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1.
Cell ; 155(3): 502-4, 2013 Oct 24.
Artigo em Inglês | MEDLINE | ID: mdl-24243009

RESUMO

Protein degradation by the ClpXP protease requires collaboration among the six AAA+ domains of ClpX. Using single-molecule optical tweezers, Sen et al. show that ClpX uses a coordinated succession of power strokes to translocate polypeptides in ATP-tunable bursts before reloading with nucleotide. This strategy allows ClpX to kinetically capture transiently unfolded intermediates.


Assuntos
Endopeptidase Clp/química , Endopeptidase Clp/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Escherichia coli/enzimologia
2.
J Biol Chem ; 291(14): 7465-76, 2016 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-26858247

RESUMO

The ClpP protease complex and its regulatory ATPases, ClpC1 and ClpX, inMycobacterium tuberculosis(Mtb) are essential and, therefore, promising drug targets. TheMtbClpP protease consists of two heptameric rings, one composed of ClpP1 and the other of ClpP2 subunits. Formation of the enzymatically active ClpP1P2 complex requires binding of N-blocked dipeptide activators. We have found a new potent activator, benzoyl-leucine-leucine (Bz-LL), that binds with higher affinity and promotes 3-4-fold higher peptidase activity than previous activators. Bz-LL-activated ClpP1P2 specifically stimulates the ATPase activity ofMtbClpC1 and ClpX. The ClpC1P1P2 and ClpXP1P2 complexes exhibit 2-3-fold enhanced ATPase activity, peptide cleavage, and ATP-dependent protein degradation. The crystal structure of ClpP1P2 with bound Bz-LL was determined at a resolution of 3.07 Å and with benzyloxycarbonyl-Leu-Leu (Z-LL) bound at 2.9 Å. Bz-LL was present in all 14 active sites, whereas Z-LL density was not resolved. Surprisingly, Bz-LL adopts opposite orientations in ClpP1 and ClpP2. In ClpP1, Bz-LL binds with the C-terminal leucine side chain in the S1 pocket. One C-terminal oxygen is close to the catalytic serine, whereas the other contacts backbone amides in the oxyanion hole. In ClpP2, Bz-LL binds with the benzoyl group in the S1 pocket, and the peptide hydrogen bonded between parallel ß-strands. The ClpP2 axial loops are extended, forming an open axial channel as has been observed with bound ADEP antibiotics. Thus occupancy of the active sites of ClpP allosterically alters sites on the surfaces thereby affecting the association of ClpP1 and ClpP2 rings, interactions with regulatory ATPases, and entry of protein substrates.


Assuntos
Proteínas de Bactérias/química , Dipeptídeos/química , Complexos Multienzimáticos/química , Mycobacterium tuberculosis/enzimologia , Serina Endopeptidases/química , Regulação Alostérica , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Dipeptídeos/metabolismo , Complexos Multienzimáticos/metabolismo , Ligação Proteica , Estrutura Quaternária de Proteína , Estrutura Secundária de Proteína , Serina Endopeptidases/metabolismo
3.
Biochim Biophys Acta ; 1862(2): 252-64, 2016 02.
Artigo em Inglês | MEDLINE | ID: mdl-26675528

RESUMO

In human cells ClpP and ClpX are imported into the mitochondrial matrix, where they interact to form the ATP-dependent protease ClpXP and play a role in the mitochondrial unfolded protein response. We find that reducing the levels of mitochondrial ClpP or ClpX renders human cancer cells more sensitive to cisplatin, a widely used anti-cancer drug. Conversely, overexpression of HClpP desensitizes cells to cisplatin. Overexpression of inactive HClpP-S97A had no effect. Cisplatin resistance correlated with decreased cellular accumulation of cisplatin and decreased levels of diguanosine-cisplatin adducts in both mitochondrial and genomic DNA. In contrast, higher levels of cisplatin-DNA adducts were found in cells in which HClpP had been depleted. Changes in the levels of ClpP had no effect on the levels of CTR1, a copper transporter that contributes to cisplatin uptake. However, the levels of ATP7A and ATP7B, copper efflux pumps that help eliminate cisplatin from cells, were increased when HClpP was overexpressed. HClpP levels were elevated in cervical carcinoma cells (KB-CP20) and hepatoma cells (BEL-7404-CP20) independently selected for cisplatin resistance. The data indicate that robust HClpXP activity positively affects the ability of cells to efflux cisplatin and suggest that targeting HClpP or HClpX would offer a novel mechanism for sensitizing cancer cells to cisplatin.


