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1.
Proteins ; 92(6): 693-704, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38179877

RESUMEN

Human acyl protein thioesterases (APTs) catalyze the depalmitoylation of S-acylated proteins attached to the plasma membrane, facilitating reversible cycles of membrane anchoring and detachment. We previously showed that a bacterial APT homologue, FTT258 from the gram-negative pathogen Francisella tularensis, exists in equilibrium between a closed and open state based on the structural dynamics of a flexible loop overlapping its active site. Although the structural dynamics of this loop are not conserved in human APTs, the amino acid sequence of this loop is highly conserved, indicating essential but divergent functions for this loop in human APTs. Herein, we investigated the role of this loop in regulating the catalytic activity, ligand binding, and protein folding of human APT1, a depalmitoylase connected with cancer, immune, and neurological signaling. Using a combination of substitutional analysis with kinetic, structural, and biophysical characterization, we show that even in its divergent structural location in human APT1 that this loop still regulates the catalytic activity of APT1 through contributions to ligand binding and substrate positioning. We confirmed previously known roles for multiple residues (Phe72 and Ile74) in substrate binding and catalysis while adding new roles in substrate selectivity (Pro69), in catalytic stabilization (Asp73 and Ile75), and in transitioning between the membrane binding ß-tongue and substrate-binding loops (Trp71). Even conservative substitution of this tryptophan (Trp71) fulcrum led to complete loss of catalytic activity, a 13°C decrease in total protein stability, and drastic drops in ligand affinity, indicating that the combination of the size, shape, and aromaticity of Trp71 are essential to the proper structure of APT1. Mixing buried hydrophobic surface area with contributions to an exposed secondary surface pocket, Trp71 represents a previously unidentified class of essential tryptophans within α/ß hydrolase structure and a potential allosteric binding site within human APTs.


Asunto(s)
Dominio Catalítico , Unión Proteica , Pliegue de Proteína , Tioléster Hidrolasas , Humanos , Tioléster Hidrolasas/química , Tioléster Hidrolasas/metabolismo , Tioléster Hidrolasas/genética , Ligandos , Modelos Moleculares , Secuencia de Aminoácidos , Cinética , Secuencia Conservada , Estabilidad de Enzimas , Francisella tularensis/enzimología , Francisella tularensis/metabolismo , Francisella tularensis/química , Cristalografía por Rayos X , Especificidad por Sustrato
2.
J Biol Chem ; 293(36): 13851-13862, 2018 09 07.
Artículo en Inglés | MEDLINE | ID: mdl-30006352

RESUMEN

Cellular esterases catalyze many essential biological functions by performing hydrolysis reactions on diverse substrates. The promiscuity of esterases complicates assignment of their substrate preferences and biological functions. To identify universal factors controlling esterase substrate recognition, we designed a 32-member structure-activity relationship (SAR) library of fluorogenic ester substrates and used this library to systematically interrogate esterase preference for chain length, branching patterns, and polarity to differentiate common classes of esterase substrates. Two structurally homologous bacterial esterases were screened against this library, refining their previously broad overlapping substrate specificity. Vibrio cholerae esterase ybfF displayed a preference for γ-position thioethers and ethers, whereas Rv0045c from Mycobacterium tuberculosis displayed a preference for branched substrates with and without thioethers. We determined that this substrate differentiation was partially controlled by individual substrate selectivity residues Tyr-119 in ybfF and His-187 in Rv0045c; reciprocal substitution of these residues shifted each esterase's substrate preference. This work demonstrates that the selectivity of esterases is tuned based on transition state stabilization, identifies thioethers as an underutilized functional group for esterase substrates, and provides a rapid method for differentiating structural isozymes. This SAR library could have multifaceted future applications, including in vivo imaging, biocatalyst screening, molecular fingerprinting, and inhibitor design.


Asunto(s)
Proteínas Bacterianas/genética , Esterasas/química , Mycobacterium tuberculosis/enzimología , Bibliotecas de Moléculas Pequeñas/química , Vibrio cholerae/enzimología , Ésteres/química , Colorantes Fluorescentes/química , Relación Estructura-Actividad , Especificidad por Sustrato , Sulfuros
3.
Drug Dev Res ; 80(1): 33-47, 2019 02.
Artículo en Inglés | MEDLINE | ID: mdl-30302779

