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1.
Microbiology (Reading) ; 170(2)2024 02.
Artigo em Inglês | MEDLINE | ID: mdl-38334478

RESUMO

YejABEF is an ATP-binding cassette transporter that is implicated in the sensitivity of Escherichia coli to anti-microbial peptides, the best-characterized example being microcin C, a peptide-nucleotide antibiotic that targets aspartyl-tRNA synthetase. Here the structure of the extracellular solute binding protein, YejA, has been determined, revealing an oligopeptide-binding protein fold enclosing a ligand-binding pocket larger than those of other peptide-binding proteins of known structure. Prominent electron density in this cavity defines an undecapeptide sequence LGEPRYAFNFN, an observation that is confirmed by mass spectrometry. In the structure, the peptide interactions with the protein are mediated by main chain hydrogen bonds with the exception of Arg5 whose guanidinium side chain makes a set of defining polar interactions with four YejA residues. More detailed characterization of purified recombinant YejA, by a combination of ESI and MALDI-mass spectrometry as well as thermal shift assays, reveals a set of YejA complexes containing overlapping peptides 10-19 residues in length. All contain the sequence LGEPRYAFN. Curiously, these peptides correspond to residues 8-26 of the mature YejA protein, which belong to a unique N-terminal extension that distinguishes YejA from other cluster C oligopeptide binding proteins of known structure. This 35-residue extension is well-ordered and packs across the surface of the protein. The undecapeptide ligand occupies only a fraction of the enclosed pocket volume suggesting the possibility that much larger peptides or peptide conjugates could be accommodated, though thermal shift assays of YejA binding to antimicrobial peptides and peptides unrelated to LGEPRYAFNFN have not provided evidence of binding. While the physiological significance of this 'auto-binding' is not clear, the experimental data suggest that it is not an artefact of the crystallization process and that it may have a function in the sensing of periplasmic or membrane stress.


Assuntos
Transportadores de Cassetes de Ligação de ATP , Proteínas de Membrana Transportadoras , Peptídeos , Ligantes , Peptídeos/metabolismo , Transportadores de Cassetes de Ligação de ATP/genética , Transportadores de Cassetes de Ligação de ATP/metabolismo , Oligopeptídeos , Escherichia coli/metabolismo , Ligação Proteica
2.
ACS Infect Dis ; 9(11): 2340-2357, 2023 11 10.
Artigo em Inglês | MEDLINE | ID: mdl-37906637

RESUMO

Leishmaniases are a collection of neglected tropical diseases caused by kinetoplastid parasites in the genus Leishmania. Current chemotherapies are severely limited, and the need for new antileishmanials is of pressing international importance. Bromodomains are epigenetic reader domains that have shown promising therapeutic potential for cancer therapy and may also present an attractive target to treat parasitic diseases. Here, we investigate Leishmania donovani bromodomain factor 5 (LdBDF5) as a target for antileishmanial drug discovery. LdBDF5 contains a pair of bromodomains (BD5.1 and BD5.2) in an N-terminal tandem repeat. We purified recombinant bromodomains of L. donovani BDF5 and determined the structure of BD5.2 by X-ray crystallography. Using a histone peptide microarray and fluorescence polarization assay, we identified binding interactions of LdBDF5 bromodomains with acetylated peptides derived from histones H2B and H4. In orthogonal biophysical assays including thermal shift assays, fluorescence polarization, and NMR, we showed that BDF5 bromodomains bind to human bromodomain inhibitors SGC-CBP30, bromosporine, and I-BRD9; moreover, SGC-CBP30 exhibited activity against Leishmania promastigotes in cell viability assays. These findings exemplify the potential BDF5 holds as a possible drug target in Leishmania and provide a foundation for the future development of optimized antileishmanial compounds targeting this epigenetic reader protein.


Assuntos
Antiprotozoários , Fator V , Humanos , Fator V/metabolismo , Histonas/química , Histonas/metabolismo , Domínios Proteicos , Antiprotozoários/farmacologia , Descoberta de Drogas , Fatores de Transcrição/metabolismo
3.
PLoS Pathog ; 16(10): e1008784, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-33108402

