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1.
J Cell Biol ; 223(4)2024 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-38323936

RESUMEN

Inosine monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in guanosine triphosphate (GTP) synthesis and assembles into filaments in cells, which desensitizes the enzyme to feedback inhibition and boosts nucleotide production. The vertebrate retina expresses two splice variants IMPDH1(546) and IMPDH1(595). In bovine retinas, residue S477 is preferentially phosphorylated in the dark, but the effects on IMPDH1 activity and regulation are unclear. Here, we generated phosphomimetic mutants to investigate structural and functional consequences of S477 phosphorylation. The S477D mutation resensitized both variants to GTP inhibition but only blocked assembly of IMPDH1(595) filaments. Cryo-EM structures of both variants showed that S477D specifically blocks assembly of a high-activity assembly interface, still allowing assembly of low-activity IMPDH1(546) filaments. Finally, we discovered that S477D exerts a dominant-negative effect in cells, preventing endogenous IMPDH filament assembly. By modulating the structure and higher-order assembly of IMPDH, S477 phosphorylation acts as a mechanism for downregulating retinal GTP synthesis in the dark when nucleotide turnover is decreased.


Asunto(s)
Citoesqueleto , Guanosina Trifosfato , IMP Deshidrogenasa , Retina , Animales , Bovinos , Guanosina Trifosfato/biosíntesis , Nucleótidos , Fosforilación , Retina/enzimología , IMP Deshidrogenasa/metabolismo
2.
Microbiol Spectr ; 11(6): e0281123, 2023 Dec 12.
Artículo en Inglés | MEDLINE | ID: mdl-37909787

RESUMEN

IMPORTANCE: Small proteins containing fewer than 70 amino acids, which were previously disregarded due to computational prediction and biochemical detection challenges, have gained increased attention in the scientific community in recent years. However, the number of functionally characterized small proteins, especially in archaea, is still limited. Here, by using biochemical and genetic approaches, we demonstrate a crucial role of the small protein sP36 in the nitrogen metabolism of M. mazei, which modulates the ammonium transporter AmtB1 according to nitrogen availability. This modulation might represent an ancient archaeal mechanism of AmtB1 inhibition, in contrast to the well-studied uridylylation-dependent regulation in bacteria.


Asunto(s)
Compuestos de Amonio , Proteínas Arqueales , Methanosarcina/genética , Methanosarcina/metabolismo , Proteínas Arqueales/genética , Proteínas Arqueales/metabolismo , Bacterias/metabolismo , Nitrógeno/metabolismo , Compuestos de Amonio/metabolismo
3.
bioRxiv ; 2023 Sep 21.
Artículo en Inglés | MEDLINE | ID: mdl-37790411

RESUMEN

Inosine monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in de novo guanosine triphosphate (GTP) synthesis and is controlled by feedback inhibition and allosteric regulation. IMPDH assembles into micron-scale filaments in cells, which desensitizes the enzyme to feedback inhibition by GTP and boosts nucleotide production. The vertebrate retina expresses two tissue-specific splice variants IMPDH1(546) and IMPDH1(595). IMPDH1(546) filaments adopt high and low activity conformations, while IMPDH1(595) filaments maintain high activity. In bovine retinas, residue S477 is preferentially phosphorylated in the dark, but the effects on IMPDH1 activity and regulation are unclear. Here, we generated phosphomimetic mutants to investigate structural and functional consequences of phosphorylation in IMPDH1 variants. The S477D mutation re-sensitized both variants to GTP inhibition, but only blocked assembly of IMPDH1(595) filaments and not IMPDH1(546) filaments. Cryo-EM structures of both variants showed that S477D specifically blocks assembly of the high activity assembly interface, still allowing assembly of low activity IMPDH1(546) filaments. Finally, we discovered that S477D exerts a dominant-negative effect in cells, preventing endogenous IMPDH filament assembly. By modulating the structure and higher-order assembly of IMPDH, phosphorylation at S477 acts as a mechanism for downregulating retinal GTP synthesis in the dark, when nucleotide turnover is decreased. Like IMPDH1, many other metabolic enzymes dynamically assemble filamentous polymers that allosterically regulate activity. Our work suggests that posttranslational modifications may be yet another layer of regulatory control to finely tune activity by modulating filament assembly in response to changing metabolic demands.

