RESUMEN
The biosynthesis of histidine, a proteinogenic amino acid, has been extensively studied due to its importance in bacterial growth and survival. Histidinol-phosphate phosphatase (Hol-Pase), which is responsible for the penultimate step of histidine biosynthesis, is generally the last enzyme to be characterized in many bacteria because its origin and evolution are more complex compared to other enzymes in histidine biosynthesis. However, none of the enzymes in histidine biosynthesis, including Hol-Pase, have been characterized in Pseudomonas aeruginosa, which is an important opportunistic Gram-negative pathogen that can cause serious human infections. In our previous work, a transposon mutant of P. aeruginosa was found to display a growth defect on glucose-containing minimal solid medium. In this study, we found that the growth defect was due to incomplete histidine auxotrophy caused by PA0335 inactivation. Subsequently, PA0335 was shown to encode Hol-Pase, and its function and enzymatic activity were investigated using genetic and biochemical methods. In addition to PA0335, the roles of 12 other predicted genes involved in histidine biosynthesis in P. aeruginosa were examined. Among them, hisC2 (PA3165), hisH2 (PA3152), and hisF2 (PA3151) were found to be dispensable for histidine synthesis, whereas hisG (PA4449), hisE (PA5067), hisF1 (PA5140), hisB (PA5143), hisI (PA5066), hisC1 (PA4447), and hisA (PA5141) were essential because deletion of each resulted in complete histidine auxotrophy; similar to the case for PA0335, hisH1 (PA5142) or hisD (PA4448) deletion caused incomplete histidine auxotrophy. Taken together, our results outline the histidine synthesis pathway of P. aeruginosaIMPORTANCE Histidine is a common amino acid in proteins. Because it plays critical roles in bacterial metabolism, its biosynthetic pathway in many bacteria has been elucidated. However, the pathway remains unclear in Pseudomonas aeruginosa, an important opportunistic pathogen in clinical settings; in particular, there is scant knowledge about histidinol-phosphate phosphatase (Hol-Pase), which has a complex origin and evolution. In this study, P. aeruginosa Hol-Pase was identified and characterized. Furthermore, the roles of all other predicted genes involved in histidine biosynthesis were examined. Our results illustrate the histidine synthesis pathway of P. aeruginosa The knowledge obtained from this study may help in developing strategies to control P. aeruginosa-related infections. In addition, some enzymes of the histidine synthesis pathway from P. aeruginosa might be used as elements of histidine synthetic biology in other industrial microorganisms.
Asunto(s)
Proteínas Bacterianas/genética , Histidina/metabolismo , Histidinol-Fosfatasa/genética , Pseudomonas aeruginosa/genética , Proteínas Bacterianas/metabolismo , Vías Biosintéticas , Histidinol-Fosfatasa/metabolismo , Pseudomonas aeruginosa/enzimología , Pseudomonas aeruginosa/metabolismoRESUMEN
The rate of reliable protein function annotation has not kept pace with the rapid advances in genome sequencing technology. This has created a gap between the number of available protein sequences, and an accurate determination of the respective physiological functions. This investigation has attempted to bridge the gap within the confines of members of the polymerase and histidinol phosphatase family of proteins in cog1387 and cog0613, which is related to the amidohydrolase superfamily. The adopted approach relies on using the mechanistic knowledge of a known enzymatic reaction, and discovering functions of closely related homologs using various tools including bioinformatics and rational library screening. The initial enzymatic reaction was that of L-histidinol phosphate phosphatase. Extensive structural, biochemical, and bioinformatic analysis of enzymes capable of hydrolyzing L-histidinol phosphate provided useful insights in predicting substrates and mechanistic studies of related enzymes. This led to the discovery of unprecedented catalytic functions such as a cyclic phosphate dihydrolase that specifically hydrolyzed a cyclic phosphodiester to inorganic phosphate and a vicinal diol; a phosphoesterase that hydrolyzes the 3'-phosphate of 3',5'-adenosine bisphosphate and similar nucleotides; and the first reported 5'-3' exonuclease for 5'-phosphorylated oligonucleotides from Escherichia coli and related organisms. This work provides a template for developing sequence-structure-function correlations within a family of enzymes that helps expedite new enzyme function discovery and more accurate annotations in protein databases.