RESUMO

Post-translational modifications such as ubiquitination are important for orchestrating the cellular transformations that occur as the Leishmania parasite differentiates between its main morphological forms, the promastigote and amastigote. 2 E1 ubiquitin-activating (E1), 13 E2 ubiquitin-conjugating (E2), 79 E3 ubiquitin ligase (E3) and 20 deubiquitinating cysteine peptidase (DUB) genes can be identified in the Leishmania mexicana genome but, currently, little is known about the role of E1, E2 and E3 enzymes in this parasite. Bar-seq analysis of 23 E1, E2 and HECT/RBR E3 null mutants generated in promastigotes using CRISPR-Cas9 revealed numerous loss-of-fitness phenotypes in promastigote to amastigote differentiation and mammalian infection. The E2s UBC1/CDC34, UBC2 and UEV1 and the HECT E3 ligase HECT2 are required for the successful transformation from promastigote to amastigote and UBA1b, UBC9, UBC14, HECT7 and HECT11 are required for normal proliferation during mouse infection. Of all ubiquitination enzyme null mutants examined in the screen, Δubc2 and Δuev1 exhibited the most extreme loss-of-fitness during differentiation. Null mutants could not be generated for the E1 UBA1a or the E2s UBC3, UBC7, UBC12 and UBC13, suggesting these genes are essential in promastigotes. X-ray crystal structure analysis of UBC2 and UEV1, orthologues of human UBE2N and UBE2V1/UBE2V2 respectively, reveal a heterodimer with a highly conserved structure and interface. Furthermore, recombinant L. mexicana UBA1a can load ubiquitin onto UBC2, allowing UBC2-UEV1 to form K63-linked di-ubiquitin chains in vitro. Notably, UBC2 can cooperate in vitro with human E3s RNF8 and BIRC2 to form non-K63-linked polyubiquitin chains, showing that UBC2 can facilitate ubiquitination independent of UEV1, but association of UBC2 with UEV1 inhibits this ability. Our study demonstrates the dual essentiality of UBC2 and UEV1 in the differentiation and intracellular survival of L. mexicana and shows that the interaction between these two proteins is crucial for regulation of their ubiquitination activity and function.


Assuntos
Leishmania/fisiologia , Leishmaniose/parasitologia , Fatores de Transcrição/metabolismo , Enzimas de Conjugação de Ubiquitina/metabolismo , Ubiquitina/metabolismo , Ubiquitinação , Sequência de Aminoácidos , Animais , Feminino , Humanos , Leishmaniose/metabolismo , Leishmaniose/patologia , Camundongos , Conformação Proteica , Homologia de Sequência de Aminoácidos , Fatores de Transcrição/química , Fatores de Transcrição/genética , Enzimas de Conjugação de Ubiquitina/química , Enzimas de Conjugação de Ubiquitina/genética
4.
Sci Rep ; 10(1): 12500, 2020 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-32719469

RESUMO

Body odour is a characteristic trait of Homo sapiens, however its role in human behaviour and evolution is poorly understood. Remarkably, body odour is linked to the presence of a few species of commensal microbes. Herein we discover a bacterial enzyme, limited to odour-forming staphylococci that are able to cleave odourless precursors of thioalcohols, the most pungent components of body odour. We demonstrated using phylogenetics, biochemistry and structural biology that this cysteine-thiol lyase (C-T lyase) is a PLP-dependent enzyme that moved horizontally into a unique monophyletic group of odour-forming staphylococci about 60 million years ago, and has subsequently tailored its enzymatic function to human-derived thioalcohol precursors. Significantly, transfer of this enzyme alone to non-odour producing staphylococci confers odour production, demonstrating that this C-T lyase is both necessary and sufficient for thioalcohol formation. The structure of the C-T lyase compared to that of other related enzymes reveals how the adaptation to thioalcohol precursors has evolved through changes in the binding site to create a constrained hydrophobic pocket that is selective for branched aliphatic thioalcohol ligands. The ancestral acquisition of this enzyme, and the subsequent evolution of the specificity for thioalcohol precursors implies that body odour production in humans is an ancient process.


Assuntos
Álcoois/metabolismo , Corpo Humano , Odorantes/análise , Compostos de Sulfidrila/metabolismo , Álcoois/química , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Teorema de Bayes , Sítios de Ligação , Liases de Carbono-Enxofre/química , Liases de Carbono-Enxofre/metabolismo , Cisteína/metabolismo , Humanos , Interações Hidrofóbicas e Hidrofílicas , Ligantes , Modelos Moleculares , Filogenia , Staphylococcus/metabolismo , Compostos de Sulfidrila/química , Fatores de Tempo
5.
Acta Crystallogr F Struct Biol Commun ; 75(Pt 4): 246-253, 2019 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-30950825

RESUMO

Peptides play an important signalling role in Bacillus subtilis, where their uptake by one of two ABC-type oligopeptide transporters, Opp and App, is required for efficient sporulation. Homologues of these transporters in Clostridium difficile have been characterized, but their role, and hence that of peptides, in regulating sporulation in this organism is less clear. Here, the oligopeptide-binding receptor proteins for these transporters, CdAppA and CdOppA, have been purified and partially characterized, and the crystal structure of CdAppA has been determined in an open unliganded form. Peptide binding to either protein could not be observed in Thermofluor assays with a set of ten peptides of varying lengths and compositions. Re-examination of the protein sequences together with structure comparisons prompts the proposal that CdAppA is not a versatile peptide-binding protein but instead may bind a restricted set of peptides. Meanwhile, CdOppA is likely to be the receptor protein for a nickel-uptake system.


Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Clostridioides difficile/metabolismo , Peptídeos/química , Peptídeos/metabolismo , Sequência de Aminoácidos , Cristalografia por Raios X , Modelos Moleculares , Níquel/metabolismo , Ligação Proteica , Transdução de Sinais , Esporos Bacterianos/metabolismo , Especificidade por Substrato
6.
Nat Chem ; 10(6): 599-606, 2018 06.
Artigo em Inglês | MEDLINE | ID: mdl-29760414

RESUMO

Rhinoviruses (RVs) are the pathogens most often responsible for the common cold, and are a frequent cause of exacerbations in asthma, chronic obstructive pulmonary disease and cystic fibrosis. Here we report the discovery of IMP-1088, a picomolar dual inhibitor of the human N-myristoyltransferases NMT1 and NMT2, and use it to demonstrate that pharmacological inhibition of host-cell N-myristoylation rapidly and completely prevents rhinoviral replication without inducing cytotoxicity. The identification of cooperative binding between weak-binding fragments led to rapid inhibitor optimization through fragment reconstruction, structure-guided fragment linking and conformational control over linker geometry. We show that inhibition of the co-translational myristoylation of a specific virus-encoded protein (VP0) by IMP-1088 potently blocks a key step in viral capsid assembly, to deliver a low nanomolar antiviral activity against multiple RV strains, poliovirus and foot and-mouth disease virus, and protection of cells against virus-induced killing, highlighting the potential of host myristoylation as a drug target in picornaviral infections.


Assuntos
Aciltransferases/antagonistas & inibidores , Antivirais/farmacologia , Capsídeo/efeitos dos fármacos , Inibidores Enzimáticos/farmacologia , Rhinovirus/efeitos dos fármacos , Montagem de Vírus/efeitos dos fármacos , Replicação Viral/efeitos dos fármacos , Antivirais/química , Inibidores Enzimáticos/química , Células HeLa , Humanos , Concentração Inibidora 50 , Estrutura Molecular , Rhinovirus/enzimologia , Rhinovirus/fisiologia
7.
Microbiologyopen ; 6(2)2017 04.
Artigo em Inglês | MEDLINE | ID: mdl-27762083

RESUMO

Rhodococcus equi (R. equi) is an important pulmonary pathogen in foals that often leads to the death of the horse. The bacterium harbors a virulence plasmid that encodes numerous virulence-associated proteins (Vaps) including VapA that is essential for intracellular survival inside macrophages. However, little is known about the precise function of VapA. Here, we demonstrate that VapA causes perturbation to late endocytic organelles with swollen endolysosome organelles having reduced Cathepsin B activity and an accumulation of LBPA, LC3 and Rab7. The data are indicative of a loss of endolysosomal function, which leads cells to upregulate lysosome biogenesis to compensate for the loss of functional endolysosomes. Although there is a high degree of homology of the core region of VapA to other Vap proteins, only the highly conserved core region of VapA, and not VapD of VapG, gives the observed effects on endolysosomes. This is the first demonstration of how VapA works and implies that VapA aids R. equi survival by reducing the impact of lysosomes on phagocytosed bacteria.


Assuntos
Infecções por Actinomycetales/patologia , Proteínas de Bactérias/metabolismo , Broncopneumonia/microbiologia , Catepsina B/metabolismo , Doenças dos Cavalos/patologia , Lisossomos/patologia , Rhodococcus equi/patogenicidade , Infecções por Actinomycetales/microbiologia , Animais , Sequência de Bases , Linhagem Celular Tumoral , Regulação Bacteriana da Expressão Gênica , Células HeLa , Doenças dos Cavalos/microbiologia , Cavalos , Humanos , Lisossomos/microbiologia , Macrófagos/microbiologia , Fagocitose , Ratos , Fatores de Virulência
8.
Biochem Soc Trans ; 43(5): 1011-7, 2015 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-26517916

RESUMO

ATP-binding cassette (ABC) transporters, although being ubiquitous in biology, often feature a subunit that is limited primarily to bacteria and archaea. This subunit, the substrate-binding protein (SBP), is a key determinant of the substrate specificity and high affinity of ABC uptake systems in these organisms. Most prokaryotes have many SBP-dependent ABC transporters that recognize a broad range of ligands from metal ions to amino acids, sugars and peptides. Herein, we review the structure and function of a number of more unusual SBPs, including an ABC transporter involved in the transport of rare furanose forms of sugars and an SBP that has evolved to specifically recognize the bacterial cell wall-derived murein tripeptide (Mtp). Both these examples illustrate that subtle changes in binding-site architecture, including changes in side chains not directly involved in ligand co-ordination, can result in significant alteration of substrate range in novel and unpredictable ways.