4.
Structure ; 31(12): 1526-1534.e4, 2023 12 07.
Artículo en Inglés | MEDLINE | ID: mdl-37875114

RESUMEN

IMP dehydrogenase and GMP reductase are enzymes from the same protein family with analogous structures and catalytic mechanisms that have gained attention because of their essential roles in nucleotide metabolism and as potential drug targets. This study focusses on GuaB3, a less-explored enzyme within this family. Phylogenetic analysis uncovers GuaB3's independent evolution from other members of the family and it predominantly occurs in Cyanobacteria. Within this group, GuaB3 functions as a unique IMP dehydrogenase, while its counterpart in Actinobacteria has a yet unknown function. Synechocystis sp. PCC6803 GuaB3 structures demonstrate differences in the active site compared to canonical IMP dehydrogenases, despite shared catalytic mechanisms. These findings highlight the essential role of GuaB3 in Cyanobacteria, provide insights into the diversity and evolution of the IMP dehydrogenase protein family, and reveal a distinctive characteristic in nucleotide metabolism, potentially aiding in combating harmful cyanobacterial blooms-a growing concern for humans and wildlife.


Asunto(s)
Cianobacterias , IMP Deshidrogenasa , Humanos , IMP Deshidrogenasa/química , IMP Deshidrogenasa/metabolismo , Filogenia , Catálisis , Nucleótidos/metabolismo , Cianobacterias/genética
5.
Protein Sci ; 31(9): e4399, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-36040265

RESUMEN

Inosine 5'-monophosphate dehydrogenase (IMPDH) is an evolutionarily conserved enzyme that mediates the first committed step in de novo guanine nucleotide biosynthetic pathway. It is an essential enzyme in purine nucleotide biosynthesis that modulates the metabolic flux at the branch point between adenine and guanine nucleotides. IMPDH plays key roles in cell homeostasis, proliferation, and the immune response, and is the cellular target of several drugs that are widely used for antiviral and immunosuppressive chemotherapy. IMPDH enzyme is tightly regulated at multiple levels, from transcriptional control to allosteric modulation, enzyme filamentation, and posttranslational modifications. Herein, we review recent developments in our understanding of the mechanisms of IMPDH regulation, including all layers of allosteric control that fine-tune the enzyme activity.


Asunto(s)
Nucleótidos de Guanina , IMP Deshidrogenasa , Regulación Alostérica , Inhibidores Enzimáticos , IMP Deshidrogenasa/genética , IMP Deshidrogenasa/metabolismo , Inosina Monofosfato
6.
Protein Sci ; 31(5): e4314, 2022 05.
Artículo en Inglés | MEDLINE | ID: mdl-35481629

RESUMEN

IMP dehydrogenase(IMPDH) is an essential enzyme that catalyzes the rate-limiting step in the guanine nucleotide pathway. In eukaryotic cells, GTP binding to the regulatory domain allosterically controls the activity of IMPDH by a mechanism that is fine-tuned by post-translational modifications and enzyme polymerization. Nonetheless, the mechanisms of regulation of IMPDH in bacterial cells remain unclear. Using biochemical, structural, and evolutionary analyses, we demonstrate that, in most bacterial phyla, (p)ppGpp compete with ATP to allosterically modulate IMPDH activity by binding to a, previously unrecognized, conserved high affinity pocket within the regulatory domain. This pocket was lost during the evolution of Proteobacteria, making their IMPDHs insensitive to these alarmones. Instead, most proteobacterial IMPDHs evolved to be directly modulated by the balance between ATP and GTP that compete for the same allosteric binding site. Altogether, we demonstrate that the activity of bacterial IMPDHs is allosterically modulated by a universally conserved nucleotide-controlled conformational switch that has divergently evolved to adapt to the specific particularities of each organism. These results reconcile the reported data on the crosstalk between (p)ppGpp signaling and the guanine nucleotide biosynthetic pathway and reinforce the essential role of IMPDH allosteric regulation on bacterial GTP homeostasis.