Asunto(s)
Amidohidrolasas/metabolismo , Proteínas Bacterianas/metabolismo , Pruebas de Enzimas/métodos , Histidinol-Fosfatasa/metabolismo , Amidohidrolasas/química , Amidohidrolasas/genética , Secuencia de Aminoácidos , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Biología Computacional/instrumentación , Biología Computacional/métodos , Cristalografía por Rayos X , Pruebas de Enzimas/instrumentación , Histidinol-Fosfatasa/química , Histidinol-Fosfatasa/genética , Hidrólisis , Modelos Moleculares , Relación Estructura-Actividad , Especificidad por SustratoRESUMEN
The absence of a histidine biosynthesis pathway in humans, coupled with histidine essentiality for survival of the important human pathogen Mycobacterium tuberculosis (Mtb), underscores the importance of the bacterial enzymes of this pathway as major antituberculosis drug targets. However, the identity of the mycobacterial enzyme that functions as the histidinol phosphate phosphatase (HolPase) of this pathway remains to be established. Here, we demonstrate that the enzyme encoded by the Rv3137 gene, belonging to the inositol monophosphatase (IMPase) family, functions as the Mtb HolPase and specifically dephosphorylates histidinol phosphate. The crystal structure of Rv3137 in apo form enabled us to dissect its distinct structural features. Furthermore, the holo-complex structure revealed that a unique cocatalytic multizinc-assisted mode of substrate binding and catalysis is the hallmark of Mtb HolPase. Interestingly, the enzyme-substrate complex structure unveiled that although monomers possess individual catalytic sites they share a common product-exit channel at the dimer interface. Furthermore, target-based screening against HolPase identified several small-molecule inhibitors of this enzyme. Taken together, our study unravels the missing enzyme link in the Mtb histidine biosynthesis pathway, augments our current mechanistic understanding of histidine production in Mtb, and has helped identify potential inhibitors of this bacterial pathway.
Asunto(s)
Histidinol-Fosfatasa/química , Histidinol-Fosfatasa/metabolismo , Mycobacterium tuberculosis/enzimología , Secuencia de Aminoácidos , Dominio Catalítico , Cristalografía por Rayos X , Inhibidores Enzimáticos/farmacología , Histidinol-Fosfatasa/antagonistas & inhibidores , Histidinol-Fosfatasa/genética , Metales/metabolismo , Mutación , Fosforilación , Multimerización de Proteína , Estructura Cuaternaria de ProteínaRESUMEN
BACKGROUND: The eighth step of L-histidine biosynthesis is carried out by an enzyme called histidinol-phosphate phosphatase (HolPase). Three unrelated HolPase families are known so far. Two of them are well studied: HAD-type HolPases known from Gammaproteobacteria like Escherichia coli or Salmonella enterica and PHP-type HolPases known from yeast and Firmicutes like Bacillus subtilis. However, the third family of HolPases, the inositol monophosphatase (IMPase)-like HolPases, present in Actinobacteria like Corynebacterium glutamicum (HisN) and plants, are poorly characterized. Moreover, there exist several IMPase-like proteins in bacteria (e.g. CysQ, ImpA, and SuhB) which are very similar to HisN but most likely do not participate in L-histidine biosynthesis. RESULTS: Deletion of hisN, the gene encoding the IMPase-like HolPase in C. glutamicum, does not result in complete L-histidine auxotrophy. Out of four hisN homologs present in the genome of C. glutamicum (impA, suhB, cysQ, and cg0911), only cg0911 encodes an enzyme with HolPase activity. The enzymatic properties of HisN and Cg0911 were determined, delivering the first available kinetic data for IMPase-like HolPases. Additionally, we analyzed the amino acid sequences of potential HisN, ImpA, SuhB, CysQ and Cg0911 orthologs from bacteria and identified six conserved sequence motifs for each group of orthologs. Mutational studies confirmed the importance of a highly conserved aspartate residue accompanied by several aromatic amino acid residues present in motif 5 for HolPase activity. Several bacterial proteins containing all identified HolPase motifs, but showing only moderate sequence similarity to HisN from C. glutamicum, were experimentally confirmed as IMPase-like HolPases, demonstrating the value of the identified motifs. Based on the confirmed IMPase-like HolPases two profile Hidden Markov Models (HMMs) were build using an iterative approach. These HMMs allow the fast, reliable detection and differentiation of the two paralog groups from each other and other IMPases. CONCLUSION: The kinetic data obtained for HisN from C. glutamicum, as an example for an IMPase-like HolPases, shows remarkable differences in enzyme properties as compared to HAD- or PHP-type HolPases. The six sequence motifs and the HMMs presented in this study can be used to reliably differentiate between IMPase-like HolPases and IMPase-like proteins with no such activity, with the potential to enhance current and future genome annotations. A phylogenetic analysis reveals that IMPase-like HolPases are not only present in Actinobacteria and plant but can be found in further bacterial phyla, including, among others, Proteobacteria, Chlorobi and Planctomycetes.