RESUMEN

The rise of antibiotic resistance necessitates the search for new platforms for drug development. Prodrugs are common tools for overcoming drawbacks typically associated with drug formulation and delivery, with ester prodrugs providing a classic strategy for masking polar alcohol and carboxylic acid functionalities and improving cell permeability. Ester prodrugs are normally designed to have simple ester groups, as they are expected to be cleaved and reactivated by a wide spectrum of cellular esterases. However, a number of pathogenic and commensal microbial esterases have been found to possess significant substrate specificity and can play an unexpected role in drug metabolism. Ester protection can also introduce antimicrobial properties into previously nontoxic drugs through alterations in cell permeability or solubility. Finally, mutation to microbial esterases is a novel mechanism for the development of antibiotic resistance. In this review, we highlight the important pathogenic and xenobiotic functions of microbial esterases and discuss the development and application of ester prodrugs for targeting microbial infections and combating antibiotic resistance. Esterases are often overlooked as therapeutic targets. Yet, with the growing need to develop new antibiotics, a thorough understanding of the specificity and function of microbial esterases and their combined action with ester prodrug antibiotics will support the design of future therapeutics.


Asunto(s)
Antibacterianos/administración & dosificación , Farmacorresistencia Microbiana/efectos de los fármacos , Esterasas/antagonistas & inhibidores , Profármacos/administración & dosificación , Animales , Antibacterianos/metabolismo , Farmacorresistencia Microbiana/fisiología , Esterasas/química , Esterasas/metabolismo , Ésteres/administración & dosificación , Ésteres/química , Ésteres/metabolismo , Humanos , Profármacos/metabolismo , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína
4.
Biochim Biophys Acta Proteins Proteom ; 1866(9): 925-932, 2018 09.
Artículo en Inglés | MEDLINE | ID: mdl-29857162

RESUMEN

The bacterial acyl protein thioesterase (APT) homologue FTT258 from the gram-negative pathogen Francisella tularensis exists in equilibrium between a closed and open state. Interconversion between these two states is dependent on structural rearrangement of a dynamic loop overlapping its active site. The dynamics and structural properties of this loop provide a simple model for how the catalytic activity of FTT258 could be spatiotemporally regulated within the cell. Herein, we characterized the dual roles of this dynamic loop in controlling its catalytic and membrane binding activity. Using a comprehensive library of loop variants, we determined the relative importance of each residue in the loop to these two biological functions. For the catalytic activity, a centrally located tryptophan residue (Trp66) was essential, with the resulting alanine variant showing complete ablation of enzyme activity. Detailed analysis of Trp66 showed that its hydrophobicity in combination with spatial arrangement defined its essential role in catalysis. Substitution of other loop residues congregated along the N-terminal side of the loop also significantly impacted catalytic activity, indicating a critical role for this loop in controlling catalytic activity. For membrane binding, the centrally located hydrophobic residues played a surprising minor role in membrane binding. Instead general electrostatic interactions regulated membrane binding with positively charged residues bracketing the dynamic loop controlling membrane binding. Overall for FTT258, this dynamic loop dually controlled its biological activities through distinct residues within the loop and this regulation provides a new model for the spatiotemporal control over FTT258 and potentially homologous APT function.


Asunto(s)
Proteínas Bacterianas/fisiología , Francisella tularensis/metabolismo , Hidrolasas/fisiología , Proteínas Bacterianas/química , Catálisis , Dominio Catalítico , Hidrolasas/química , Modelos Biológicos , Modelos Moleculares , Mutagénesis Sitio-Dirigida , Estructura Terciaria de Proteína , Triptófano/química , Triptófano/metabolismo
5.
Chembiochem ; 18(18): 1807-1813, 2017 09 19.
Artículo en Inglés | MEDLINE | ID: mdl-28703362

RESUMEN

Protein expression and localization are often studied in vivo by tagging molecules with green fluorescent protein (GFP), yet subtle changes in protein levels are not easily detected. To develop a sensitive in vivo method to amplify fluorescence signals and allow cell-specific quantification of protein abundance changes, we sought to apply an enzyme-activated cellular fluorescence system in vivo by delivering ester-masked fluorophores to Caenorhabditis elegans neurons expressing porcine liver esterase (PLE). To aid uptake into sensory neuron membranes, we synthesized two novel fluorogenic hydrolase substrates with long hydrocarbon tails. Recombinant PLE activated these fluorophores in vitro. In vivo activation occurred in sensory neurons, along with potent activation in intestinal lysosomes quantifiable by imaging and microplate and partially attributable to gut esterase 1 (GES-1) activity. These data demonstrate the promise of biorthogonal hydrolases and their fluorogenic substrates as in vivo neuronal imaging tools and for characterizing endogenous C. elegans hydrolase substrate specificities.