Asunto(s)
Nucleótidos de Guanina , IMP Deshidrogenasa , Adenina , Adenosina Trifosfato , Guanosina Pentafosfato , Guanosina Trifosfato/metabolismo , Homeostasis , IMP Deshidrogenasa/genética , IMP Deshidrogenasa/metabolismo , Modelos Moleculares
7.
Nat Struct Mol Biol ; 29(1): 47-58, 2022 01.
Artículo en Inglés | MEDLINE | ID: mdl-35013599

RESUMEN

Inosine-5'-monophosphate dehydrogenase (IMPDH), a key regulatory enzyme in purine nucleotide biosynthesis, dynamically assembles filaments in response to changes in metabolic demand. Humans have two isoforms: IMPDH2 filaments reduce sensitivity to feedback inhibition, while IMPDH1 assembly remains uncharacterized. IMPDH1 plays a unique role in retinal metabolism, and point mutants cause blindness. Here, in a series of cryogenic-electron microscopy structures we show that human IMPDH1 assembles polymorphic filaments with different assembly interfaces in extended and compressed states. Retina-specific splice variants introduce structural elements that reduce sensitivity to GTP inhibition, including stabilization of the extended filament form. Finally, we show that IMPDH1 disease mutations fall into two classes: one disrupts GTP regulation and the other has no effect on GTP regulation or filament assembly. These findings provide a foundation for understanding the role of IMPDH1 in retinal function and disease and demonstrate the diverse mechanisms by which metabolic enzyme filaments are allosterically regulated.


Asunto(s)
IMP Deshidrogenasa/genética , Retina/enzimología , Adenosina Trifosfato/metabolismo , Regulación Alostérica , Sitios de Unión , Dominio Catalítico , Guanosina Trifosfato/metabolismo , Células HEK293 , Humanos , IMP Deshidrogenasa/química , IMP Deshidrogenasa/ultraestructura , Modelos Moleculares , NAD/metabolismo , Enfermedades de la Retina/genética
8.
Front Microbiol ; 12: 740914, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34777288

RESUMEN

We have structurally and functionally characterized Skl and Pal endolysins, the latter being the first endolysin shown to kill effectively Streptococcus pneumoniae, a leading cause of deathly diseases. We have proved that Skl and Pal are cysteine-amidases whose catalytic domains, from CHAP and Amidase_5 families, respectively, share an α3ß6-fold with papain-like topology. Catalytic triads are identified (for the first time in Amidase_5 family), and residues relevant for substrate binding and catalysis inferred from in silico models, including a calcium-binding site accounting for Skl dependence on this cation for activity. Both endolysins contain a choline-binding domain (CBD) with a ß-solenoid fold (homology modeled) and six conserved choline-binding loci whose saturation induced dimerization. Remarkably, Pal and Skl dimers display a common overall architecture, preserved in choline-bound dimers of pneumococcal lysins with other catalytic domains and bond specificities, as disclosed using small angle X-ray scattering (SAXS). Additionally, Skl is proved to be an efficient anti-pneumococcal agent that kills multi-resistant strains and clinical emergent-serotype isolates. Interestingly, Skl and Pal time-courses of pneumococcal lysis were sigmoidal, which might denote a limited access of both endolysins to target bonds at first stages of lysis. Furthermore, their DTT-mediated activation, of relevance for other cysteine-peptidases, cannot be solely ascribed to reversal of catalytic-cysteine oxidation.