Assuntos
Antineoplásicos/farmacologia , Apoptose/efeitos dos fármacos , Cisplatino/farmacologia , Resistencia a Medicamentos Antineoplásicos , Endopeptidase Clp/metabolismo , Mitocôndrias/efeitos dos fármacos , Neoplasias/tratamento farmacológico , Linhagem Celular Tumoral , Adutos de DNA/genética , Adutos de DNA/metabolismo , Endopeptidase Clp/genética , Humanos , Mitocôndrias/genética , Mitocôndrias/metabolismo , Neoplasias/genética , Neoplasias/metabolismo , Regulação para Cima
4.
J Biol Chem ; 288(40): 28913-24, 2013 Oct 04.
Artigo em Inglês | MEDLINE | ID: mdl-23960079

RESUMO

The N-end rule is a conserved mechanism found in Gram-negative bacteria and eukaryotes for marking proteins to be degraded by ATP-dependent proteases. Specific N-terminal amino acids (N-degrons) are sufficient to target a protein to the degradation machinery. In Escherichia coli, the adaptor ClpS binds an N-degron and delivers the protein to ClpAP for degradation. As ClpS recognizes N-terminal Phe, Trp, Tyr, and Leu, which are not found at the N terminus of proteins translated and processed by the canonical pathway, proteins must be post-translationally modified to expose an N-degron. One modification is catalyzed by Aat, an enzyme that adds leucine or phenylalanine to proteins with N-terminal lysine or arginine; however, such proteins are also not generated by the canonical protein synthesis pathway. Thus, the mechanisms producing N-degrons in proteins and the frequency of their occurrence largely remain a mystery. To address these issues, we used a ClpS affinity column to isolate interacting proteins from E. coli cell lysates under non-denaturing conditions. We identified more than 100 proteins that differentially bound to a column charged with wild-type ClpS and eluted with a peptide bearing an N-degron. Thirty-two of 37 determined N-terminal peptides had N-degrons. Most of the proteins were N-terminally truncated by endoproteases or exopeptidases, and many were further modified by Aat. The identities of the proteins point to possible physiological roles for the N-end rule in cell division, translation, transcription, and DNA replication and reveal widespread proteolytic processing of cellular proteins to generate N-end rule substrates.


Assuntos
Aminoácidos/metabolismo , Proteínas de Escherichia coli/metabolismo , Escherichia coli/metabolismo , Proteólise , Sequência de Aminoácidos , Cromatografia de Afinidade , Eletroforese em Gel Bidimensional , Proteínas de Escherichia coli/isolamento & purificação , Proteínas Imobilizadas/metabolismo , Espectrometria de Massas , Dados de Sequência Molecular , Peptídeos/metabolismo , Proteínas Recombinantes de Fusão/metabolismo , Análise de Sequência de Proteína
5.
EMBO J ; 29(20): 3520-30, 2010 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-20834233

RESUMO

Lon proteases are distributed in all kingdoms of life and are required for survival of cells under stress. Lon is a tandem fusion of an AAA+ molecular chaperone and a protease with a serine-lysine catalytic dyad. We report the 2.0-Å resolution crystal structure of Thermococcus onnurineus NA1 Lon (TonLon). The structure is a three-tiered hexagonal cylinder with a large sequestered chamber accessible through an axial channel. Conserved loops extending from the AAA+ domain combine with an insertion domain containing the membrane anchor to form an apical domain that serves as a gate governing substrate access to an internal unfolding and degradation chamber. Alternating AAA+ domains are in tight- and weak-binding nucleotide states with different domain orientations and intersubunit contacts, reflecting intramolecular dynamics during ATP-driven protein unfolding and translocation. The bowl-shaped proteolytic chamber is contiguous with the chaperone chamber allowing internalized proteins direct access to the proteolytic sites without further gating restrictions.


Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Protease La/química , Protease La/metabolismo , Estrutura Quaternária de Proteína , Estrutura Terciária de Proteína , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Cristalografia por Raios X , Modelos Moleculares , Dados de Sequência Molecular , Protease La/genética , Multimerização Proteica , Alinhamento de Sequência , Thermococcus/enzimologia
6.
J Biol Chem ; 287(19): 15661-71, 2012 May 04.
Artigo em Inglês | MEDLINE | ID: mdl-22433868