Asunto(s)
Caenorhabditis elegans/metabolismo , Esterasas/metabolismo , Colorantes Fluorescentes/metabolismo , Animales , Medios de Contraste/química , Medios de Contraste/metabolismo , Esterasas/genética , Colorantes Fluorescentes/química , Microscopía Fluorescente , Neuronas/metabolismo , ARN Mensajero/metabolismo , Especificidad por Sustrato , Porcinos
6.
Bioorg Med Chem Lett ; 27(19): 4544-4547, 2017 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-28882482

RESUMEN

M. tuberculosis contains an unusually high number of serine hydrolases by proteome percentage compared to other common bacteria or humans. This letter describes a method to probe the global substrate specificity of mycobacterial serine hydrolases with ester-protected prodrugs of ethambutol, a first-line antibiotic treatment for TB. These compounds were synthesized directly from ethambutol using a selective o-acylation to yield products in high yield and purity with minimal workup. A library of derivatives was screened against M. smegmatis, a non-infectious model for M. tuberculosis, which displayed significantly lowered biological activity compared to ethambutol. Incubation with a general serine hydrolase reactivated each derivative to near-ethambutol levels, demonstrating that esterification of ethambutol should provide a simple screen for mycobacterial hydrolase activity.


Asunto(s)
Antibacterianos/farmacología , Inhibidores Enzimáticos/farmacología , Ésteres/farmacología , Etambutol/farmacología , Hidrolasas/antagonistas & inhibidores , Profármacos/farmacología , Antibacterianos/síntesis química , Antibacterianos/química , Relación Dosis-Respuesta a Droga , Evaluación Preclínica de Medicamentos , Inhibidores Enzimáticos/síntesis química , Inhibidores Enzimáticos/química , Ésteres/síntesis química , Ésteres/química , Etambutol/síntesis química , Etambutol/química , Hidrolasas/metabolismo , Pruebas de Sensibilidad Microbiana , Estructura Molecular , Mycobacterium smegmatis/efectos de los fármacos , Mycobacterium smegmatis/metabolismo , Mycobacterium tuberculosis/efectos de los fármacos , Mycobacterium tuberculosis/metabolismo , Profármacos/síntesis química , Profármacos/química , Relación Estructura-Actividad
7.
Biochemistry ; 55(51): 7099-7111, 2016 Dec 27.
Artículo en Inglés | MEDLINE | ID: mdl-27936614

RESUMEN

The complex life cycle of Mycobacterium tuberculosis requires diverse energy mobilization and utilization strategies facilitated by a battery of lipid metabolism enzymes. Among lipid metabolism enzymes, the Lip family of mycobacterial serine hydrolases is essential to lipid scavenging, metabolic cycles, and reactivation from dormancy. On the basis of the homologous rescue strategy for mycobacterial drug targets, we have characterized the three-dimensional structure of full length LipW from Mycobacterium marinum, the first structure of a catalytically active Lip family member. LipW contains a deep, expansive substrate-binding pocket with only a narrow, restrictive active site, suggesting tight substrate selectivity for short, unbranched esters. Structural alignment reinforced this strict substrate selectivity of LipW, as the binding pocket of LipW aligned most closely with the bacterial acyl esterase superfamily. Detailed kinetic analysis of two different LipW homologues confirmed this strict substrate selectivity, as each homologue selected for unbranched propionyl ester substrates, irrespective of the alcohol portion of the ester. Using comprehensive substitutional analysis across the binding pocket, the strict substrate selectivity of LipW for propionyl esters was assigned to a narrow funnel in the acyl-binding pocket capped by a key hydrophobic valine residue. The polar, negatively charged alcohol-binding pocket also contributed to substrate orientation and stabilization of rotameric states in the catalytic serine. Together, the structural, enzymatic, and substitutional analyses of LipW provide a connection between the structure and metabolic properties of a Lip family hydrolase that refines its biological function in active and dormant tuberculosis infection.