9.
Plant Physiol ; 186(1): 285-296, 2021 05 27.
Artículo en Inglés | MEDLINE | ID: mdl-33599267

RESUMEN

Thioredoxin reductases control the redox state of thioredoxins (Trxs)-ubiquitous proteins that regulate a spectrum of enzymes by dithiol-disulfide exchange reactions. In most organisms, Trx is reduced by NADPH via a thioredoxin reductase flavoenzyme (NTR), but in oxygenic photosynthetic organisms, this function can also be performed by an iron-sulfur ferredoxin (Fdx)-dependent thioredoxin reductase (FTR) that links light to metabolic regulation. We have recently found that some cyanobacteria, such as the thylakoid-less Gloeobacter and the ocean-dwelling green oxyphotobacterium Prochlorococcus, lack NTR and FTR but contain a thioredoxin reductase flavoenzyme (formerly tentatively called deeply-rooted thioredoxin reductase or DTR), whose electron donor remained undefined. Here, we demonstrate that Fdx functions in this capacity and report the crystallographic structure of the transient complex between the plant-type Fdx1 and the thioredoxin reductase flavoenzyme from Gloeobacter violaceus. Thereby, our data demonstrate that this cyanobacterial enzyme belongs to the Fdx flavin-thioredoxin reductase (FFTR) family, originally described in the anaerobic bacterium Clostridium pasteurianum. Accordingly, the enzyme hitherto termed DTR is renamed FFTR. Our experiments further show that the redox-sensitive peptide CP12 is modulated in vitro by the FFTR/Trx system, demonstrating that FFTR functionally substitutes for FTR in light-linked enzyme regulation in Gloeobacter. Altogether, we demonstrate the FFTR is spread within the cyanobacteria phylum and propose that, by substituting for FTR, it connects the reduction of target proteins to photosynthesis. Besides, the results indicate that FFTR acquisition constitutes a mechanism of evolutionary adaptation in marine phytoplankton such as Prochlorococcus that live in low-iron environments.


Asunto(s)
Proteínas Bacterianas/metabolismo , Cianobacterias/enzimología , Proteínas Hierro-Azufre/metabolismo , Oxidorreductasas/metabolismo , Proteínas Bacterianas/química , Cianobacterias/química , Proteínas Hierro-Azufre/química , Oxidorreductasas/química
10.
Elife ; 92020 04 07.
Artículo en Inglés | MEDLINE | ID: mdl-32254022

RESUMEN

We report the in vivo regulation of Inosine-5´-monophosphate dehydrogenase 1 (IMPDH1) in the retina. IMPDH1 catalyzes the rate-limiting step in the de novo synthesis of guanine nucleotides, impacting the cellular pools of GMP, GDP and GTP. Guanine nucleotide homeostasis is central to photoreceptor cells, where cGMP is the signal transducing molecule in the light response. Mutations in IMPDH1 lead to inherited blindness. We unveil a light-dependent phosphorylation of retinal IMPDH1 at Thr159/Ser160 in the Bateman domain that desensitizes the enzyme to allosteric inhibition by GDP/GTP. When exposed to bright light, living mice increase the rate of GTP and ATP synthesis in their retinas; concomitant with IMPDH1 aggregate formation at the outer segment layer. Inhibiting IMPDH activity in living mice delays rod mass recovery. We unveil a novel mechanism of regulation of IMPDH1 in vivo, important for understanding GTP homeostasis in the retina and the pathogenesis of adRP10 IMPDH1 mutations.


Asunto(s)
Guanosina Trifosfato/biosíntesis , IMP Deshidrogenasa/genética , Luz , Procesamiento Proteico-Postraduccional , Retina/metabolismo , Retina/efectos de la radiación , Adenosina Trifosfato/biosíntesis , Animales , Fenómenos Bioquímicos , Regulación de la Expresión Génica , Homeostasis , Ratones , Ratones Endogámicos C57BL , Mutación , Fosforilación , Estimulación Luminosa , Células Fotorreceptoras/fisiología
11.
Elife ; 92020 03 10.
Artículo en Inglés | MEDLINE | ID: mdl-32151315

RESUMEN

Microtubules (MTs) are hollow cylinders made of tubulin, a GTPase responsible for essential functions during cell growth and division, and thus, key target for anti-tumor drugs. In MTs, GTP hydrolysis triggers structural changes in the lattice, which are responsible for interaction with regulatory factors. The stabilizing GTP-cap is a hallmark of MTs and the mechanism of the chemical-structural link between the GTP hydrolysis site and the MT lattice is a matter of debate. We have analyzed the structure of tubulin and MTs assembled in the presence of fluoride salts that mimic the GTP-bound and GDP•Pi transition states. Our results challenge current models because tubulin does not change axial length upon GTP hydrolysis. Moreover, analysis of the structure of MTs assembled in the presence of several nucleotide analogues and of taxol allows us to propose that previously described lattice expansion could be a post-hydrolysis stage involved in Pi release.