RESUMO

The synthetic derivative of ascochlorin, 4-O-carboxymethyl ascochlorin (AS-6) is an agonist of the nuclear hormone receptor PPARγ and has been shown to induce differentiation in mouse pre-adipocytes and to ameliorate type II diabetes in a murine model. AS-6 was cytotoxic when added at micromolar concentrations to cultures of three different human cancer cell lines. We used gel electrophoresis and mass spectrometry to identify proteins with altered expression in human hepatocarcinoma cells (HepG2) cells after 12 h in the presence of AS-6 and found 58 proteins that were differentially expressed. Many of the proteins showing increased expression in cells treated with AS-6 are involved in protein quality control, including glucose-regulated protein 78 (GRP78/BiP), a regulator of ER stress responses, and the transcriptional regulator CHOP, which mediates ER stress-induced apoptosis. Cells treated with AS-6 undergo an autophagic response accompanied by increased expression of beclin1, ATG5, and LC3-II and autophagosome formation marked by the appearance of large vesicles containing LC3-II. Grp78 induction was inhibited when the PPARγ antagonist, GW9662, was added together with AS-6, and autophagy and cell death were partially blocked. 3-methyl-adenine (3-MA), an inhibitor of phosphatidyl inositol 3-kinase (PI3-kinase) prevented induction of ATG5 and activation of LC3-II and blocked autophagosome formation. 3-MA also blocked induction of GRP78 and CHOP, suggesting that PI3-kinase, which is known to mediate ER stress-induced autophagy, also plays a role in initiating apoptosis in response to ER stress. Together these data establish that the cytotoxicity of AS-6 operates by a mechanism dependent on ER stress-induced autophagy and apoptosis.


Assuntos
Autofagia/efeitos dos fármacos , Estresse do Retículo Endoplasmático/efeitos dos fármacos , Glicolatos/farmacologia , Proteínas Reguladoras de Apoptose/genética , Proteínas Reguladoras de Apoptose/metabolismo , Proteína 5 Relacionada à Autofagia , Proteína Beclina-1 , Western Blotting , Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/metabolismo , Carcinoma Hepatocelular/patologia , Linhagem Celular Tumoral , Sobrevivência Celular/efeitos dos fármacos , Relação Dose-Resposta a Droga , Eletroforese em Gel Bidimensional , Chaperona BiP do Retículo Endoplasmático , Expressão Gênica/efeitos dos fármacos , Células Hep G2 , Humanos , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/metabolismo , Neoplasias Hepáticas/patologia , Proteínas de Membrana/genética , Proteínas de Membrana/metabolismo , Microscopia de Fluorescência , Proteínas Associadas aos Microtúbulos/genética , Proteínas Associadas aos Microtúbulos/metabolismo , Fagossomos/efeitos dos fármacos , Fagossomos/metabolismo , Proteômica/métodos , Interferência de RNA , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Resposta a Proteínas não Dobradas/efeitos dos fármacos
7.
Plant Mol Biol ; 80(2): 189-202, 2012 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-22772861

RESUMO

The ClpP peptidase is a major constituent of the proteolytic machinery of bacteria and organelles. The chloroplast ClpP complex is unusual, in that it associates a large number of subunits, one of which (ClpP1) is encoded in the chloroplast, the others in the nucleus. The complexity of these large hetero-oligomeric complexes has been a major difficulty in their overproduction and biochemical characterization. In this paper, we describe the purification of native chloroplast ClpP complex from the green alga Chlamydomonas reinhardtii, using a strain that carries the Strep-tag II at the C-terminus of the ClpP1 subunit. Similar to land plants, the algal complex comprises active and inactive subunits (3 ClpP and 5 ClpR, respectively). Evidence is presented that a sub-complex can be produced by dissociation, comprising ClpP1 and ClpR1, 2, 3 and 4, similar to the ClpR-ring described in land plants. Our Chlamydomonas ClpP preparation also contains two ClpT subunits, ClpT3 and ClpT4, which like the land plant ClpT1 and ClpT2 show 2 Clp-N domains. ClpTs are believed to function in substrate binding and/or assembly of the two heptameric rings. Phylogenetic analysis indicates that ClpT subunits have appeared independently in Chlorophycean algae, in land plants and in dispersed cyanobacterial genomes. Negative staining electron microscopy shows that the Chlamydomonas complex retains the barrel-like shape of homo-oligomeric ClpPs, with 4 additional peripheral masses that we speculate represent either the additional IS1 domain of ClpP1 (a feature unique to algae) or ClpTs or extensions of ClpR subunits.