Asunto(s)
Proteínas Bacterianas/metabolismo , Ésteres/metabolismo , Hidrolasas/metabolismo , Mycobacterium marinum/enzimología , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Biocatálisis , Dominio Catalítico , Cristalografía por Rayos X , Estabilidad de Enzimas , Ésteres/química , Hidrolasas/química , Hidrolasas/genética , Interacciones Hidrofóbicas e Hidrofílicas , Cinética , Modelos Moleculares , Estructura Molecular , Mutación , Mycobacterium marinum/genética , Unión Proteica , Dominios Proteicos , Serina/química , Serina/genética , Serina/metabolismo , Especificidad por Sustrato , Temperatura , Valina/química , Valina/genética , Valina/metabolismo
8.
Biochemistry ; 53(47): 7386-95, 2014 Dec 02.
Artículo en Inglés | MEDLINE | ID: mdl-25354081

RESUMEN

The transition between dormant and active Mycobacterium tuberculosis infection requires reorganization of its lipid metabolism and activation of a battery of serine hydrolase enzymes. Among these serine hydrolases, Rv0045c is a mycobacterial-specific serine hydrolase with limited sequence homology outside mycobacteria but structural homology to divergent bacterial hydrolase families. Herein, we determined the global substrate specificity of Rv0045c against a library of fluorogenic hydrolase substrates, constructed a combined experimental and computational model for its binding pocket, and performed comprehensive substitutional analysis to develop a structural map of its binding pocket. Rv0045c showed strong substrate selectivity toward short, straight chain alkyl esters with the highest activity toward four atom chains. This strong substrate preference was maintained through the combined action of residues in a flexible loop connecting the cap and α/ß hydrolase domains and in residues close to the catalytic triad. Two residues bracketing the substrate-binding pocket (Gly90 and His187) were essential to maintaining the narrow substrate selectivity of Rv0045c toward various acyl ester substituents, as independent conversion of these residues significantly increased its catalytic activity and broadened its substrate specificity. Focused saturation mutagenesis of position 187 implicated this residue, as the differentiation point between the substrate specificity of Rv0045c and the structurally homologous ybfF hydrolase family. Insertion of the analogous tyrosine residue from ybfF hydrolases into Rv0045c increased the catalytic activity of Rv0045 by over 20-fold toward diverse ester substrates. The unique binding pocket structure and selectivity of Rv0045c provide molecular indications of its biological role and evidence for expanded substrate diversity in serine hydrolases from M. tuberculosis.


Asunto(s)
Hidrolasas/metabolismo , Mycobacterium tuberculosis/enzimología , Dominio Catalítico , Hidrolasas/química , Cinética , Modelos Moleculares , Serina , Especificidad por Sustrato
9.
J Biol Chem ; 288(15): 10522-35, 2013 Apr 12.
Artículo en Inglés | MEDLINE | ID: mdl-23430251

RESUMEN

Tularemia is a deadly, febrile disease caused by infection by the gram-negative bacterium, Francisella tularensis. Members of the ubiquitous serine hydrolase protein family are among current targets to treat diverse bacterial infections. Herein we present a structural and functional study of a novel bacterial carboxylesterase (FTT258) from F. tularensis, a homologue of human acyl protein thioesterase (hAPT1). The structure of FTT258 has been determined in multiple forms, and unexpectedly large conformational changes of a peripheral flexible loop occur in the presence of a mechanistic cyclobutanone ligand. The concomitant changes in this hydrophobic loop and the newly exposed hydrophobic substrate binding pocket suggest that the observed structural changes are essential to the biological function and catalytic activity of FTT258. Using diverse substrate libraries, site-directed mutagenesis, and liposome binding assays, we determined the importance of these structural changes to the catalytic activity and membrane binding activity of FTT258. Residues within the newly exposed hydrophobic binding pocket and within the peripheral flexible loop proved essential to the hydrolytic activity of FTT258, indicating that structural rearrangement is required for catalytic activity. Both FTT258 and hAPT1 also showed significant association with liposomes designed to mimic bacterial or human membranes, respectively, even though similar structural rearrangements for hAPT1 have not been reported. The necessity for acyl protein thioesterases to have maximal catalytic activity near the membrane surface suggests that these conformational changes in the protein may dually regulate catalytic activity and membrane association in bacterial and human homologues.


Asunto(s)
Proteínas Bacterianas/química , Membrana Celular/enzimología , Francisella tularensis/enzimología , Serina Endopeptidasas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Membrana Celular/genética , Francisella tularensis/genética , Humanos , Mutagénesis Sitio-Dirigida , Serina Endopeptidasas/genética , Serina Endopeptidasas/metabolismo , Homología Estructural de Proteína , Relación Estructura-Actividad , Tioléster Hidrolasas/química , Tioléster Hidrolasas/genética , Tioléster Hidrolasas/metabolismo
10.
Biochim Biophys Acta ; 1824(9): 1024-30, 2012 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-22659119

