin chains upon heat shock, a condition in which more proteins require ubiquitin conjugation, was mediated in part by Doa4 and Rfu1. Thus, regulation of ubiquitin homeostasis is controlled by a balance between a deubiquitinating enzyme and its inhibitor. We propose that free ubiquitin chains function as a ubiquitin reservoir that allows maintenance of monomeric ubiquitins at adequate levels under normal conditions and rapid supply for substrate conjugation under stress conditions.
Topics: Allosteric Regulation; Endopeptidases; Endosomal Sorting Complexes Required for Transport; Endosomes; Humans; Mutation; Proteasome Endopeptidase Complex; Protein Binding; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Signal Transduction; Stress, Physiological; Ubiquitin; Ubiquitin Thiolesterase; Ubiquitin-Protein Ligase Complexes
PubMed: 19410548
DOI: 10.1016/j.cell.2009.02.028 -
The Biochemical Journal Apr 1993
Review
Topics: Amino Acid Sequence; Animals; Cell Nucleus; Cysteine Endopeptidases; Cytoplasm; Molecular Sequence Data; Multienzyme Complexes; Peptides; Proteasome Endopeptidase Complex; RNA
PubMed: 7682410
DOI: 10.1042/bj2910001 -
The Journal of Biological Chemistry Oct 1985Single-chain pro-urokinase is an inactive proenzyme form of human urokinase with a single-chain structure and a Mr of 50,000 and converted to the active two-chain form...
Single-chain pro-urokinase is an inactive proenzyme form of human urokinase with a single-chain structure and a Mr of 50,000 and converted to the active two-chain form by catalytic amounts of plasmin. It was isolated from culture fluid of human kidney cells and subjected to chemical (CNBr) and proteolytic (lysyl endopeptidase) degradation. The resulting peptides were separated by reverse-phase high performance liquid chromatography and subjected to automated sequence analysis. Amino acid sequence of 85% of the 411 residues recovered in 17 peptides were found to be consistent with those of the A chain (157 amino acids) and B chain (253 amino acids) of human urokinase reported by Günzler and co-workers (Günzler, W. A., Steffens, G.J., Otting, F., Kim, S.-M., A., Frankus, E., and Flohé, L. (1982) Hoppe-Seyler's Z. Physiol. Chem. 363, 133-141; 1155-1165; Steffens, G.J., Günzler, W.A., Otting, F., Frankus, E., and Flohé, L. (1982) Hoppe-Seyler's Z. Physiol. Chem. 363, 1043-1058). It revealed the presence of Lys at position 158 in single-chain pro-urokinase through which the two polypeptide chains of human urokinase are unified into one molecule. In addition, firm evidence was found that upon activation by plasmin single-chain pro-urokinase is cleaved at the Lys-Ile bond between residues 158 and 159, resulting in the formation of a two-chain urokinase molecule held together by one disulfide linkage. These results indicate that the cleavage at the Lys-Ile bond between residues 158 and 159 is responsible for conformational change, appearance of enzyme activity and reduction of its high affinity for fibrin.
Topics: Amino Acid Sequence; Cyanogen Bromide; Endopeptidases; Fibrinolysin; Humans; Kidney; Molecular Weight; Peptide Fragments; Plasminogen Activators; Urokinase-Type Plasminogen Activator
PubMed: 2931434
DOI: No ID Found -
Archaea (Vancouver, B.C.) 2015Pseudomurein endoisopeptidases cause lysis of the cell walls of methanogens by cleaving the isopeptide bond Ala-ε-Lys in the peptide chain of pseudomurein. PeiW and...
Pseudomurein endoisopeptidases cause lysis of the cell walls of methanogens by cleaving the isopeptide bond Ala-ε-Lys in the peptide chain of pseudomurein. PeiW and PeiP are two thermostable pseudomurein endoisopeptidases encoded by phage ΨM100 of Methanothermobacter wolfei and phages ΨM1 and ΨM2 of Methanothermobacter marburgensis, respectively. A continuous assay using synthetic peptide substrates was developed and used in the biochemical characterisation of recombinant PeiW and PeiP. The advantages of these synthetic peptide substrates over natural substrates are sensitivity, high purity, and characterisation and the fact that they are more easily obtained than natural substrates. In the presence of a reducing agent, purified PeiW and PeiP each showed similar activity under aerobic and anaerobic conditions. Both enzymes required a divalent metal for activity and showed greater thermostability in the presence of Ca(2+). PeiW and PeiP involve a cysteine residue in catalysis and have a monomeric native conformation. The kinetic parameters, K(M) and k(cat), were determined, and the ε-isopeptide bond between alanine and lysine was confirmed as the bond lysed by these enzymes in pseudomurein. The new assay may have wider applications for the general study of peptidases and the identification of specific methanogens susceptible to lysis by specific pseudomurein endoisopeptidases.