Assuntos
Proteínas de Algas/genética , Chlamydomonas reinhardtii/genética , Proteínas de Cloroplastos/genética , Endopeptidase Clp/genética , Proteínas de Algas/classificação , Proteínas de Algas/metabolismo , Sequência de Aminoácidos , Sítios de Ligação/genética , Chlamydomonas reinhardtii/enzimologia , Proteínas de Cloroplastos/isolamento & purificação , Proteínas de Cloroplastos/metabolismo , Eletroforese em Gel de Poliacrilamida , Endopeptidase Clp/metabolismo , Endopeptidase Clp/ultraestrutura , Microscopia Eletrônica , Dados de Sequência Molecular , Filogenia , Multimerização Proteica , Subunidades Proteicas/química , Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo , Homologia de Sequência de Aminoácidos , Tripsina/metabolismo
8.
J Biol Chem ; 285(19): 14834-40, 2010 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-20236930

RESUMO

ClpP is a serine protease whose active sites are sequestered in a cavity enclosed between two heptameric rings of subunits. The ability of ClpP to process folded protein substrates depends on its being partnered by an AAA+ ATPase/unfoldase, ClpA or ClpX. In active complexes, substrates are unfolded and fed along an axial channel to the degradation chamber inside ClpP. We have used cryoelectron microscopy at approximately 11-A resolution to investigate the three-dimensional structure of ClpP complexed with either one or two end-mounted ClpA hexamers. In the absence of ClpA, the apical region of ClpP is sealed; however, it opens on ClpA binding, creating an access channel. This region is occupied by the N-terminal loops (residues 1-17) of ClpP, which tend to be poorly visible in crystal structures, indicative of conformational variability. Nevertheless, we were able to model the closed-to-open transition that accompanies ClpA binding in terms of movements of these loops; in particular, "up" conformations of the loops correlate with the open state. The main part of ClpP, the barrel formed by 14 copies of residues 18-193, is essentially unchanged by the interaction with ClpA. Using difference mapping, we localized the binding site for ClpA to a peripheral pocket between adjacent ClpP subunits. Based on these observations, we propose that access to the ClpP degradation chamber is controlled allosterically by hinged movements of its N-terminal loops, which the symmetry-mismatched binding of ClpA suffices to induce.


Assuntos
Endopeptidase Clp/química , Endopeptidase Clp/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Escherichia coli/enzimologia , Sítios de Ligação , Microscopia Crioeletrônica , Cristalografia por Raios X , Modelos Moleculares , Conformação Proteica
9.
J Biol Chem ; 285(12): 8771-81, 2010 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-20068042

RESUMO

ClpS is an adaptor protein that interacts with ClpA and promotes degradation of proteins with N-end rule degradation motifs (N-degrons) by ClpAP while blocking degradation of substrates with other motifs. Although monomeric ClpS forms a 1:1 complex with an isolated N-domain of ClpA, only one molecule of ClpS binds with high affinity to ClpA hexamers (ClpA(6)). One or two additional molecules per hexamer bind with lower affinity. Tightly bound ClpS dissociates slowly from ClpA(6) with a t((1/2)) of approximately 3 min at 37 degrees C. Maximum activation of degradation of the N-end rule substrate, LR-GFP(Venus), occurs with a single ClpS bound per ClpA(6); one ClpS is also sufficient to inhibit degradation of proteins without N-degrons. ClpS competitively inhibits degradation of unfolded substrates that interact with ClpA N-domains and is a non-competitive inhibitor with substrates that depend on internal binding sites in ClpA. ClpS inhibition of substrate binding is dependent on the order of addition. When added first, ClpS blocks binding of both high and low affinity substrates; however, when substrates first form committed complexes with ClpA(6), ClpS cannot displace them or block their degradation by ClpP. We propose that the first molecule of ClpS binds to the N-domain and to an additional functional binding site, sterically blocking binding of non-N-end rule substrates as well as additional ClpS molecules to ClpA(6). Limiting ClpS-mediated substrate delivery to one per ClpA(6) avoids congestion at the axial channel and allows facile transfer of proteins to the unfolding and translocation apparatus.