Asunto(s)
Microtúbulos/química , Modelos Moleculares , Conformación Molecular , Microscopía por Crioelectrón , Guanosina Difosfato/química , Guanosina Difosfato/metabolismo , Guanosina Trifosfato/química , Enlace de Hidrógeno , Microtúbulos/metabolismo , Relación Estructura-Actividad , Tubulina (Proteína)/química , Tubulina (Proteína)/metabolismo
12.
J Biol Chem ; 294(40): 14768-14775, 2019 10 04.
Artículo en Inglés | MEDLINE | ID: mdl-31416831

RESUMEN

IMP dehydrogenase (IMPDH) is an essential enzyme that catalyzes the rate-limiting step in the de novo guanine nucleotide biosynthetic pathway. Because of its involvement in the control of cell division and proliferation, IMPDH represents a therapeutic for managing several diseases, including microbial infections and cancer. IMPDH must be tightly regulated, but the molecular mechanisms responsible for its physiological regulation remain unknown. To this end, we recently reported an important role of adenine and guanine mononucleotides that bind to the regulatory Bateman domain to allosterically modulate the catalytic activity of eukaryotic IMPDHs. Here, we have used enzyme kinetics, X-ray crystallography, and small-angle X-ray scattering (SAXS) methodologies to demonstrate that adenine/guanine dinucleoside polyphosphates bind to the Bateman domain of IMPDH from the fungus Ashbya gossypii with submicromolar affinities. We found that these dinucleoside polyphosphates modulate the catalytic activity of IMPDHs in vitro by efficiently competing with the adenine/guanine mononucleotides for the allosteric sites. These results suggest that dinucleoside polyphosphates play important physiological roles in the allosteric regulation of IMPDHs by adding an additional mechanism for fine-tuning the activities of these enzymes. We propose that these findings may have important implications for the design of therapeutic strategies to inhibit IMPDHs.


Asunto(s)
Fosfatos de Dinucleósidos/química , IMP Deshidrogenasa/química , Conformación Proteica , Dominios Proteicos/genética , Regulación Alostérica/genética , Infecciones Bacterianas/genética , Infecciones Bacterianas/microbiología , Sitios de Unión/genética , Catálisis , Cristalografía por Rayos X , Fosfatos de Dinucleósidos/genética , Eremothecium/genética , Nucleótidos de Guanina , Humanos , IMP Deshidrogenasa/genética , IMP Deshidrogenasa/ultraestructura , Modelos Moleculares , Neoplasias/genética , Dispersión del Ángulo Pequeño , Difracción de Rayos X
13.
Microb Biotechnol ; 12(6): 1293-1301, 2019 11.
Artículo en Inglés | MEDLINE | ID: mdl-31055883

RESUMEN

The filamentous fungus Ashbya gossypii is currently used for the industrial production of vitamin B2. Furthermore, the ability of A. gossypii to grow using low-cost substrates together with the inexpensive downstream processing makes this fungus an attractive biotechnological chassis. Indeed, the production in A. gossypii of other high-added value compounds such as folic acid, nucleosides and biolipids has been described. Hence, the development of new methods to expand the molecular toolkit for A. gossypii genomic manipulation constitutes an important issue for the biotechnology of this fungus. In this work, we present a one-vector CRISPR/Cas9 system for genomic engineering of A. gossypii. We demonstrate the efficiency of the system as a marker-less approach for nucleotide deletions and substitutions both with visible and invisible phenotypes. Particularly, the system has been validated for three types of genomic editions: gene inactivation, the genomic erasure of loxP scars and the introduction of point mutations. We anticipate that the use of the CRISPR/Cas9 system for A. gossypii will largely contribute to facilitate the genomic manipulations of this industrial fungus in a marker-less manner.