Asunto(s)
Proteínas Bacterianas/genética , Corynebacterium glutamicum/enzimología , Histidinol-Fosfatasa/genética , Actinobacteria/química , Actinobacteria/clasificación , Actinobacteria/enzimología , Actinobacteria/genética , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Corynebacterium glutamicum/química , Corynebacterium glutamicum/genética , Regulación Bacteriana de la Expresión Génica , Histidinol-Fosfatasa/química , Histidinol-Fosfatasa/metabolismo , Cinética , Datos de Secuencia Molecular , Monoéster Fosfórico Hidrolasas/química , Monoéster Fosfórico Hidrolasas/genética , Monoéster Fosfórico Hidrolasas/metabolismo , Filogenia , Homología de Secuencia de AminoácidoRESUMEN
The penultimate enzyme in the histidine biosynthetic pathway catalyzes dephosphorylation of l-histidinol 1-phosphate (HOLP) into l-histidinol. The recently discovered in Arabidopsis thaliana plant-type histidinol phosphate phosphatase (HPP) shares no homology with the two other HPP superfamilies known previously in prokaryotes and resembles myo-inositol monophosphatases (IMPases). In this work, identification of an HPP enzyme from a model legume, Medicago truncatula (MtHPP) was based on the highest sequence identity to A. thaliana enzyme. Biochemical assays confirmed that MtHPP was able to cleave inorganic phosphate from HOLP but not from d-myo-inositol-1-phosphate, the main substrate of IMPases. Dimers of MtHPP, determined by size exclusion chromatography, in the presence of CO2 or formaldehyde form mutual, methylene-bridged cross-links between Lys(158) and Cys(245) residues. Four high resolution crystal structures, namely complexes with HOLP (substrate), l-histidinol (product), and PO4 (3-) (by-product) as well as the structure showing the cross-linking between two MtHPP molecules, provide detailed structural information on the enzyme. Based on the crystal structures, the enzymatic reaction mechanism of IMPases is accustomed to fit the data for MtHPP. The enzymatic reaction, which requires Mg(2+) cations, is catalyzed mainly by amino acid residues from the N-terminal domain. The C-terminal domain, sharing little identity with IMPases, is responsible for the substrate specificity (i.e. allows the enzyme to distinguish between HOLP and d-myo-inositol-1-phosphate). Structural features, mainly the presence of a conserved Asp(246), allow MtHPP to bind HOLP specifically.
Asunto(s)
Histidinol-Fosfatasa/química , Medicago truncatula/enzimología , Proteínas de Plantas/química , Arabidopsis/enzimología , Arabidopsis/genética , Cristalografía por Rayos X , Histidina/biosíntesis , Histidina/química , Histidina/genética , Histidinol-Fosfatasa/genética , Histidinol-Fosfatasa/metabolismo , Medicago truncatula/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Estructura Terciaria de Proteína , Homología de Secuencia de AminoácidoRESUMEN
Many enzymes exhibit some catalytic promiscuity or substrate ambiguity. These weak activities do not affect the fitness of the organism under ordinary circumstances, but can serve as potential evolutionary precursors of new catalytic functions. We wondered whether different proteins with the same substrate ambiguous activity evolve differently under identical selection conditions. Patrick et al. (Patrick WM, Quandt EM, Swartzlander DB, Matsumura I. 2007. Multicopy suppression underpins metabolic evolvability. Mol Biol Evol. 24:2716-2722.) previously showed that three multicopy suppressors, gph, hisB, and ytjC, rescue ΔserB Escherichia coli cells from starvation on minimal media. We directed the evolution of variants of Gph, histidinol phosphatase (HisB), and YtjC that complemented ΔserB more efficiently, and characterized the effects of the amino acid changes, alone and in combination, upon the evolved phosphoserine phosphatase (PSP) activity. Gph and HisB are members of the HAD superfamily of hydrolases, but they adapted through different, kinetically distinguishable, biochemical mechanisms. All of the selected mutations, except N102T in YtjC, proved to be beneficial in isolation. They exhibited a pattern of antagonistic epistasis, as their effects in combination upon the kinetic parameters of the three proteins in reactions with phosphoserine were nonmultiplicative. The N102T mutation exhibited sign epistasis, as it was deleterious in isolation but beneficial in the context of other mutations. We also showed that the D57N mutation in the chromosomal copy of hisB is sufficient to suppress the ΔserB deletion. These results in combination show that proteomes can offer multiple mechanistic solutions to a molecular recognition problem.