Assuntos
Proteínas de Transporte/metabolismo , Endopeptidase Clp/fisiologia , Proteínas de Escherichia coli/metabolismo , Escherichia coli/enzimologia , Regulação Bacteriana da Expressão Gênica , Chaperoninas/química , Relação Dose-Resposta a Droga , Endopeptidase Clp/química , Endopeptidase Clp/metabolismo , Cinética , Peptídeo Hidrolases/química , Plasmídeos/metabolismo , Ligação Proteica , Conformação Proteica , Desnaturação Proteica , Mapeamento de Interação de Proteínas , Fatores de Tempo
10.
Acta Crystallogr D Biol Crystallogr ; 66(Pt 8): 865-73, 2010 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-20693685

RESUMO

The structure of a recombinant construct consisting of residues 1-245 of Escherichia coli Lon protease, the prototypical member of the A-type Lon family, is reported. This construct encompasses all or most of the N-terminal domain of the enzyme. The structure was solved by SeMet SAD to 2.6 A resolution utilizing trigonal crystals that contained one molecule in the asymmetric unit. The molecule consists of two compact subdomains and a very long C-terminal alpha-helix. The structure of the first subdomain (residues 1-117), which consists mostly of beta-strands, is similar to that of the shorter fragment previously expressed and crystallized, whereas the second subdomain is almost entirely helical. The fold and spatial relationship of the two subdomains, with the exception of the C-terminal helix, closely resemble the structure of BPP1347, a 203-amino-acid protein of unknown function from Bordetella parapertussis, and more distantly several other proteins. It was not possible to refine the structure to satisfactory convergence; however, since almost all of the Se atoms could be located on the basis of their anomalous scattering the correctness of the overall structure is not in question. The structure reported here was also compared with the structures of the putative substrate-binding domains of several proteins, showing topological similarities that should help in defining the binding sites used by Lon substrates.


Assuntos
Escherichia coli/enzimologia , Fragmentos de Peptídeos/química , Protease La/química , Bordetella parapertussis/enzimologia , Cristalografia por Raios X , Modelos Moleculares , Estrutura Terciária de Proteína , Homologia Estrutural de Proteína
11.
Mol Endocrinol ; 21(9): 2164-77, 2007 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-17579211

RESUMO

Steroidogenic acute regulatory protein (StAR) is a vital mitochondrial protein promoting transfer of cholesterol into steroid making mitochondria in specialized cells of the adrenal cortex and gonads. Our previous work has demonstrated that StAR is rapidly degraded upon import into the mitochondrial matrix. To identify the protease(s) responsible for this rapid turnover, murine StAR was expressed in wild-type Escherichia coli or in mutant strains lacking one of the four ATP-dependent proteolytic systems, three of which are conserved in mammalian mitochondria-ClpP, FtsH, and Lon. StAR was rapidly degraded in wild-type bacteria and stabilized only in lon (-)mutants; in such cells, StAR turnover was fully restored upon coexpression of human mitochondrial Lon. In mammalian cells, the rate of StAR turnover was proportional to the cell content of Lon protease after expression of a Lon-targeted small interfering RNA, or overexpression of the protein. In vitro assays using purified proteins showed that Lon-mediated degradation of StAR was ATP-dependent and blocked by the proteasome inhibitors MG132 (IC(50) = 20 microm) and clasto-lactacystin beta-lactone (cLbetaL, IC(50) = 3 microm); by contrast, epoxomicin, representing a different class of proteasome inhibitors, had no effect. Such inhibition is consistent with results in cultured rat ovarian granulosa cells demonstrating that degradation of StAR in the mitochondrial matrix is blocked by MG132 and cLbetaL but not by epoxomicin. Both inhibitors also blocked Lon-mediated cleavage of the model substrate fluorescein isothiocyanate-casein. Taken together, our former studies and the present results suggest that Lon is the primary ATP-dependent protease responsible for StAR turnover in mitochondria of steroidogenic cells.


Assuntos
Mitocôndrias/metabolismo , Fosfoproteínas/metabolismo , Protease La/fisiologia , Inibidores de Proteassoma , Trifosfato de Adenosina/fisiologia , Animais , Células Cultivadas , Feminino , Hormônios Esteroides Gonadais/biossíntese , Células da Granulosa/metabolismo , Camundongos , Fosfoproteínas/genética , Ratos , Ratos Sprague-Dawley
12.
Protein Sci ; 15(8): 1815-28, 2006 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-16877706