Assuntos
Transportadores de Cassetes de Ligação de ATP/metabolismo , Trifosfato de Adenosina/metabolismo , Bactérias/metabolismo , Proteínas de Bactérias/metabolismo , Transportadores de Cassetes de Ligação de ATP/química , Proteínas de Bactérias/química , Sítios de Ligação , Evolução Biológica , Modelos Moleculares , Monossacarídeos/química , Monossacarídeos/metabolismo , Ligação Proteica , Estrutura Terciária de Proteína
9.
Protein Sci ; 24(10): 1660-70, 2015 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-26243007

RESUMO

Penicillin acylases are industrially important enzymes for the production of 6-APA, which is used extensively in the synthesis of secondary antibiotics. The enzyme translates into an inactive single chain precursor that subsequently gets processed by the removal of a spacer peptide connecting the chains of the mature active heterodimer. We have cloned the penicillin G acylase from Kluyvera citrophila (KcPGA) and prepared two mutants by site-directed mutagenesis. Replacement of N-terminal serine of the ß-subunit with cysteine (Serß1Cys) resulted in a fully processed but inactive enzyme. The second mutant in which this serine is replaced by glycine (Serß1Gly) remained in the unprocessed and inactive form. The crystals of both mutants belonged to space group P1 with four molecules in the asymmetric unit. The three-dimensional structures of these mutants were refined at resolutions 2.8 and 2.5 Å, respectively. Comparison of these structures with similar structures of Escherichia coli PGA (EcPGA) revealed various conformational changes that lead to autocatalytic processing and consequent removal of the spacer peptide. The large displacements of residues such as Arg168 and Arg477 toward the N-terminal cleavage site of the spacer peptide or the conformational changes of Arg145 and Phe146 near the active site in these structures suggested probable steps in the processing dynamics. A comparison between the structures of the processed Serß1Cys mutant and that of the processed form of EcPGA showed conformational differences in residues Argα145, Pheα146, and Pheß24 at the substrate binding pocket. Three conformational transitions of Argα145 and Pheα146 residues were seen when processed and unprocessed forms of KcPGA were compared with the substrate bound structure of EcPGA. Structure mediation in activity difference between KcPGA and EcPGA toward acyl homoserine lactone (AHL) is elucidated.


Assuntos
Kluyvera/enzimologia , Kluyvera/genética , Penicilina Amidase/química , Penicilina Amidase/metabolismo , Processamento de Proteína Pós-Traducional , Sítios de Ligação , Cristalografia por Raios X , Kluyvera/química , Conformação Molecular , Mutagênese Sítio-Dirigida , Mutação , Penicilina Amidase/genética , Ligação Proteica , Percepção de Quorum , Relação Estrutura-Atividade , Especificidade por Substrato
10.
Anal Biochem ; 421(1): 342-4, 2012 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-22051857

RESUMO

N-myristoylation is the irreversible attachment of a C(14) fatty acid, myristic acid, to the N-terminal glycine of a protein via formation of an amide bond. This modification is catalyzed by myristoyl-coenzyme A (CoA):protein N-myristoyltransferase (NMT), an enzyme ubiquitous in eukaryotes that is up-regulated in several cancers. Here we report a sensitive fluorescence-based assay to study the enzymatic activity of human NMT1 and NMT2 based on detection of CoA by 7-diethylamino-3-(4-maleimido-phenyl)-4-methylcoumarin. We also describe expression and characterization of NMT1 and NMT2 and assay validation with small molecule inhibitors. This assay should be broadly applicable to NMTs from a range of organisms.