Asunto(s)
Proteínas de Escherichia coli/metabolismo , Escherichia coli/genética , Regulación Bacteriana de la Expresión Génica , Histidinol-Fosfatasa/metabolismo , Monoéster Fosfórico Hidrolasas/metabolismo , Proteoma/metabolismo , Biocatálisis , Evolución Biológica , Epistasis Genética , Escherichia coli/enzimología , Proteínas de Escherichia coli/genética , Genes Supresores , Prueba de Complementación Genética , Histidinol-Fosfatasa/genética , Cinética , Modelos Moleculares , Mutación , Monoéster Fosfórico Hidrolasas/genética , Fosfoserina/metabolismo , Proteoma/genética , Especificidad por SustratoRESUMEN
L-Histidinol phosphate phosphatase (HPP) catalyzes the hydrolysis of L-histidinol phosphate to L-histidinol and inorganic phosphate, the penultimate step in the biosynthesis of L-histidine. HPP from the polymerase and histidinol phosphatase (PHP) family of proteins possesses a trinuclear active site and a distorted (ß/α)(7)-barrel protein fold. This group of enzymes is closely related to the amidohydrolase superfamily of enzymes. The mechanism of phosphomonoester bond hydrolysis by the PHP family of HPP enzymes was addressed. Recombinant HPP from Lactococcus lactis subsp. lactis that was expressed in Escherichia coli contained a mixture of iron and zinc in the active site and had a catalytic efficiency of ~10(3) M(-1) s(-1). Expression of the protein under iron-free conditions resulted in the production of an enzyme with a 2 order of magnitude improvement in catalytic efficiency and a mixture of zinc and manganese in the active site. Solvent isotope and viscosity effects demonstrated that proton transfer steps and product dissociation steps are not rate-limiting. X-ray structures of HPP were determined with sulfate, L-histidinol phosphate, and a complex of L-histidinol and arsenate bound in the active site. These crystal structures and the catalytic properties of variants were used to identify the structural elements required for catalysis and substrate recognition by the HPP family of enzymes within the amidohydrolase superfamily.
Asunto(s)
Arseniatos/metabolismo , Escherichia coli/enzimología , Histidina/metabolismo , Histidinol-Fosfatasa/química , Lactococcus lactis/enzimología , Secuencia de Aminoácidos , Catálisis , Dominio Catalítico , Biología Computacional , Cristalografía por Rayos X , Escherichia coli/genética , Histidinol-Fosfatasa/genética , Histidinol-Fosfatasa/metabolismo , Concentración de Iones de Hidrógeno , Lactococcus lactis/genética , Modelos Moleculares , Datos de Secuencia Molecular , Familia de Multigenes , Mutagénesis Sitio-Dirigida , Mutación/genética , Proteínas Recombinantes , Homología de Secuencia de AminoácidoRESUMEN
The crystal structures of an unliganded and adenosine 5'-monophosphate (AMP) bound, metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis are reported at 2.4 and 1.94 Å, respectively. Functional characterization of this enzyme was guided by computational analysis and then confirmed by experiment. The structure consists of a polymerase and histidinol phosphatase (PHP, Pfam: PF02811) domain with a second domain (residues 105-178) inserted in the middle of the PHP sequence. The insert domain functions in binding AMP, but the precise function and substrate specificity of this domain are unknown. Initial bioinformatics analyses yielded multiple potential functional leads, with most of them suggesting DNA polymerase or DNA replication activity. Phylogenetic analysis indicated a potential DNA polymerase function that was somewhat supported by global structural comparisons identifying the closest structural match to the alpha subunit of DNA polymerase III. However, several other functional predictions, including phosphoesterase, could not be excluded. Theoretical microscopic anomalous titration curve shapes, a computational method for the prediction of active sites from protein 3D structures, identified potential reactive residues in YP_910028.1. Further analysis of the predicted active site and local comparison with its closest structure matches strongly suggested phosphoesterase activity, which was confirmed experimentally. Primer extension assays on both normal and mismatched DNA show neither extension nor degradation and provide evidence that YP_910028.1 has neither DNA polymerase activity nor DNA-proofreading activity. These results suggest that many of the sequence neighbors previously annotated as having DNA polymerase activity may actually be misannotated.