RESUMEN

Acetyl esterases from carbohydrate esterase family 7 exhibit unusual substrate specificity. These proteins catalyze the cleavage of disparate acetate esters with high efficiency, but are unreactive to larger acyl groups. The structural basis for this distinct selectivity profile is unknown. Here, we investigate a thermostable acetyl esterase (TM0077) from Thermotoga maritima using evolutionary relationships, structural information, fluorescent kinetic measurements, and site directed mutagenesis. We measured the kinetic and structural determinants for this specificity using a diverse series of small molecule enzyme substrates, including novel fluorogenic esters. These experiments identified two hydrophobic plasticity residues (Pro228, and Ile276) surrounding the nucleophilic serine that impart this specificity of TM0077 for small, straight-chain esters. Substitution of these residues with alanine imparts broader specificity to TM0077 for the hydrolysis of longer and bulkier esters. Our results suggest the specificity of acetyl esterases have been finely tuned by evolution to catalyze the removal of acetate groups from diverse substrates, but can be modified by focused amino acid substitutions to yield enzymes capable of cleaving larger ester functionalities.


Asunto(s)
Acetilesterasa/química , Proteínas Bacterianas/química , Thermotoga maritima/enzimología , Acetilesterasa/metabolismo , Proteínas Bacterianas/metabolismo , Sitios de Unión , Catálisis , Ésteres/química , Ésteres/metabolismo , Fluoresceínas/química , Fluoresceínas/metabolismo , Colorantes Fluorescentes , Hidrólisis , Cinética , Modelos Moleculares , Mutagénesis Sitio-Dirigida , Especificidad por Sustrato
11.
Chembiochem ; 14(9): 1134-44, 2013 Jun 17.
Artículo en Inglés | MEDLINE | ID: mdl-23670977

RESUMEN

Serine hydrolases have diverse intracellular substrates, biological functions, and structural plasticity, and are thus important for biocatalyst design. Amongst serine hydrolases, the recently described ybfF enzyme family are promising novel biocatalysts with an unusual bifurcated substrate-binding cleft and the ability to recognize commercially relevant substrates. We characterized in detail the substrate selectivity of a novel ybfF enzyme from Vibrio cholerae (Vc-ybfF) by using a 21-member library of fluorogenic ester substrates. We assigned the roles of the two substrate-binding clefts in controlling the substrate selectivity and folded stability of Vc-ybfF by comprehensive substitution analysis. The overall substrate preference of Vc-ybfF was for short polar chains, but it retained significant activity with a range of cyclic and extended esters. This broad substrate specificity combined with the substitutional analysis demonstrates that the larger binding cleft controls the substrate specificity of Vc-ybfF. Key selectivity residues (Tyr116, Arg120, Tyr209) are also located at the larger binding pocket and control the substrate specificity profile. In the structure of ybfF the narrower binding cleft contains water molecules prepositioned for hydrolysis, but based on substitution this cleft showed only minimal contribution to catalysis. Instead, the residues surrounding the narrow binding cleft and at the entrance to the binding pocket contributed significantly to the folded stability of Vc-ybfF. The relative contributions of each cleft of the binding pocket to the catalytic activity and folded stability of Vc-ybfF provide a valuable map for designing future biocatalysts based on the ybfF scaffold.


Asunto(s)
Proteínas Bacterianas/química , Esterasas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Sitios de Unión , Biocatálisis , Dominio Catalítico , Esterasas/genética , Esterasas/metabolismo , Cinética , Simulación del Acoplamiento Molecular , Mutagénesis Sitio-Dirigida , Estabilidad Proteica , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Especificidad por Sustrato , Temperatura , Vibrio cholerae/enzimología
12.
ACS Omega ; 8(14): 13252-13264, 2023 Apr 11.
Artículo en Inglés | MEDLINE | ID: mdl-37065048

RESUMEN

Mycobacterium tuberculosis has a complex life cycle transitioning between active and dormant growth states depending on environmental conditions. LipN (Rv2970c) is a conserved mycobacterial serine hydrolase with regulated catalytic activity at the interface between active and dormant growth conditions. LipN also catalyzes the xenobiotic degradation of a tertiary ester substrate and contains multiple conserved motifs connected with the ability to catalyze the hydrolysis of difficult tertiary ester substrates. Herein, we expanded a library of fluorogenic ester substrates to include more tertiary and constrained esters and screened 33 fluorogenic substrates for activation by LipN, identifying its unique substrate signature. LipN preferred short, unbranched ester substrates, but had its second highest activity against a heteroaromatic five-membered oxazole ester. Oxazole esters are present in multiple mycobacterial serine hydrolase inhibitors but have not been tested widely as ester substrates. Combined structural modeling, kinetic measurements, and substitutional analysis of LipN showcased a fairly rigid binding pocket preorganized for catalysis of short ester substrates. Substitution of diverse amino acids across the binding pocket significantly impacted the folded stability and catalytic activity of LipN with two conserved motifs (HGGGW and GDSAG) playing interconnected, multidimensional roles in regulating its substrate specificity. Together this detailed substrate specificity profile of LipN illustrates the complex interplay between structure and function in mycobacterial hormone-sensitive lipase homologues and indicates oxazole esters as promising inhibitor and substrate scaffolds for mycobacterial hydrolases.