Assuntos
Aciltransferases/análise , Aciltransferases/antagonistas & inibidores , Aciltransferases/genética , Aciltransferases/metabolismo , Coenzima A , Cumarínicos , Fluorescência , Corantes Fluorescentes , Humanos , Cinética , Ácidos Mirísticos/metabolismo , Processamento de Proteína Pós-Traducional
11.
Protein Eng Des Sel ; 23(11): 817-25, 2010 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-20817757

RESUMO

SpoIIE is a dual function protein that plays important roles during sporulation in Bacillus subtilis. It binds to the tubulin-like protein FtsZ causing the cell division septum to relocate from mid-cell to the cell pole, and it dephosphorylates SpoIIAA phosphate leading to establishment of differential gene expression in the two compartments following the asymmetric septation. Its 872 residue polypeptide contains a multiple-membrane spanning sequence at the N-terminus and a PP2C phosphatase domain at the C-terminus. The central segment that binds to FtsZ is unlike domains of known structure or function, moreover the domain boundaries are poorly defined and this has hampered the expression of soluble fragments of SpoIIE at the levels required for structural studies. Here we have screened over 9000 genetic constructs of spoIIE using a random incremental truncation library approach, ESPRIT, to identify a number of soluble C-terminal fragments of SpoIIE that were aligned with the protein sequence to map putative domains and domain boundaries. The expression and purification of three fragments were optimised, yielding multimilligram quantities of the PP2C phosphatase domain, the putative FtsZ-binding domain and a larger fragment encompassing both these domains. All three fragments are monomeric and the PP2C domain-containing fragments have phosphatase activity.


Assuntos
Bacillus subtilis/genética , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Clonagem Molecular/métodos , Bacillus subtilis/química , Bacillus subtilis/metabolismo , Proteínas de Bactérias/isolamento & purificação , Proteínas de Bactérias/metabolismo , Proteínas do Citoesqueleto/metabolismo , Expressão Gênica , Mutagênese , Ligação Proteica , Estrutura Quaternária de Proteína , Estrutura Terciária de Proteína , Solubilidade
12.
Biochem J ; 428(3): 499-509, 2010 May 27.
Artigo em Inglês | MEDLINE | ID: mdl-20353400

RESUMO

Plasmodium falciparum is the causative agent of malaria, a disease where new drug targets are required due to increasing resistance to current anti-malarials. TMPK (thymidylate kinase) is a good candidate as it is essential for the synthesis of dTTP, a critical precursor of DNA and has been much studied due to its role in prodrug activation and as a drug target. Type I TMPKs, such as the human enzyme, phosphorylate the substrate AZT (3'-azido-3'-deoxythymidine)-MP (monophosphate) inefficiently compared with type II TMPKs (e.g. Escherichia coli TMPK). In the present paper we report that eukaryotic PfTMPK (P. falciparum TMPK) presents sequence features of a type I enzyme yet the kinetic parameters for AZT-MP phosphorylation are similar to those of the highly efficient E. coli enzyme. Structural information shows that this is explained by a different juxtaposition of the P-loop and the azide of AZT-MP. Subsequent formation of the transition state requires no further movement of the PfTMPK P-loop, with no steric conflicts for the azide moiety, allowing efficient phosphate transfer. Likewise, we present results that confirm the ability of the enzyme to uniquely accept dGMP as a substrate and shed light on the basis for its wider substrate specificity. Information resulting from two ternary complexes (dTMP-ADP and AZT-MP-ADP) and a binary complex with the transition state analogue AP5dT [P1-(5'-adenosyl)-P5-(5'-thymidyl) pentaphosphate] all reveal significant differences with the human enzyme, notably in the lid region and in the P-loop which may be exploited in the rational design of Plasmodium-specific TMPK inhibitors with therapeutic potential.


Assuntos
Nucleotídeos de Desoxiguanina/metabolismo , Didesoxinucleotídeos/química , Didesoxinucleotídeos/metabolismo , Núcleosídeo-Fosfato Quinase/química , Plasmodium falciparum/enzimologia , Nucleotídeos de Timina/química , Nucleotídeos de Timina/metabolismo , Zidovudina/análogos & derivados , Nucleotídeos de Desoxiguanina/química , Cinética , Núcleosídeo-Fosfato Quinase/metabolismo , Fosforilação , Plasmodium falciparum/metabolismo , Especificidade por Substrato , Zidovudina/química , Zidovudina/metabolismo
13.
Protein Sci ; 19(5): 987-99, 2010 May.
Artigo em Inglês | MEDLINE | ID: mdl-20222013