Asunto(s)
Proteína 9 Asociada a CRISPR , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas , Edición Génica/métodos , Saccharomycetales/genética , Microbiología Industrial/métodos , Ingeniería Metabólica/métodos
14.
J Mol Biol ; 431(5): 956-969, 2019 03 01.
Artículo en Inglés | MEDLINE | ID: mdl-30664871

RESUMEN

Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the rate-limiting step in the de novo GTP biosynthetic pathway and plays essential roles in cell proliferation. As a clinical target, IMPDH has been studied for decades, but it has only been within the last years that we are starting to understand the complexity of the mechanisms of its physiological regulation. Here, we report structural and functional insights into how adenine and guanine nucleotides control a conformational switch that modulates the assembly of the two human IMPDH enzymes into cytoophidia and allosterically regulates their catalytic activity. In vitro reconstituted micron-length cytoophidia-like structures show catalytic activity comparable to unassembled IMPDH but, in turn, are more resistant to GTP/GDP allosteric inhibition. Therefore, IMPDH cytoophidia formation facilitates the accumulation of high levels of guanine nucleotides when the cell requires it. Finally, we demonstrate that most of the IMPDH retinopathy-associated mutations abrogate GTP/GDP-induced allosteric inhibition and alter cytoophidia dynamics.


Asunto(s)
IMP Deshidrogenasa/metabolismo , Nucleótidos/metabolismo , Catálisis , Línea Celular Tumoral , Proliferación Celular/fisiología , Guanosina Trifosfato/metabolismo , Células HeLa , Humanos , Conformación Molecular , Polimerizacion
15.
Proc Natl Acad Sci U S A ; 115(51): 12967-12972, 2018 12 18.
Artículo en Inglés | MEDLINE | ID: mdl-30510005

RESUMEN

Ferredoxin-dependent thioredoxin reductase was identified 35 y ago in the fermentative bacterium Clostridium pasteurianum [Hammel KE, Cornwell KL, Buchanan BB (1983) Proc Natl Acad Sci USA 80:3681-3685]. The enzyme, a flavoprotein, was strictly dependent on ferredoxin as reductant and was inactive with either NADPH or NADH. This early work has not been further pursued. We have recently reinvestigated the problem and confirmed that the enzyme, here designated ferredoxin-dependent flavin thioredoxin reductase (FFTR), is a flavoprotein. The enzyme differs from ferredoxin-thioredoxin reductase (FTR), which has a signature [4Fe-4S] cluster, but shows structural similarities to NADP-dependent thioredoxin reductase (NTR). Comparative amino acid sequence analysis showed that FFTR is present in a number of clostridial species, some of which lack both FTR and an archetypal NTR. We have isolated, crystallized, and determined the structural properties of FFTR from a member of this group, Clostridium acetobutylicum, both alone and in complex with Trx. The structures showed an elongated FFTR homodimer, each monomer comprising two Rossmann domains and a noncovalently bound FAD cofactor that exposes the isoalloxazine ring to the solvent. The FFTR structures revealed an alternative domain organization compared with NTR that enables the enzyme to accommodate Fdx rather than NADPH. The results suggest that FFTR exists in a range of conformations with varying degrees of domain separation in solution and that the stacking between the two redox-active groups for the transfer of reducing equivalents results in a profound structural reorganization. A mechanism in accord with the findings is proposed.


Asunto(s)
Clostridium acetobutylicum/enzimología , Ferredoxinas/química , Flavoproteínas/química , Cristalografía por Rayos X , Flavoproteínas/metabolismo , Flavoproteínas/fisiología , Modelos Moleculares , NADP/química , Oxidación-Reducción , Conformación Proteica , Análisis de Secuencia de Proteína , Homología de Secuencia
16.
Antioxidants (Basel) ; 7(11)2018 Nov 17.
Artículo en Inglés | MEDLINE | ID: mdl-30453601