Asunto(s)
Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Bifidobacterium/enzimología , Esterasas/química , Esterasas/metabolismo , 4-Nitrofenilfosfatasa/química , 4-Nitrofenilfosfatasa/metabolismo , Adenosina Difosfato/química , Adenosina Difosfato/metabolismo , Secuencia de Aminoácidos , Sitios de Unión , Dominio Catalítico , Simulación por Computador , Cristalografía , ADN Polimerasa III/química , ADN Polimerasa III/metabolismo , Histidinol-Fosfatasa/química , Histidinol-Fosfatasa/metabolismo , Modelos Moleculares , Datos de Secuencia Molecular , Filogenia , Reproducibilidad de los Resultados , Relación Estructura-ActividadRESUMEN
Histidine (His) plays a critical role in plant growth and development, both as one of the standard amino acids in proteins, and as a metal-binding ligand. While genes encoding seven of the eight enzymes in the pathway of His biosynthesis have been characterized from a number of plant species, the identity of the enzyme catalyzing the dephosphorylation of histidinol-phosphate to histidinol has remained elusive. Recently, members of a novel family of histidinol-phosphate phosphatase proteins, displaying significant sequence similarity to known myoinositol monophosphatases (IMPs) have been identified from several Actinobacteria. Here we demonstrate that a member of the IMP family from Arabidopsis (Arabidopsis thaliana), myoinositol monophosphatase-like2 (IMPL2; encoded by At4g39120), has histidinol-phosphate phosphatase activity. Heterologous expression of IMPL2, but not the related IMPL1 protein, was sufficient to rescue the His auxotrophy of a Streptomyces coelicolor hisN mutant. Homozygous null impl2 Arabidopsis mutants displayed embryonic lethality, which could be rescued by supplying plants heterozygous for null impl2 alleles with His. In common with the previously characterized HISN genes from Arabidopsis, IMPL2 was expressed in all plant tissues and throughout development, and an IMPL2:green fluorescent protein fusion protein was targeted to the plastid, where His biosynthesis occurs in plants. Our data demonstrate that IMPL2 is the HISN7 gene product, and suggest a lack of genetic redundancy at this metabolic step in Arabidopsis, which is characteristic of the His biosynthetic pathway.
Asunto(s)
Proteínas de Arabidopsis/metabolismo , Arabidopsis/enzimología , Histidina/biosíntesis , Histidinol-Fosfatasa/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/genética , ADN Bacteriano/genética , ADN de Plantas/genética , Regulación de la Expresión Génica de las Plantas , Prueba de Complementación Genética , Histidinol/metabolismo , Histidinol-Fosfatasa/genética , Modelos Moleculares , Mutagénesis Insercional , Mutación , Fosforilación , Filogenia , Estructura Terciaria de Proteína , Proteínas Recombinantes de Fusión/genética , Proteínas Recombinantes de Fusión/metabolismoRESUMEN
The TON_0887 gene product from Thermococcus onnurineus NA1 is a 240-residue protein that has histidinol-phosphate phosphatase (HolPase) activity. According to analysis of its primary structure, the TON_0887 gene product is a monofunctional HolPase that belongs to the DDDD superfamily. This contrasts with the generally accepted classification that bifunctional HolPases belong to the DDDD superfamily. The TON_0887 gene product was purified and crystallized at 295 K. A 2.2 A resolution data set was collected using synchrotron radiation. The TON-HolPase crystals belonged to space group P222(1), with unit-cell parameters a = 40.88, b = 46.89, c = 148.03 A. Assuming the presence of one molecule in the asymmetric unit, the solvent content was estimated to be about 48.3%.