RESUMO

ATP-dependent proteases are crucial for cellular homeostasis. By degrading short-lived regulatory proteins, they play an important role in the control of many cellular pathways and, through the degradation of abnormally misfolded proteins, protect the cell from a buildup of aggregates. Disruption or disregulation of mammalian mitochondrial Lon protease leads to severe changes in the cell, linked with carcinogenesis, apoptosis, and necrosis. Here we present the structure of the proteolytic domain of human mitochondrial Lon at 2 A resolution. The fold resembles those of the three previously determined Lon proteolytic domains from Escherichia coli, Methanococcus jannaschii, and Archaeoglobus fulgidus. There are six protomers in the asymmetric unit, four arranged as two dimers. The intersubunit interactions within the two dimers are similar to those between adjacent subunits of the hexameric ring of E. coli Lon, suggesting that the human Lon proteolytic domain also forms hexamers. The active site contains a 3(10) helix attached to the N-terminal end of alpha-helix 2, which leads to the insertion of Asp852 into the active site, as seen in M. jannaschii. Structural considerations make it likely that this conformation is proteolytically inactive. When comparing the intersubunit interactions of human with those of E. coli Lon taken with biochemical data leads us to propose a mechanism relating the formation of Lon oligomers with a conformational shift in the active site region coupled to a movement of a loop in the oligomer interface, converting the proteolytically inactive form seen here to the active one in the E. coli hexamer.


Assuntos
Protease La/química , Protease La/metabolismo , Sequência de Aminoácidos , Domínio Catalítico , Cristalografia por Raios X , Humanos , Modelos Moleculares , Dados de Sequência Molecular , Protease La/genética , Conformação Proteica , Multimerização Proteica , Subunidades Proteicas , Alinhamento de Sequência
14.
Protein Sci ; 18(12): 2578-91, 2009 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-19827093

RESUMO

Malaria, caused by Plasmodium falciparum and related parasites, is responsible for millions of deaths each year, mainly from complications arising from the blood stages of its life cycle. Macrophage migration inhibitory factor (MIF), a protein expressed by the parasite during these stages, has been characterized in mammals as a cytokine involved in a broad spectrum of immune responses. It also possesses two catalytic activities, a tautomerase and an oxidoreductase, though the physiological significance of neither reaction is known. Here, we have determined the crystal structure of MIF from two malaria parasites, Plasmodium falciparum and Plasmodium berghei at 2.2 A and 1.8 A, respectively. The structures have an alpha/beta fold and each reveals a trimer, in agreement with the results of analytical ultracentrifugation. We observed open and closed active sites, these being distinguished by movements of proline-1, the catalytic base in the tautomerase reaction. These states correlate with the covalent modification of cysteine 2 to form a mercaptoethanol adduct, an observation confirmed by mass spectrometry. The Plasmodium MIFs have a different pattern of conserved cysteine residues to the mammalian MIFs and the side chain of Cys58, which is implicated in the oxidoreductase activity, is buried. This observation and the evident redox reactivity of Cys2 suggest quite different oxidoreductase characteristics. Finally, we show in pull-down assays that Plasmodium MIF binds to the cell surface receptor CD74, a known mammalian MIF receptor implying that parasite MIF has the ability to interfere with, or modulate, host MIF activity through a competitive binding mechanism.


Assuntos
Cristalografia por Raios X , Fatores Inibidores da Migração de Macrófagos/química , Malária/parasitologia , Plasmodium berghei/química , Plasmodium falciparum/química , Sequência de Aminoácidos , Animais , Domínio Catalítico , Expressão Gênica , Humanos , Fatores Inibidores da Migração de Macrófagos/genética , Modelos Moleculares , Dados de Sequência Molecular , Conformação Proteica , Multimerização Proteica , Alinhamento de Sequência , Ultracentrifugação
15.
J Mol Biol ; 390(5): 1007-18, 2009 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-19500589

RESUMO

The GAF domain is a simple module widespread in proteins of diverse function, including cell signalling proteins and transcription factors. Its structure, typically spanning 150 residues, has three tiers: a basal layer of two or more alpha-helices, a middle layer of beta-pleated sheet and a top layer formed by segments of the polypeptide that connect strands of the beta-sheet. In structures of GAF domains in complex with their effectors, these polypeptide segments envelop the ligand, enclosing it in a cavity whose base is formed by the beta-sheet, such that ligand binding and release must be accompanied by conformational rearrangements of the distal portion of the structure. Descriptions of binding are presently limited by the absence of a GAF domain for which both liganded and unliganded structures are known. Earlier, we solved the crystal structure of the GAF domain of CodY, a branched-chain amino acid and GTP-responsive regulator of the transcription of stationary-phase and virulence genes in Bacillus, in complexes with isoleucine and valine. Here, we report the structure of this domain in its unliganded form, allowing definition of the structural changes accompanying ligand binding. The core of the protein and its dimerisation interface are essentially unchanged, in agreement with circular dichroism spectroscopy experiments that show that the secondary structure composition is unperturbed by ligand binding. There is however extensive refolding of the binding site loops, with up to 15-A movements of the coiled segment linking beta3 and beta4, such that the binding pocket is not formed in the absence of the ligand. The implications of these structural rearrangements for ligand affinity and specificity are discussed. Finally, saturation-transfer-difference NMR spectroscopy showed binding of isoleucine but not that of GTP to the GAF domain, suggesting that the two cofactors do not have a common binding site.