RESUMO

ATP-dependent Lon proteases are multi-domain enzymes found in all living organisms. All Lon proteases contain an ATPase domain belonging to the AAA(+) superfamily of molecular machines and a proteolytic domain with a serine-lysine catalytic dyad. Lon proteases can be divided into two subfamilies, LonA and LonB, exemplified by the Escherichia coli and Archaeoglobus fulgidus paralogs, respectively. The LonA subfamily is defined by the presence of a large N-terminal domain, whereas the LonB subfamily has no such domain, but has a membrane-spanning domain that anchors the protein to the cytoplasmic side of the membrane. The two subfamilies also differ in their consensus sequences. Recent crystal structures for several individual domains and sub-fragments of Lon proteases have begun to illuminate similarities and differences in structure-function relationships between the two subfamilies. Differences in orientation of the active site residues in several isolated Lon protease domains point to possible roles for the AAA(+) domains and/or substrates in positioning the catalytic residues within the active site. Structures of the proteolytic domains have also indicated a possible hexameric arrangement of subunits in the native state of bacterial Lon proteases. The structure of a large segment of the N-terminal domain has revealed a folding motif present in other protein families of unknown function and should lead to new insights regarding ways in which Lon interacts with substrates or other cellular factors. These first glimpses of the structure of Lon are heralding an exciting new era of research on this ancient family of proteases.


Assuntos
Protease La/química , Trifosfato de Adenosina/metabolismo , Archaeoglobus fulgidus/enzimologia , Sítios de Ligação/genética , Sequência Consenso/genética , Proteínas de Escherichia coli/química , Modelos Moleculares , Protease La/metabolismo , Estrutura Quaternária de Proteína , Estrutura Terciária de Proteína
13.
Structure ; 12(2): 175-83, 2004 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-14962378

RESUMO

Clp/Hsp100 chaperones work with other cellular chaperones and proteases to control the quality and amounts of many intracellular proteins. They employ an ATP-dependent protein unfoldase activity to solubilize protein aggregates or to target specific classes of proteins for degradation. The structural complexity of Clp/Hsp100 proteins combined with the complexity of the interactions with their macromolecular substrates presents a considerable challenge to understanding the mechanisms by which they recognize and unfold substrates and deliver them to downstream enzymes. Fortunately, high-resolution structural data is now available for several of the chaperones and their functional partners, which together with mutational data on the chaperones and their substrates has provided a glimmer of light at the end of the Clp/Hsp100 tunnel.


Assuntos
Proteínas de Choque Térmico/química , Chaperonas Moleculares/química , Subunidades Proteicas/química , Proteínas de Protozoários/química , Endopeptidase Clp , Ligação Proteica , Dobramento de Proteína , Estrutura Terciária de Proteína/fisiologia
14.
Protein Sci ; 14(11): 2895-900, 2005 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-16199667

RESUMO

We report here the first crystal structure of the N-terminal domain of an A-type Lon protease. Lon proteases are ubiquitous, multidomain, ATP-dependent enzymes with both highly specific and non-specific protein binding, unfolding, and degrading activities. We expressed and purified a stable, monomeric 119-amino acid N-terminal subdomain of the Escherichia coli A-type Lon protease and determined its crystal structure at 2.03 A (Protein Data Bank [PDB] code 2ANE). The structure was solved in two crystal forms, yielding 14 independent views. The domain exhibits a unique fold consisting primarily of three twisted beta-sheets and a single long alpha-helix. Analysis of recent PDB depositions identified a similar fold in BPP1347 (PDB code 1ZBO), a 203-amino acid protein of unknown function from Bordetella parapertussis, crystallized as part of a structural genomics effort. BPP1347 shares sequence homology with Lon N-domains and with a family of other independently expressed proteins of unknown functions. We postulate that, as is the case in Lon proteases, this structural domain represents a general protein and polypeptide interaction domain.


Assuntos
Proteínas de Escherichia coli/química , Modelos Moleculares , Protease La/química , Sequência de Aminoácidos , Cristalografia por Raios X , Dados de Sequência Molecular , Estrutura Terciária de Proteína , Alinhamento de Sequência , Homologia Estrutural de Proteína
16.
Structure ; 18(5): 553-62, 2010 May 12.
Artigo em Inglês | MEDLINE | ID: mdl-20462489

RESUMO

The ClpA chaperone combines with the ClpP peptidase to perform targeted proteolysis in the bacterial cytoplasm. ClpA monomer has an N-terminal substrate-binding domain and two AAA+ ATPase domains (D1 and D2). ClpA hexamers stack axially on ClpP heptamers to form the symmetry-mismatched protease. We used cryo-electron microscopy to visualize the ClpA-ATPgammaS hexamer, in the context of ClpAP complexes. Two segments lining the axial channel show anomalously low density, indicating that these motifs, which have been implicated in substrate translocation, are mobile. We infer that ATP hydrolysis is accompanied by substantial structural changes in the D2 but not the D1 tier. The entire N domain is rendered invisible by large-scale fluctuations. When deletions of 10 and 15 residues were introduced into the linker, N domain mobility was reduced but not eliminated and changes were observed in enzymatic activities. Based on these observations, we present a pseudo-atomic model of ClpAP holoenzyme, a dynamic proteolytic nanomachine.