Asunto(s)
Histidinol-Fosfatasa/química , Thermococcus/enzimología , Cristalización , Cristalografía por Rayos X , Histidinol-Fosfatasa/genética , Histidinol-Fosfatasa/metabolismo , Thermococcus/genéticaAsunto(s)
Escherichia coli/genética , Histidina/genética , Biología Molecular/historia , Mutación , Proteínas/genética , ADN Recombinante/genética , ADN Recombinante/metabolismo , Escherichia coli/metabolismo , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Expresión Génica , Histidina/metabolismo , Histidinol-Fosfatasa/genética , Histidinol-Fosfatasa/metabolismo , Historia del Siglo XX , Hidroliasas/genética , Hidroliasas/metabolismo , Proteínas/metabolismoRESUMEN
BACKGROUND: Reversible phosphorylation events within a polymerisation complex have been proposed to modulate capsular polysaccharide synthesis in Streptococcus pneumoniae. Similar phosphatase and kinase genes are present in the exopolysaccharide (EPS) biosynthesis loci of numerous lactic acid bacteria genomes. RESULTS: The protein sequence deduced from the wzb gene in Lactobacillus rhamnosus ATCC 9595 reveals four motifs of the polymerase and histidinol phosphatase (PHP) superfamily of prokaryotic O-phosphatases. Native and modified His-tag fusion Wzb proteins were purified from Escherichia coli cultures. Extracts showed phosphatase activity towards tyrosine-containing peptides. The purified fusion protein Wzb was active on p-nitrophenyl-phosphate (pNPP), with an optimal activity in presence of bovine serum albumin (BSA 1%) at pH 7.3 and a temperature of 75 degrees C. At 50 degrees C, residual activity decreased to 10 %. Copper ions were essential for phosphatase activity, which was significantly increased by addition of cobalt. Mutated fusion Wzb proteins exhibited reduced phosphatase activity on p-nitrophenyl-phosphate. However, one variant (C6S) showed close to 20% increase in phosphatase activity. CONCLUSION: These characteristics reveal significant differences with the manganese-dependent CpsB protein tyrosine phosphatase described for Streptococcus pneumoniae as well as with the polysaccharide-related phosphatases of Gram negative bacteria.
Asunto(s)
Proteínas Bacterianas/metabolismo , Lactobacillus/enzimología , Mutagénesis Sitio-Dirigida/métodos , Monoéster Fosfórico Hidrolasas/metabolismo , Secuencia de Aminoácidos , Proteínas Bacterianas/genética , Catálisis/efectos de los fármacos , Cobalto/farmacología , Electroforesis en Gel de Poliacrilamida , Histidinol-Fosfatasa/genética , Histidinol-Fosfatasa/metabolismo , Concentración de Iones de Hidrógeno , Lactobacillus/genética , Datos de Secuencia Molecular , Monoéster Fosfórico Hidrolasas/antagonistas & inhibidores , Monoéster Fosfórico Hidrolasas/genética , Proteínas Recombinantes/antagonistas & inhibidores , Proteínas Recombinantes/metabolismo , Homología de Secuencia de Aminoácido , Especificidad por Sustrato , Temperatura , Vanadatos/farmacologíaRESUMEN
The TON_0887 gene was identified as the missing histidinol-phosphate phosphatase (HolPase) in the hyperthermophilic archaeon "Thermococcus onnurineus" NA1. The protein contained conserved motifs of the DDDD superfamily of phosphohydrolase, and the recombinantly expressed protein exhibited strong HolPase activity. In this study, we functionally assessed for the first time the monofunctional DDDD-type HolPase, which is organized in the gene cluster.
Asunto(s)
Proteínas Arqueales/metabolismo , Histidinol-Fosfatasa/metabolismo , Thermococcus/enzimología , Secuencia de Aminoácidos , Proteínas Arqueales/química , Proteínas Arqueales/genética , ADN de Archaea/química , ADN de Archaea/genética , Electroforesis en Gel de Poliacrilamida , Histidinol-Fosfatasa/química , Histidinol-Fosfatasa/genética , Cinética , Modelos Genéticos , Datos de Secuencia Molecular , Familia de Multigenes , Análisis de Secuencia de ADN , Homología de Secuencia de Aminoácido , Thermococcus/genéticaRESUMEN
Monofunctional histidinol phosphate phosphatase from Thermus thermophilus HB8, which catalyzes the dephosphorylation of l-histidinol phosphate, belongs to the PHP family, together with the PHP domain of bacterial DNA polymerase III and family X DNA polymerase. We have determined the structures of the complex with a sulfate ion, the complex with a phosphate ion, and the unliganded form at 1.6, 2.1, and 1.8 A resolution, respectively. The enzyme exists as a tetramer, and the subunit consists of a distorted (betaalpha)7 barrel with one linker and one C-terminal tail. Three metal sites located on the C-terminal side of the barrel are occupied by Fe1, Fe2, and Zn ions, respectively, forming a trinuclear metal center liganded by seven histidines, one aspartate, one glutamate, and one hydroxide with two Fe ions bridged by the hydroxide. In the complexes, the sulfate or phosphate ion is coordinated to three metal ions, resulting in octahedral, trigonal bipyramidal, and tetrahedral geometries around the Fe1, Fe2, and Zn ions, respectively. The ligand residues are derived from the four motifs that characterize the PHP family and from two motifs conserved in histidinol phosphate phosphatases. The (betaalpha)7 barrel and the metal cluster are closely related in nature and architecture to the (betaalpha)8 barrel and the mononuclear or dinuclear metal center in the amidohydrolase superfamily, respectively. The coordination behavior of the phosphate ion toward the metal center supports the mechanism in which the bridging hydroxide makes a direct attack on the substrate phosphate tridentately bound to the two Fe ions and Zn ion to hydrolyze the phosphoester bond.