13.
Biochem Mol Biol Educ ; 49(5): 707-719, 2021 09.
Artículo en Inglés | MEDLINE | ID: mdl-34080750

RESUMEN

Proteopedia (proteopedia.org) is an open resource to explore the structure-function relationship of proteins and other biomolecules. This guide provides practical advice on how to incorporate Proteopedia into teaching the structure and function of proteins and other biomolecules. For 11 activities, we discuss desired outcomes, setting expectations, preparing students for the tasks, using resources within Proteopedia, and evaluating student work. We point out features of Proteopedia that make it especially suitable for teaching and give examples of how to avoid common pitfalls.


Asunto(s)
Proteínas , Estudiantes , Humanos , Enseñanza
14.
Protein Sci ; 30(8): 1554-1565, 2021 08.
Artículo en Inglés | MEDLINE | ID: mdl-33914998

RESUMEN

Mycobacterium tuberculosis virulence is highly metal-dependent with metal availability modulating the shift from the dormant to active states of M. tuberculosis infection. Rv0045c from M. tuberculosis is a proposed metabolic serine hydrolase whose folded stability is dependent on divalent metal concentration. Herein, we measured the divalent metal inhibition profile of the enzymatic activity of Rv0045c and found specific divalent transition metal cations (Cu2+ ≥ Zn2+ > Ni2+ > Co2+ ) strongly inhibited its enzymatic activity. The metal cations bind allosterically, largely affecting values for kcat rather than KM . Removal of the artificial N-terminal 6xHis-tag did not change the metal-dependent inhibition, indicating that the allosteric inhibition site is native to Rv0045c. To isolate the site of this allosteric regulation in Rv0045c, the structures of Rv0045c were determined at 1.8 Å and 2.0 Å resolution in the presence and absence of Zn2+ with each structure containing a previously unresolved dynamic loop spanning the binding pocket. Through the combination of structural analysis with and without zinc and targeted mutagenesis, this metal-dependent inhibition was traced to multiple chelating residues (H202A/E204A) on a flexible loop, suggesting dynamic allosteric regulation of Rv0045c by divalent metals. Although serine hydrolases like Rv0045c are a large and diverse enzyme superfamily, this is the first structural confirmation of allosteric regulation of their enzymatic activity by divalent metals.


Asunto(s)
Proteínas Bacterianas , Inhibidores Enzimáticos/química , Esterasas , Metales Pesados/química , Mycobacterium tuberculosis , Regulación Alostérica , Proteínas Bacterianas/antagonistas & inhibidores , Proteínas Bacterianas/metabolismo , Cationes/química , Esterasas/antagonistas & inhibidores , Esterasas/metabolismo , Modelos Moleculares , Mycobacterium tuberculosis/enzimología , Mycobacterium tuberculosis/genética , Conformación Proteica , Elementos de Transición/química
15.
Elife ; 102021 07 19.
Artículo en Inglés | MEDLINE | ID: mdl-34279224

RESUMEN

Carboxy ester prodrugs are widely employed to increase oral absorption and potency of phosphonate antibiotics. Prodrugging can mask problematic chemical features that prevent cellular uptake and may enable tissue-specific compound delivery. However, many carboxy ester promoieties are rapidly hydrolyzed by serum esterases, limiting their therapeutic potential. While carboxy ester-based prodrug targeting is feasible, it has seen limited use in microbes as microbial esterase-specific promoieties have not been described. Here we identify the bacterial esterases, GloB and FrmB, that activate carboxy ester prodrugs in Staphylococcus aureus. Additionally, we determine the substrate specificities for FrmB and GloB and demonstrate the structural basis of these preferences. Finally, we establish the carboxy ester substrate specificities of human and mouse sera, ultimately identifying several promoieties likely to be serum esterase-resistant and microbially labile. These studies will enable structure-guided design of antistaphylococcal promoieties and expand the range of molecules to target staphylococcal pathogens.