RESUMEN

The redox regulation of proteins via reversible dithiol/disulfide exchange reactions involves the thioredoxin system, which is composed of a reductant, a thioredoxin reductase (TR), and thioredoxin (Trx). In the pyridine nucleotide-dependent Trx reduction pathway, reducing equivalents, typically from reduced nicotinamide adenine dinucleotide phosphate (NADPH), are transferred from NADPH-TR (NTR) to Trx and, in turn, to target proteins, thus resulting in the reversible modification of the structural and functional properties of the targets. NTR enzymes contain three functional sites: an NADPH binding pocket, a non-covalently bound flavin cofactor, and a redox-active disulfide in the form of CxxC. With the aim of increasing our knowledge of the thioredoxin system in archaea, we here report the high-resolution crystal structure of NTR from the methane-generating organism Methanosarcina mazei strain Gö1 (MmNTR) at 2.6 Å resolution. Based on the crystals presently described, MmNTR assumes an overall fold that is nearly identical to the archetypal fold of authentic NTRs; however, surprisingly, we observed no electron density for flavin adenine dinucleotide (FAD) despite the well-defined and conserved FAD-binding cavity in the folded module. Remarkably, the dimers of the apo-protein within the crystal were different from those observed by small angle X-ray scattering (SAXS) for the holo-protein, suggesting that the binding of the flavin cofactor does not require major protein structural rearrangements. Rather, binding results in the stabilization of essential parts of the structure, such as those involved in dimer stabilization. Altogether, this structure represents the example of an apo-form of an NTR that yields important insight into the effects of the cofactor on protein folding.

17.
Sci Rep ; 7(1): 16494, 2017 11 28.
Artículo en Inglés | MEDLINE | ID: mdl-29184076

RESUMEN

Endolysins, the cell wall lytic enzymes encoded by bacteriophages to release the phage progeny, are among the top alternatives to fight against multiresistant pathogenic bacteria; one of the current biggest challenges to global health. Their narrow range of susceptible bacteria relies, primarily, on targeting specific cell-wall receptors through specialized modules. The cell wall-binding domain of Cpl-7 endolysin, made of three CW_7 repeats, accounts for its extended-range of substrates. Using as model system the cell wall-binding domain of Cpl-7, here we describe the molecular basis for the bacterial cell wall recognition by the CW_7 motif, which is widely represented in sequences of cell wall hydrolases. We report the crystal and solution structure of the full-length domain, identify N-acetyl-D-glucosaminyl-(ß1,4)-N-acetylmuramyl-L-alanyl-D-isoglutamine (GMDP) as the peptidoglycan (PG) target recognized by the CW_7 motifs, and characterize feasible GMDP-CW_7 contacts. Our data suggest that Cpl-7 cell wall-binding domain might simultaneously bind to three PG chains, and also highlight the potential use of CW_7-containing lysins as novel anti-infectives.


Asunto(s)
Bacterias/metabolismo , Bacterias/virología , Bacteriófagos/enzimología , Pared Celular/metabolismo , Endopeptidasas/metabolismo , Peptidoglicano/metabolismo , Dominios y Motivos de Interacción de Proteínas , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Bacteriólisis , Bacteriófagos/fisiología , Sitios de Unión , Endopeptidasas/química , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Unión Proteica , Conformación Proteica , Relación Estructura-Actividad
18.
Proc Natl Acad Sci U S A ; 114(48): 12725-12730, 2017 11 28.
Artículo en Inglés | MEDLINE | ID: mdl-29133410

RESUMEN

Flavoproteins participate in a wide variety of physiologically relevant processes that typically involve redox reactions. Within this protein superfamily, there exists a group that is able to transfer reducing equivalents from FAD to a redox-active disulfide bridge, which further reduces disulfide bridges in target proteins to regulate their structure and function. We have identified a previously undescribed type of flavin enzyme that is exclusive to oxygenic photosynthetic prokaryotes and that is based on the primary sequence that had been assigned as an NADPH-dependent thioredoxin reductase (NTR). However, our experimental data show that the protein does not transfer reducing equivalents from flavins to disulfides as in NTRs but functions in the opposite direction. High-resolution structures of the protein from Gloeobacter violaceus and Synechocystis sp. PCC6803 obtained by X-ray crystallography showed two juxtaposed FAD molecules per monomer in redox communication with an active disulfide bridge in a variant of the fold adopted by NTRs. We have tentatively named the flavoprotein "DDOR" (diflavin-linked disulfide oxidoreductase) and propose that its activity is linked to a thiol-based transfer of reducing equivalents in bacterial membranes. These findings expand the structural and mechanistic repertoire of flavoenzymes with oxidoreductase activity and pave the way to explore new protein engineering approaches aimed at designing redox-active proteins for diverse biotechnological applications.


