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1.
Tuberculosis (Edinb) ; 147: 102516, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38735123

ABSTRACT

Although studies on non-tuberculous mycobacteria have increased in recent years because they cause a considerable proportion of infections, their cellulolytic system is still poorly studied. This study presents a characterization of the cellulolytic activities of environmental mycobacterial isolates derived from soil and water samples from the central region of Argentina, aimed to evaluate the conservation of the mechanism for the degradation of cellulose in this group of bacteria. The molecular and genomic identification revealed identity with Mycolicibacterium septicum. The endoglucanase and total cellulase activities were assessed both qualitatively and quantitatively and the optimal enzymatic conditions were characterized. A specific protein of around 56 kDa with cellulolytic activity was detected in a zymogram. Protein sequences possibly arising from a cellulase were identified by mass spectrometry-based shotgun proteomics. Results showed that M. septicum encodes for cellulose- and hemicellulose-related degrading enzymes, including at least an active ß-1,4 endoglucanase enzyme that could be useful to improve its survival in the environment. Given the important health issues related to mycobacteria, the results of the present study may contribute to the knowledge of their cellulolytic system, which could be important for their ability to survive in many different types of environments.


Subject(s)
Bacterial Proteins , Cellulase , Cellulose , Soil Microbiology , Cellulose/metabolism , Cellulase/metabolism , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Argentina , Water Microbiology , Proteomics/methods , Mycobacteriaceae/genetics , Mycobacteriaceae/enzymology
2.
J Biol Chem ; 300(2): 105621, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38176649

ABSTRACT

Phenazine-1-carboxylic acid decarboxylase (PhdA) is a prenylated-FMN-dependent (prFMN) enzyme belonging to the UbiD family of decarboxylases. Many UbiD-like enzymes catalyze (de)carboxylation reactions on aromatic rings and conjugated double bonds and are potentially valuable industrial catalysts. We have investigated the mechanism of PhdA using a slow turnover substrate, 2,3-dimethylquinoxaline-5-carboxylic acid (DQCA). Detailed analysis of the pH dependence and solvent deuterium isotope effects associated with the reaction uncovered unusual kinetic behavior. At low substrate concentrations, a substantial inverse solvent isotope effect (SIE) is observed on Vmax/KM of ∼ 0.5 when reaction rates of DQCA in H2O and D2O are compared. Under the same conditions, a normal SIE of 4.15 is measured by internal competition for proton transfer to the product. These apparently contradictory results indicate that the SIE values report on different steps in the mechanism. A proton inventory analysis of the reaction under Vmax/KM and Vmax conditions points to a "medium effect" as the source of the inverse SIE. Molecular dynamics simulations of the effect of D2O on PhdA structure support that D2O reduces the conformational lability of the enzyme and results in a more compact structure, akin to the active, "closed" conformer observed in crystal structures of some UbiD-like enzymes. Consistent with the simulations, PhdA was found to be more stable in D2O and to bind DQCA more tightly, leading to the observed rate enhancement under Vmax/KM conditions.


Subject(s)
Carboxy-Lyases , Carboxy-Lyases/chemistry , Isotopes , Kinetics , Phenazines , Protons , Solvents , Mycobacteriaceae/enzymology
3.
Appl Environ Microbiol ; 87(24): e0032121, 2021 11 24.
Article in English | MEDLINE | ID: mdl-34586911

ABSTRACT

Steroidal 17-carbonyl reduction is crucial to the production of natural bioactive steroid medicines, and boldenone (BD) is one of the important C-17-hydroxylated steroids. Although efforts have been made to produce BD through biotransformation, the challenges of the complex transformation process, high substrate costs, and low catalytic efficiencies have yet to be mastered. Phytosterol (PS) is the most widely accepted substrate for the production of steroid medicines due to its similar foundational structure and ubiquitous sources. 17ß-Hydroxysteroid dehydrogenase (17ßHSD) and its native electron donor play significant roles in the 17ß-carbonyl reduction reaction of steroids. In this study, we bridged 17ßHSD with a cofactor regeneration strategy in Mycobacterium neoaurum to establish a one-step biocatalytic carbonyl reduction strategy for the efficient biosynthesis of BD from PS for the first time. After investigating different intracellular electron transfer strategies, we rationally designed the engineered strain with the coexpression of 17ßhsd and the glucose-6-phosphate dehydrogenase (G6PDH) gene in M. neoaurum. With the establishment of an intracellular cofactor regeneration strategy, the ratio of [NADPH]/[NADP+] was maintained at a relatively high level, the yield of BD increased from 17% (in MNR M3M-ayr1S.c) to 78% (in MNR M3M-ayr1&g6p with glucose supplementation), and the productivity was increased by 6.5-fold. Furthermore, under optimal glucose supplementation conditions, the yield of BD reached 82%, which is the highest yield reported for transformation from PS in one step. This study demonstrated an excellent strategy for the production of many other valuable carbonyl reduction steroidal products from natural inexpensive raw materials. IMPORTANCE Steroid C-17-carbonyl reduction is one of the important transformations for the production of valuable steroidal medicines or intermediates for the further synthesis of steroidal medicines, but it remains a challenge through either chemical or biological synthesis. Phytosterol can be obtained from low-cost residues of waste natural materials, and it is preferred as the economical and applicable substrate for steroid medicine production by Mycobacterium. This study explored a green and efficient one-step biocatalytic carbonyl reduction strategy for the direct conversion of phytosterol to C-17-hydroxylated steroids by bridging 17ß-hydroxysteroid dehydrogenase with a cofactor regeneration strategy in Mycobacterium neoaurum. This work has practical value for the production of many valuable hydroxylated steroids from natural inexpensive raw materials.