Asunto(s)
Antibacterianos/farmacología , Proteínas Bacterianas/química , Profármacos/farmacología , Staphylococcus/efectos de los fármacos , Animales , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Carboxilesterasa/metabolismo , Esterasas/química , Esterasas/metabolismo , Ésteres/metabolismo , Humanos , Hidrólisis , Ratones , Staphylococcus aureus/efectos de los fármacos , Staphylococcus aureus/genética
16.
PLoS One ; 15(3): e0230166, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32182256

RESUMEN

Over 100 metabolic serine hydrolases are present in humans with confirmed functions in metabolism, immune response, and neurotransmission. Among potentially clinically-relevant but uncharacterized human serine hydrolases is OVCA2, a serine hydrolase that has been linked with a variety of cancer-related processes. Herein, we developed a heterologous expression system for OVCA2 and determined the comprehensive substrate specificity of OVCA2 against two ester substrate libraries. Based on this analysis, OVCA2 was confirmed as a serine hydrolase with a strong preference for long-chain alkyl ester substrates (>10-carbons) and high selectivity against a variety of short, branched, and substituted esters. Substitutional analysis was used to identify the catalytic residues of OVCA2 with a Ser117-His206-Asp179 classic catalytic triad. Comparison of the substrate specificity of OVCA2 to the model homologue FSH1 from Saccharomyces cerevisiae illustrated the tighter substrate selectivity of OVCA2, but their overlapping substrate preference for extended straight-chain alkyl esters. Conformation of the overlapping biochemical properties of OVCA2 and FSH1 was used to model structural information about OVCA2. Together our analysis provides detailed substrate specificity information about a previously, uncharacterized human serine hydrolase and begins to define the biological properties of OVCA2.


Asunto(s)
Proteínas/química , Proteínas de Saccharomyces cerevisiae/química , Serina Proteasas/química , Secuencia de Aminoácidos , Ésteres/metabolismo , Humanos , Modelos Moleculares , Conformación Proteica , Proteínas/metabolismo , Saccharomyces cerevisiae , Homología de Secuencia de Aminoácido , Serina Proteasas/metabolismo , Homología Estructural de Proteína , Especificidad por Sustrato
17.
J Mol Biol ; 368(2): 434-49, 2007 Apr 27.
Artículo en Inglés | MEDLINE | ID: mdl-17350650

RESUMEN

The ribonuclease inhibitor protein (RI) binds to members of the bovine pancreatic ribonuclease (RNase A) superfamily with an affinity in the femtomolar range. Here, we report on structural and energetic aspects of the interaction between human RI (hRI) and human pancreatic ribonuclease (RNase 1). The structure of the crystalline hRI x RNase 1 complex was determined at a resolution of 1.95 A, revealing the formation of 19 intermolecular hydrogen bonds involving 13 residues of RNase 1. In contrast, only nine such hydrogen bonds are apparent in the structure of the complex between porcine RI and RNase A. hRI, which is anionic, also appears to use its horseshoe-shaped structure to engender long-range Coulombic interactions with RNase 1, which is cationic. In accordance with the structural data, the hRI.RNase 1 complex was found to be extremely stable (t(1/2)=81 days; K(d)=2.9 x 10(-16) M). Site-directed mutagenesis experiments enabled the identification of two cationic residues in RNase 1, Arg39 and Arg91, that are especially important for both the formation and stability of the complex, and are thus termed "electrostatic targeting residues". Disturbing the electrostatic attraction between hRI and RNase 1 yielded a variant of RNase 1 that maintained ribonucleolytic activity and conformational stability but had a 2.8 x 10(3)-fold lower association rate for complex formation and 5.9 x 10(9)-fold lower affinity for hRI. This variant of RNase 1, which exhibits the largest decrease in RI affinity of any engineered ribonuclease, is also toxic to human erythroleukemia cells. Together, these results provide new insight into an unusual and important protein-protein interaction, and could expedite the development of human ribonucleases as chemotherapeutic agents.