Asunto(s)
Histidinol-Fosfatasa/química , Thermus thermophilus/enzimología , Amidohidrolasas/química , Sitios de Unión , Cristalografía por Rayos X , Dimerización , Histidinol-Fosfatasa/metabolismo , Metales/metabolismo , Modelos Biológicos , Modelos Moleculares , Unión ProteicaRESUMEN
HisB from Escherichia coli is a bifunctional enzyme catalyzing the sixth and eighth steps of l-histidine biosynthesis. The N-terminal domain (HisB-N) possesses histidinol phosphate phosphatase activity, and its crystal structure shows a single domain with fold similarity to the haloacid dehalogenase (HAD) enzyme family. HisB-N forms dimers in the crystal and in solution. The structure shows the presence of a structural Zn(2+) ion stabilizing the conformation of an extended loop. Two metal binding sites were also identified in the active site. Their presence was further confirmed by isothermal titration calorimetry. HisB-N is active in the presence of Mg(2+), Mn(2+), Co(2+), or Zn(2+), but Ca(2+) has an inhibitory effect. We have determined structures of several intermediate states corresponding to snapshots along the reaction pathway, including that of the phosphoaspartate intermediate. A catalytic mechanism, different from that described for other HAD enzymes, is proposed requiring the presence of the second metal ion not found in the active sites of previously characterized HAD enzymes, to complete the second half-reaction. The proposed mechanism is reminiscent of two-Mg(2+) ion catalysis utilized by DNA and RNA polymerases and many nucleases. The structure also provides an explanation for the inhibitory effect of Ca(2+).
Asunto(s)
Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Escherichia coli/enzimología , Histidinol-Fosfatasa/química , Histidinol-Fosfatasa/metabolismo , Secuencia de Aminoácidos , Sustitución de Aminoácidos , Dominio Catalítico , Cationes Bivalentes/metabolismo , Cristalografía por Rayos X , Dimerización , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Histidinol-Fosfatasa/genética , Cinética , Modelos Moleculares , Datos de Secuencia Molecular , Mutagénesis Sitio-Dirigida , Conformación Proteica , Estructura Cuaternaria de Proteína , Estructura Terciaria de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Homología de Secuencia de Aminoácido , Electricidad Estática , TermodinámicaRESUMEN
Recently a family X DNA polymerase (PolXDr) was identified in the radioresistant bacterium Deinococcus radiodurans. Knockout cells show a delay in double-strand break repair (DSBR) and an increased sensitivity to gamma-irradiation. Here we show that PolXDr possesses 3'-->5' exonuclease activity that stops cutting close to a loop. PolXDr consists of a DNA polymerase X domain (PolXc) and a Polymerase and Histidinol Phosphatase (PHP) domain. Deletion of the PHP domain abolishes only the structure-modulated but not the canonical 3'-->5' exonuclease activity. Thus, the exonuclease resides in the PolXc domain, but the structure-specificity requires additionally the PHP domain. Mutation of two conserved glycines in the PolXc domain leads to a specific loss of the structure-modulated exonuclease activity but not the exonuclease activity in general. The PHP domain itself does not show any activity. PolXDr is the first family X DNA polymerase that harbours an exonuclease activity. The wild-type protein, the glycine mutant and the two domains were expressed separately in DeltapolXDr cells. The wild-type protein could restore the radiation resistance, whereas intriguingly the mutant proteins showed a significant negative effect on survival of gamma-irradiated cells. Taken together our in vivo results suggest that both PolXDr domains play important roles in DSBR in D. radiodurans.