Assuntos
Bacillus subtilis/química , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Cristalografia por Raios X , Guanosina Trifosfato/metabolismo , Ligantes , Modelos Moleculares , Ligação Proteica , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Análise Espectral , Relação Estrutura-Atividade
16.
Mol Microbiol ; 68(5): 1315-27, 2008 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-18430139

RESUMO

The fluid mosaic model of membrane structure has been revised in recent years as it has become evident that domains of different lipid composition are present in eukaryotic and prokaryotic cells. Using membrane binding fluorescent dyes, we demonstrate the presence of lipid spirals extending along the long axis of cells of the rod-shaped bacterium Bacillus subtilis. These spiral structures are absent from cells in which the synthesis of phosphatidylglycerol is disrupted, suggesting an enrichment in anionic phospholipids. Green fluorescent protein fusions of the cell division protein MinD also form spiral structures and these were shown by fluorescence resonance energy transfer to be coincident with the lipid spirals. These data indicate a higher level of membrane lipid organization than previously observed and a primary role for lipid spirals in determining the site of cell division in bacterial cells.


Assuntos
Bacillus subtilis/fisiologia , Divisão Celular/fisiologia , Lipídeos/fisiologia , Adenosina Trifosfatases/química , Adenosina Trifosfatases/metabolismo , Bacillus subtilis/química , Membrana Celular/química , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Corantes Fluorescentes , Proteínas de Fluorescência Verde/análise , Proteínas de Fluorescência Verde/genética , Lipídeos/química , Proteínas Luminescentes/genética , Fosfatidilgliceróis
17.
J Mol Biol ; 364(3): 309-22, 2006 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-17010379

RESUMO

Cbl is a member of the large family of LysR-type transcriptional regulators (LTTRs) common in bacteria and found also in Archaea and algal chloroplasts. The function of Cbl is required in Escherichia coli for expression of sulphate starvation-inducible (ssi) genes, associated with the biosynthesis of cysteine from organic sulphur sources (sulphonates). Here, we report the crystal structure of the cofactor-binding domain of Cbl (c-Cbl) from E. coli. The overall fold of c-Cbl is very similar to the regulatory domain (RD) of another LysR family member, CysB. The RD is composed of two subdomains enclosing a cavity, which is expected to bind effector molecules. We have constructed and analysed several full-length Cbl variants bearing single residue substitutions in the RD that affect cofactor responses. Using in vivo and in vitro transcription assays, we demonstrate that pssuE, a Cbl responsive promoter, is down-regulated not only by the cofactor, adenosine phosphosulphate (APS), but also by thiosulphate, and, that the same RD determinants are important for the response to both cofactors. We also demonstrate the effects of selected site-directed mutations on Cbl oligomerization and discuss these in the context of the structure. Based on the crystal structure and molecular modelling, we propose a model for the interaction of Cbl with adenosine phosphosulphate.


Assuntos
Adenosina Fosfossulfato/química , Proteínas de Escherichia coli/química , Escherichia coli/metabolismo , Modelos Moleculares , Tiossulfatos/química , Fatores de Transcrição/química , Sítios de Ligação , Cristalografia por Raios X , Regulação para Baixo , Proteínas de Escherichia coli/genética , Mutação , Regiões Promotoras Genéticas , Ligação Proteica , Estrutura Secundária de Proteína , Fatores de Transcrição/genética
18.
J Biol Chem ; 281(31): 22212-22222, 2006 Aug 04.
Artigo em Inglês | MEDLINE | ID: mdl-16702222

RESUMO

Extracytoplasmic solute receptors (ESRs) are important components of solute uptake systems in bacteria, having been studied extensively as parts of ATP binding cassette transporters. Herein we report the first crystal structure of an ESR protein from a functionally characterized electrochemical ion gradient dependent secondary transporter. This protein, SiaP, forms part of a tripartite ATP-independent periplasmic transporter specific for sialic acid in Haemophilus influenzae. Surprisingly, the structure reveals an overall topology similar to ATP binding cassette ESR proteins, which is not apparent from the sequence, demonstrating that primary and secondary transporters can share a common structural component. The structure of SiaP in the presence of the sialic acid analogue 2,3-didehydro-2-deoxy-N-acetylneuraminic acid reveals the ligand bound in a deep cavity with its carboxylate group forming a salt bridge with a highly conserved Arg residue. Sialic acid binding, which obeys simple bimolecular association kinetics as determined by stopped-flow fluorescence spectroscopy, is accompanied by domain closure about a hinge region and the kinking of an alpha-helix hinge component. The structure provides insight into the evolution, mechanism, and substrate specificity of ESR-dependent secondary transporters that are widespread in prokaryotes.