Asunto(s)
Hormonas Placentarias/metabolismo , Ribonucleasa Pancreática/antagonistas & inhibidores , Secuencia de Aminoácidos , Animales , Bovinos , Muerte Celular , Cristalografía por Rayos X , Estabilidad de Enzimas , Humanos , Enlace de Hidrógeno , Células K562 , Cinética , Modelos Moleculares , Datos de Secuencia Molecular , Proteínas Mutantes/metabolismo , Hormonas Placentarias/química , Unión Proteica , Estructura Secundaria de Proteína , Ribonucleasa Pancreática/química , Ribonucleasa Pancreática/metabolismo , Electricidad Estática , Porcinos
18.
ACS Infect Dis ; 4(6): 904-911, 2018 06 08.
Artículo en Inglés | MEDLINE | ID: mdl-29648787

RESUMEN

Among the proteins required for lipid metabolism in Mycobacterium tuberculosis are a significant number of uncharacterized serine hydrolases, especially lipases and esterases. Using a streamlined synthetic method, a library of immolative fluorogenic ester substrates was expanded to better represent the natural lipidomic diversity of Mycobacterium. This expanded fluorogenic library was then used to rapidly characterize the global structure activity relationship (SAR) of mycobacterial serine hydrolases in M. smegmatis under different growth conditions. Confirmation of fluorogenic substrate activation by mycobacterial serine hydrolases was performed using nonspecific serine hydrolase inhibitors and reinforced the biological significance of the SAR. The hydrolases responsible for the global SAR were then assigned using gel-resolved activity measurements, and these assignments were used to rapidly identify the relative substrate specificity of previously uncharacterized mycobacterial hydrolases. These measurements provide a global SAR of mycobacterial hydrolase activity, a picture of cycling hydrolase activity, and a detailed substrate specificity profile for previously uncharacterized hydrolases.


Asunto(s)
Colorantes Fluorescentes/química , Colorantes Fluorescentes/metabolismo , Mycobacterium/enzimología , Serina Endopeptidasas/química , Serina Endopeptidasas/metabolismo , Análisis por Conglomerados , Ésteres , Hidrólisis , Estructura Molecular , Relación Estructura-Actividad , Especificidad por Sustrato
19.
Protein Sci ; 16(8): 1609-16, 2007 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-17656580

RESUMEN

The burial of nonpolar surface area is known to enhance markedly the conformational stability of proteins. The contribution from the burial of polar surface area is less clear. Here, we report on the tolerance to substitution of Ser75 of bovine pancreatic ribonuclease (RNase A), a residue that has the unusual attributes of being buried, conserved, and polar. To identify variants that retain biological function, we used a genetic selection based on the intrinsic cytotoxicity of ribonucleolytic activity. Cell growth at 30 degrees C, 37 degrees C, and 44 degrees C correlated with residue size, indicating that the primary attribute of Ser75 is its small size. The side-chain hydroxyl group of Ser75 forms a hydrogen bond with a main-chain nitrogen. The conformational stability of the S75A variant, which lacks this hydrogen bond, was diminished by DeltaDeltaG = 2.5 kcal/mol. Threonine, which can reinstate this hydrogen bond, provided a catalytically active RNase A variant at higher temperatures than did some smaller residues (including aspartate), indicating that a secondary attribute of Ser75 is the ability of its uncharged side chain to accept a hydrogen bond. These results provide insight on the imperatives for the conservation of a buried polar residue.


Asunto(s)
Ribonucleasa Pancreática/química , Serina/química , Animales , Secuencia Conservada , Cristalografía por Rayos X , Humanos , Enlace de Hidrógeno , Interacciones Hidrofóbicas e Hidrofílicas , Conformación Proteica , Ribonucleasa Pancreática/genética , Serina/genética , Temperatura , Termodinámica
20.
Biochem Biophys Rep ; 7: 415-422, 2016 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-28955933

RESUMEN

Francisella tularensis is the causative agent of the highly, infectious disease, tularemia. Amongst the genes identified as essential to the virulence of F. tularensis was the proposed serine hydrolase FTT0941c. Herein, we purified FTT0941c to homogeneity and then characterized the folded stability, enzymatic activity, and substrate specificity of FTT0941c. Based on phylogenetic analysis, FTT0941c was classified within a divergent Francisella subbranch of the bacterial hormone sensitive lipase (HSL) superfamily, but with the conserved sequence motifs of a bacterial serine hydrolase. FTT0941c showed broad hydrolase activity against diverse libraries of ester substrates, including significant hydrolytic activity across alkyl ester substrates from 2 to 8 carbons in length. Among a diverse library of fluorogenic substrates, FTT0941c preferred α-cyclohexyl ester substrates, matching with the substrate specificity of structural homologues and the broad open architecture of its modeled binding pocket. By substitutional analysis, FTT0941c was confirmed to have a classic catalytic triad of Ser115, His278, and Asp248 and to remain thermally stable even after substitution. Its overall substrate specificity profile, divergent phylogenetic homology, and preliminary pathway analysis suggested potential biological functions for FTT0941c in diverse metabolic degradation pathways in F. tularensis.

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