Assuntos
Endopeptidase Clp/química , Endopeptidases/metabolismo , Chaperonas Moleculares/metabolismo , Trifosfato de Adenosina/análogos & derivados , Antígenos de Neoplasias , Microscopia Crioeletrônica , DNA Topoisomerases Tipo II , Proteínas de Ligação a DNA , Hidrólise , Substâncias Macromoleculares , Chaperonas Moleculares/química , Ligação Proteica , Estrutura Terciária de Proteína
17.
Chem Biol ; 17(9): 959-69, 2010 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-20851345

RESUMO

In ClpXP and ClpAP complexes, ClpA and ClpX use the energy of ATP hydrolysis to unfold proteins and translocate them into the self-compartmentalized ClpP protease. ClpP requires the ATPases to degrade folded or unfolded substrates, but binding of acyldepsipeptide antibiotics (ADEPs) to ClpP bypasses this requirement with unfolded proteins. We present the crystal structure of Escherichia coli ClpP bound to ADEP1 and report the structural changes underlying ClpP activation. ADEP1 binds in the hydrophobic groove that serves as the primary docking site for ClpP ATPases. Binding of ADEP1 locks the N-terminal loops of ClpP in a ß-hairpin conformation, generating a stable pore through which extended polypeptides can be threaded. This structure serves as a model for ClpP in the holoenzyme ClpAP and ClpXP complexes and provides critical information to further develop this class of antibiotics.


Assuntos
Antibacterianos/química , Depsipeptídeos/química , Endopeptidase Clp/química , Proteínas de Escherichia coli/química , Modelos Moleculares , ATPases Associadas a Diversas Atividades Celulares , Adenosina Trifosfatases/química , Adenosina Trifosfatases/metabolismo , Endopeptidase Clp/metabolismo , Escherichia coli/enzimologia , Proteínas de Escherichia coli/metabolismo , Cinética , Chaperonas Moleculares/química , Chaperonas Moleculares/metabolismo , Ligação Proteica , Dobramento de Proteína , Estrutura Terciária de Proteína , Especificidade por Substrato
18.
J Biol Chem ; 283(34): 22918-29, 2008 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-18550539

RESUMO

Formation and degradation of SsrA-tagged proteins enable ribosome recycling and elimination of defective products of incomplete translation. We produced an antibody against the SsrA peptide and used it to measure the amounts of SsrA-tagged proteins in Escherichia coli cells without interfering with tagging or altering the context of the tag added at the ends of nascent polypeptides. SsrA-tagged proteins were present in very small amounts unless a component of the ClpXP protease was missing. From the levels of tagged proteins in cells in which degradation is essentially blocked, we calculate that > or =1 in 200 translation products receives an SsrA tag. ClpXP is responsible for > or =90% of the degradation of SsrA-tagged proteins. The degradation rate in wild type cells is > or =1.4 min(-1) and decreases to approximately 0.10 min(-1) in a clpX mutant. The rate of degradation by ClpXP is decreased approximately 3-fold in mutants lacking the adaptor SspB, whereas degradation by ClpAP is increased 3-5-fold. However, ClpAP degrades SsrA-tagged proteins slowly even in the absence of SspB, possibly because of interference from ClpA-specific substrates. Lon protease degrades SsrA-tagged proteins at a rate of approximately 0.05 min(-1) in the presence or absence of SspB. We conclude that ClpXP, together with SspB, is uniquely adapted for degradation of SsrA-tagged proteins and is responsible for the major part of their degradation in vivo.


Assuntos
Trifosfato de Adenosina/química , Escherichia coli/metabolismo , Regulação Bacteriana da Expressão Gênica , RNA Bacteriano/metabolismo , ATPases Associadas a Diversas Atividades Celulares , Adenosina Trifosfatases/metabolismo , Fenômenos Fisiológicos Bacterianos , Proteínas de Transporte/metabolismo , Endopeptidase Clp/metabolismo , Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Cinética , Modelos Biológicos , Chaperonas Moleculares/metabolismo , Mutação
19.
J Struct Biol ; 156(1): 165-74, 2006 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-16682229