Asunto(s)
ADN Polimerasa Dirigida por ADN , Deinococcus/efectos de la radiación , Exonucleasas/metabolismo , Tolerancia a Radiación , ADN/metabolismo , ADN/efectos de la radiación , Daño del ADN , Reparación del ADN , ADN Bacteriano/metabolismo , ADN Bacteriano/efectos de la radiación , ADN Polimerasa Dirigida por ADN/química , ADN Polimerasa Dirigida por ADN/genética , ADN Polimerasa Dirigida por ADN/metabolismo , Deinococcus/enzimología , Deinococcus/genética , Exonucleasas/química , Rayos gamma , Histidinol-Fosfatasa/genética , Histidinol-Fosfatasa/metabolismoRESUMEN
Histidinol phosphate phosphatase (HisPPase) catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to give histidinol. A recombinant form of the histidinol phosphate phosphatase from Thermus thermophilus HB8 has been expressed in Escherichia coli, purified and crystallized in two crystal forms by the hanging-drop vapour-diffusion technique. Crystal form I belongs to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 84.8, b = 97.2, c = 74.9 A, and crystal form II belongs to the orthorhombic space group C222(1), with unit-cell parameters a = 76.9, b = 157.6, c = 116.7 A. The crystals probably contain two monomers in the asymmetric unit, with V(M) values of 2.57 A(3) Da(-1) for form I and 2.96 A(3) Da(-1) for form II. X-ray data have been collected to 1.70 and 1.75 A resolution for crystal forms I and II, respectively.
Asunto(s)
Proteínas Bacterianas/química , Proteínas Bacterianas/aislamiento & purificación , Histidinol-Fosfatasa/química , Histidinol-Fosfatasa/aislamiento & purificación , Thermus thermophilus/enzimología , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Cristalización , Cristalografía por Rayos X , Escherichia coli/genética , Expresión Génica , Histidinol/metabolismo , Histidinol-Fosfatasa/genética , Histidinol-Fosfatasa/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/aislamiento & purificación , Proteínas Recombinantes/metabolismo , Thermus thermophilus/genéticaRESUMEN
The deduced product of the Bacillus subtilis ytvP gene is similar to that of ORF13, a gene of unknown function in the Lactococcus lactis histidine biosynthesis operon. A B. subtilis ytvP mutant was auxotrophic for histidine. The only enzyme of the histidine biosynthesis pathway that remained uncharacterized in B. subtilis was histidinol phosphate phosphatase (HolPase), catalyzing the penultimate step of this pathway. HolPase activity could not be detected in crude extracts of the ytvP mutant, while purified glutathione S-transferase-YtvP fusion protein exhibited strong HolPase activity. These observations demonstrated that HolPase is encoded by ytvP in B. subtilis and led us to rename this gene hisJ. Together with the HolPase of Saccharomyces cerevisiae and the presumed HolPases of L. lactis and Schizosaccharomyces pombe, HisJ constitutes a family of related enzymes that are not homologous to the HolPases of Escherichia coli, Salmonella typhimurium, and Haemophilus influenzae.
Asunto(s)
Bacillus subtilis/enzimología , Genes Bacterianos/genética , Histidina/biosíntesis , Histidinol-Fosfatasa/genética , Secuencia de Aminoácidos , Bacillus subtilis/genética , Bacillus subtilis/crecimiento & desarrollo , Catálisis/efectos de los fármacos , Regulación Bacteriana de la Expresión Génica/efectos de los fármacos , Histidina/genética , Histidina/metabolismo , Histidina/farmacología , Histidinol/metabolismo , Histidinol/farmacología , Histidinol-Fosfatasa/química , Histidinol-Fosfatasa/aislamiento & purificación , Histidinol-Fosfatasa/metabolismo , Lactococcus lactis/genética , Datos de Secuencia Molecular , Mutación , Sistemas de Lectura Abierta/genética , Fenotipo , Regiones Promotoras Genéticas/genética , Proteínas Recombinantes de Fusión/biosíntesis , Proteínas Recombinantes de Fusión/química , Proteínas Recombinantes de Fusión/aislamiento & purificación , Proteínas Recombinantes de Fusión/metabolismo , Alineación de Secuencia , Homología de Secuencia de Aminoácido , Transcripción Genética/efectos de los fármacosRESUMEN
Expression of the histidine operon in Escherichia coli cells in contrast to the one in Salmonella typhimurium is changed proportionally to cells growth rate on the different carbon sources. The specific activity of histidinol-dehydrogenase is repressed by addition of 19 amino acids both in Escherichia coli and Salmonella typhimurium independent of the growth medium used. Using of Escherichia coli and Salmonella typhimurium strains containing the heterologous histidine operons made possible to demonstrate the dependence of the histidine operon metabolic regulation to be determined by the operon itself but not by the specificity of the recipient cells. ppGpp was shown to be a positive regulator of the histidine operon expression in Escherichia coli.