Assuntos
Haemophilus influenzae/química , Proteínas de Membrana Transportadoras/química , Ácido N-Acetilneuramínico/química , Transportadores de Ânions Orgânicos/química , Simportadores/química , Fatores de Virulência/química , Transportadores de Cassetes de Ligação de ATP/química , Sequência de Aminoácidos , Sítios de Ligação , Cristalização , Cristalografia por Raios X , Cinética , Ácido N-Acetilneuramínico/análogos & derivados , Conformação Proteica , Alinhamento de Sequência , Especificidade por Substrato
19.
Trends Cell Biol ; 16(5): 229-33, 2006 May.
Artigo em Inglês | MEDLINE | ID: mdl-16581249

RESUMO

Gankyrin is a new oncoprotein with potent cell cycle and apoptotic properties that is overexpressed early in hepatocarcinogenesis and in hepatocellular carcinomas. Gankyrin regulates the phosphorylation of the retinoblastoma protein (pRb) by CDK4 and enhances the ubiquitylation of p53 by the RING ubiquitin ligase MDM2. Purified preparations of the 26S proteasome contain gankyrin, which specifically interacts with the S6b (Rpt3) ATPase of the 19S regulator. In conclusion, gankyrin is a small versatile cell cycle regulator that illustrates the essential interplay between the ubiquitin proteasome system and gene expression in the cell. Here, we discuss the activities of gankyrin and present a model for its function in the regulation of pRb and p53.


Assuntos
Complexo de Endopeptidases do Proteassoma/metabolismo , Proteínas Proto-Oncogênicas/metabolismo , Proteína do Retinoblastoma/metabolismo , Proteína Supressora de Tumor p53/metabolismo , Animais , Anquirinas/metabolismo , Humanos , Fosforilação , Complexo de Endopeptidases do Proteassoma/genética , Proteínas Proto-Oncogênicas/genética , Ubiquitina/metabolismo
20.
Mol Microbiol ; 57(1): 143-55, 2005 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-15948956

RESUMO

Campylobacter jejuni is a Gram-negative food-borne pathogen associated with gastroenteritis in humans as well as cases of the autoimmune disease Guillain-Barré syndrome. C. jejuni is asaccharolytic because it lacks an active glycolytic pathway for the use of sugars as a carbon source. This suggests an increased reliance on amino acids as nutrients and indeed the genome sequence of this organism indicates the presence of a number of amino acid uptake systems. Cj0982, also known as CjaA, is a putative extracytoplasmic solute receptor for one such uptake system as well as a major surface antigen and vaccine candidate. The crystal structure of Cj0982 reveals a two-domain protein with density in the enclosed cavity between the domains that clearly defines the presence of a bound cysteine ligand. Fluorescence titration experiments were used to demonstrate that Cj0982 binds cysteine tightly and specifically with a K(d) of approximately 10(-7) M consistent with a role as a receptor for a high-affinity transporter. These data imply that Cj0982 is the binding protein component of an ABC-type cysteine transporter system and that cysteine uptake is important in the physiology of C. jejuni.


Assuntos
Transportadores de Cassetes de Ligação de ATP/química , Transportadores de Cassetes de Ligação de ATP/metabolismo , Sistemas de Transporte de Aminoácidos Neutros/química , Sistemas de Transporte de Aminoácidos Neutros/metabolismo , Campylobacter jejuni/química , Cisteína/metabolismo , Transportadores de Cassetes de Ligação de ATP/genética , Transportadores de Cassetes de Ligação de ATP/isolamento & purificação , Sequência de Aminoácidos , Sistemas de Transporte de Aminoácidos Neutros/genética , Sistemas de Transporte de Aminoácidos Neutros/isolamento & purificação , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Sequência de Bases , Sítios de Ligação , Proteínas de Transporte/química , Proteínas de Transporte/metabolismo , Cristalografia por Raios X , Cisteína/química , Citoplasma/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Conformação Proteica , Estrutura Terciária de Proteína , Homologia de Sequência de Aminoácidos , Espectrometria de Fluorescência , Tirosina/química , Tirosina/metabolismo
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