RESUMO

ClpP, the proteolytic component of the ATP-dependent ClpAP and ClpXP chaperone/protease complexes, has 14 identical subunits organized in two stacked heptameric rings. The active sites are in an interior aqueous chamber accessible through axial channels. We have determined a 1.9 A crystal structure of Escherichia coli ClpP with benzyloxycarbonyl-leucyltyrosine chloromethyl ketone (Z-LY-CMK) bound at each active site. The complex mimics a tetrahedral intermediate during peptide cleavage, with the inhibitor covalently linked to the active site residues, Ser97 and His122. Binding is further stabilized by six hydrogen bonds between backbone atoms of the peptide and ClpP as well as by hydrophobic binding of the phenolic ring of tyrosine in the S1 pocket. The peptide portion of Z-LY-CMK displaces three water molecules in the native enzyme resulting in little change in the conformation of the peptide binding groove. The heptameric rings of ClpP-CMK are slightly more compact than in native ClpP, but overall structural changes were minimal (rmsd approximately 0.5 A). The side chain of Ser97 is rotated approximately 90 degrees in forming the covalent adduct with Z-LY-CMK, indicating that rearrangement of the active site residues to a active configuration occurs upon substrate binding. The N-terminal peptide of ClpP-CMK is stabilized in a beta-hairpin conformation with the proximal N-terminal residues lining the axial channel and the loop extending beyond the apical surface of the heptameric ring. The lack of major substrate-induced conformational changes suggests that changes in ClpP structure needed to facilitate substrate entry or product release must be limited to rigid body motions affecting subunit packing or contacts between ClpP rings.


Assuntos
Cristalografia por Raios X , Endopeptidase Clp/química , Endopeptidase Clp/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Sequência de Aminoácidos , Sítios de Ligação , Domínio Catalítico , Endopeptidase Clp/genética , Endopeptidase Clp/isolamento & purificação , Escherichia coli/química , Escherichia coli/crescimento & desenvolvimento , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/isolamento & purificação , Humanos , Modelos Moleculares , Dados de Sequência Molecular , Peptídeos/química , Ligação Proteica , Conformação Proteica , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Homologia de Sequência de Aminoácidos , Serina/química , Streptococcus pneumoniae/enzimologia , Streptococcus pneumoniae/genética , Relação Estrutura-Atividade , Especificidade por Substrato , Água/química
20.
J Biol Chem ; 280(42): 35424-32, 2005 Oct 21.
Artigo em Inglês | MEDLINE | ID: mdl-16115876

RESUMO

The functional form of ClpP, the proteolytic component of ATP-dependent Clp proteases, is a hollow-cored particle composed of two heptameric rings joined face-to-face forming an aqueous chamber containing the proteolytic active sites. We have found that isolated human mitochondrial ClpP (hClpP) is stable as a heptamer and remains a monodisperse species (s(20,w) 7.0 S; M(app) 169, 200) at concentrations > or = 3 mg/ml. Heptameric hClpP has no proteolytic activity and very low peptidase activity. In the presence of ATP, hClpX interacts with hClpP forming a complex, which by equilibrium sedimentation measurements has a M(app) of 1 x 10(6). Electron microscopy confirmed that the complex consisted of a double ring of hClpP with an hClpX ring axially aligned on each end. The hClpXP complex has protease activity and greatly increased peptidase activity, indicating that interaction with hClpX affects the conformation of the hClpP catalytic active site. A mutant of hClpP, in which a cysteine residue was introduced into the handle region at the interface between the two rings formed stable tetradecamers under oxidizing conditions but spontaneously dissociated into two heptamers upon reduction. Thus, hClpP rings interact transiently but very weakly in solution, and hClpX must exert an allosteric effect on hClpP to promote a conformation that stabilizes the tetradecamer. These data suggest that hClpX can regulate the appearance of hClpP peptidase activity in mitochondria and might affect the nature of the degradation products released during ATP-dependent proteolytic cycles.


Assuntos
Endopeptidase Clp/química , Mitocôndrias/enzimologia , Trifosfato de Adenosina/química , Sítio Alostérico , Animais , Sítios de Ligação , Imunoprecipitação da Cromatina , Cromatografia em Gel , Reagentes de Ligações Cruzadas/farmacologia , Cisteína/química , Dimerização , Dissulfetos/química , Glutaral/farmacologia , Proteínas de Fluorescência Verde/química , Histidina/química , Humanos , Concentração de Íons de Hidrogênio , Hidrólise , Fígado/metabolismo , Microscopia Eletrônica , Mitocôndrias/metabolismo , Mutagênese , Mutação , Peptídeo Hidrolases/química , Ligação Proteica , Conformação Proteica , Estrutura Terciária de Proteína , Ratos , Proteínas Recombinantes/química , Fatores de Tempo , Tripsina/farmacologia , Ultracentrifugação
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