Asunto(s)
Proteínas Bacterianas/química , Cianobacterias/enzimología , Disulfuros/química , Flavina-Adenina Dinucleótido/química , Oxidorreductasas/química , Synechocystis/enzimología , Secuencia de Aminoácidos , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Sitios de Unión , Biocatálisis , Membrana Celular/química , Membrana Celular/enzimología , Cristalografía por Rayos X , Cianobacterias/genética , Disulfuros/metabolismo , Flavina-Adenina Dinucleótido/metabolismo , Expresión Génica , Cinética , Modelos Moleculares , Oxidorreductasas/genética , Oxidorreductasas/metabolismo , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Pliegue de Proteína , Dominios y Motivos de Interacción de Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alineación de Secuencia , Homología Estructural de Proteína , Especificidad por Sustrato , Synechocystis/genética , Reductasa de Tiorredoxina-Disulfuro/química , Reductasa de Tiorredoxina-Disulfuro/genética , Reductasa de Tiorredoxina-Disulfuro/metabolismo
19.
Sci Rep ; 7(1): 2648, 2017 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-28572600

RESUMEN

Inosine-5'-monophosphate dehydrogenase (IMPDH) is an essential enzyme for nucleotide metabolism and cell proliferation. Despite IMPDH is the target of drugs with antiviral, immunosuppressive and antitumor activities, its physiological mechanisms of regulation remain largely unknown. Using the enzyme from the industrial fungus Ashbya gossypii, we demonstrate that the binding of adenine and guanine nucleotides to the canonical nucleotide binding sites of the regulatory Bateman domain induces different enzyme conformations with significantly distinct catalytic activities. Thereby, the comparison of their high-resolution structures defines the mechanistic and structural details of a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity of eukaryotic IMPDHs. Remarkably, retinopathy-associated mutations lie within the mechanical hinges of the conformational change, highlighting its physiological relevance. Our results expand the mechanistic repertoire of Bateman domains and pave the road to new approaches targeting IMPDHs.


Asunto(s)
Nucleótidos de Adenina/metabolismo , Nucleótidos de Guanina/metabolismo , IMP Deshidrogenasa/metabolismo , Nucleótidos de Adenina/química , Sitios de Unión , Nucleótidos de Guanina/química , IMP Deshidrogenasa/química , Modelos Moleculares , Conformación Molecular , Saccharomycetales
20.
Biotechnol Biofuels ; 10: 3, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28053663

RESUMEN

BACKGROUND: Ashbya gossypii is a filamentous fungus that is currently exploited for the industrial production of riboflavin. The utilization of A. gossypii as a microbial biocatalyst is further supported by its ability to grow in low-cost feedstocks, inexpensive downstream processing and the availability of an ease to use molecular toolbox for genetic and genomic modifications. Consequently, A. gossypii has been also introduced as an ideal biotechnological chassis for the production of inosine, folic acid, and microbial oils. However, A. gossypii cannot use xylose, the most common pentose in hydrolysates of plant biomass. RESULTS: In this work, we aimed at designing A. gossypii strains able to utilize xylose as the carbon source for the production of biolipids. An endogenous xylose utilization pathway was identified and overexpressed, resulting in an A. gossypii xylose-metabolizing strain showing prominent conversion rates of xylose to xylitol (up to 97% after 48 h). In addition, metabolic flux channeling from xylulose-5-phosphate to acetyl-CoA, using aheterologous phosphoketolase pathway, increased the lipid content in the xylose-metabolizing strain a 54% over the parental strain growing in glucose-based media. This increase raised to 69% when lipid accumulation was further boosted by blocking the beta-oxidation pathway. CONCLUSIONS: Ashbya gossypii has been engineered for the utilization of xylose. We present here a proof-of-concept study for the production of microbial oils from xylose in A. gossypii, thus introducing a novel biocatalyst with very promising properties in developing consolidated bioprocessing to produce fine chemicals and biofuels from xylose-rich hydrolysates of plant biomass.

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