Topics: Bacteriophages; Cations, Divalent; Coenzymes; Endopeptidases; Enzyme Stability; Kinetics; Metals; Methanobacteriaceae; Peptides; Recombinant Proteins; Temperature
PubMed: 26483615
DOI: 10.1155/2015/828693 -
Scientific Reports Jul 2017We introduce LytU, a short member of the lysostaphin family of zinc-dependent pentaglycine endopeptidases. It is a potential antimicrobial agent for S. aureus infections...
We introduce LytU, a short member of the lysostaphin family of zinc-dependent pentaglycine endopeptidases. It is a potential antimicrobial agent for S. aureus infections and its gene transcription is highly upregulated upon antibiotic treatments along with other genes involved in cell wall synthesis. We found this enzyme to be responsible for the opening of the cell wall peptidoglycan layer during cell divisions in S. aureus. LytU is anchored in the plasma membrane with the active part residing in the periplasmic space. It has a unique Ile/Lys insertion at position 151 that resides in the catalytic site-neighbouring loop and is vital for the enzymatic activity but not affecting the overall structure common to the lysostaphin family. Purified LytU lyses S. aureus cells and cleaves pentaglycine, a reaction conveniently monitored by NMR spectroscopy. Substituting the cofactor zinc ion with a copper or cobalt ion remarkably increases the rate of pentaglycine cleavage. NMR and isothermal titration calorimetry further reveal that, uniquely for its family, LytU is able to bind a second zinc ion which is coordinated by catalytic histidines and is therefore inhibitory. The pH-dependence and high affinity of binding carry further physiological implications.
Topics: Amino Acid Sequence; Anti-Bacterial Agents; Binding Sites; Catalytic Domain; Cell Membrane; Endopeptidases; Hydrogen-Ion Concentration; Lysostaphin; Mutation; Protein Binding; Protein Interaction Domains and Motifs; Proteolysis; Staphylococcus aureus; Structure-Activity Relationship; Zinc
PubMed: 28729697
DOI: 10.1038/s41598-017-06135-w -
Nature Communications Jan 2020Assembly of the peptidoglycan is crucial in maintaining viability of bacteria and in defining bacterial cell shapes, both of which are important for existence in the...
Assembly of the peptidoglycan is crucial in maintaining viability of bacteria and in defining bacterial cell shapes, both of which are important for existence in the ecological niche that the organism occupies. Here, eight crystal structures for a member of the cell-shape-determining class of Campylobacter jejuni, the peptidoglycan peptidase 3 (Pgp3), are reported. Characterization of the turnover chemistry of Pgp3 reveals cell wall D,D-endopeptidase and D,D-carboxypeptidase activities. Catalysis is accompanied by large conformational changes upon peptidoglycan binding, whereby a loop regulates access to the active site. Furthermore, prior hydrolysis of the crosslinked peptide stem from the saccharide backbone of the peptidoglycan on one side is a pre-requisite for its recognition and turnover by Pgp3. These analyses reveal the noncanonical nature of the transformations at the core of the events that define the morphological shape for C. jejuni as an intestinal pathogen.
Topics: Bacterial Proteins; Campylobacter jejuni; Catalytic Domain; Citric Acid; Crystallography, X-Ray; Endopeptidases; Hydrolysis; Metalloproteases; Models, Molecular; Mutation; Peptidoglycan; Protein Conformation; Virulence Factors
PubMed: 31974386
DOI: 10.1038/s41467-019-13934-4 -
Genes & Development Apr 1997
Review
Topics: ATP-Dependent Proteases; Adenosine Triphosphatases; Bacterial Proteins; Endopeptidase Clp; Endopeptidases; Heat-Shock Proteins; Membrane Proteins; Models, Biological; Molecular Chaperones; Protein Denaturation; Protein Folding; Serine Endopeptidases
PubMed: 9106654
DOI: 10.1101/gad.11.7.815 -
Reproduction, Nutrition, Development 1998The ubiquitin-proteasome proteolytic pathway has recently been reported to be of major importance in the breakdown of skeletal muscle proteins. The first step in this... (Review)
Review
The ubiquitin-proteasome proteolytic pathway has recently been reported to be of major importance in the breakdown of skeletal muscle proteins. The first step in this pathway is the covalent attachment of polyubiquitin chains to the targeted protein. Polyubiquitylated proteins are then recognized and degraded by the 26S proteasome complex. In this review, we critically analyse recent findings in the regulation of this pathway, both in animal models of muscle wasting and in some human diseases. The identification of regulatory steps of ubiquitin conjugation to protein substrates and/or of the proteolytic activities of the proteasome should lead to new concepts that can be used to manipulate muscle protein mass. Such concepts are essential for the development of anti-cachectic therapies for many clinical situations.
Topics: Animals; Cysteine Endopeptidases; Endopeptidases; Humans; Multienzyme Complexes; Muscle Proteins; Muscle, Skeletal; Proteasome Endopeptidase Complex; Ubiquitins
PubMed: 9638789
DOI: 10.1051/rnd:19980202