Subject(s)
17-Hydroxycorticosteroids/metabolism , 17-Hydroxysteroid Dehydrogenases/metabolism , Glucosephosphate Dehydrogenase/metabolism , Mycobacteriaceae/enzymology , Phytosterols , Biocatalysis , Biotransformation , Phytosterols/metabolism
4.
Angew Chem Int Ed Engl ; 60(10): 5414-5420, 2021 03 01.
Article in English | MEDLINE | ID: mdl-33258169

ABSTRACT

4-Androstenedione (4-AD) and progesterone (PG) are two of the most important precursors for synthesis of steroid drugs, however their current manufacturing processes suffer from low efficiency and severe environmental issues. In this study, we decipher a dual-role reductase (mnOpccR) in the phytosterols catabolism, which engages in two different metabolic branches to produce the key intermediate 20-hydroxymethyl pregn-4-ene-3-one (4-HBC) through a 4-e reduction of 3-oxo-4-pregnene-20-carboxyl-CoA (3-OPC-CoA) and 2-e reduction of 3-oxo-4-pregnene-20-carboxyl aldehyde (3-OPA), respectively. Inactivation or overexpression of mnOpccR in the Mycobacterium neoaurum can achieve exclusive production of either 4-AD or 4-HBC from phytosterols. By utilizing a two-step synthesis, 4-HBC can be efficiently converted into PG in a scalable manner (100 gram scale). This study deciphers a pivotal biosynthetic mechanism of phytosterol catabolism and provides very efficient production routes of 4-AD and PG.


Subject(s)
Bacterial Proteins/metabolism , Oxidoreductases/metabolism , Phytosterols/metabolism , Pregnenes/metabolism , Androstenedione/chemical synthesis , Bacterial Proteins/genetics , Biocatalysis , Mycobacteriaceae/enzymology , Mycobacteriaceae/genetics , Oxidoreductases/genetics , Pregnenes/chemistry , Progesterone/chemical synthesis
5.
Dalton Trans ; 49(48): 17745-17757, 2020 Dec 22.
Article in English | MEDLINE | ID: mdl-33241840

ABSTRACT

Two mononuclear iron(ii)-thiolate complexes have been prepared that represent structural models of the nonheme iron enzymes EgtB and OvoA, which catalyze the O2-dependent formation of carbon-sulfur bonds in the biosynthesis of thiohistidine compounds. The series of Fe(ii) complexes reported here feature tripodal N4 chelates (LA and LB) that contain both pyridyl and imidazolyl donors (LA = (1H-imidazol-4-yl)-N,N-bis((pyridin-2-yl)methyl)methanamine; LB = N,N-bis((1-methylimidazol-2-yl)methyl)-2-pyridylmethylamine). Further coordination with monodentate aromatic or aliphatic thiolate ligands yielded the five-coordinate, high-spin Fe(ii) complexes [FeII(LA)(SMes)]BPh4 (1) and [FeII(LB)(SCy)]BPh4 (2), where SMes = 2,4,6-trimethylthiophenolate and SCy = cyclohexanethiolate. X-ray crystal structures revealed that 1 and 2 possess trigonal bipyramidal geometries formed by the N4S ligand set. In each case, the thiolate ligand is positioned cis to an imidazole donor, replicating the arrangement of Cys- and His-based substrates in the active site of EgtB. The geometric and electronic structures of 1 and 2 were analyzed with UV-vis absorption and Mössbauer spectroscopies in tandem with density functional theory (DFT) calculations. Exposure of 1 and 2 to nitric oxide (NO) yielded six-coordinate FeNO adducts that were characterized with infrared and electron paramagnetic resonance (EPR) spectroscopies, confirming that these complexes are capable of binding diatomic molecules. Reaction of 1 and 2 with O2 causes oxidation of the thiolate ligands to disulfide products. The implications of these results for the development of functional models of EgtB and OvoA are discussed.


Subject(s)
Ferrous Compounds/pharmacology , Nonheme Iron Proteins/metabolism , Oxidoreductases/metabolism , Sulfhydryl Compounds/pharmacology , Catalytic Domain/drug effects , Crystallography, X-Ray , Density Functional Theory , Ferrous Compounds/chemical synthesis , Ferrous Compounds/chemistry , Models, Molecular , Molecular Structure , Mycobacteriaceae/enzymology , Sulfhydryl Compounds/chemistry
6.
Microb Cell Fact ; 19(1): 187, 2020 Oct 02.
Article in English | MEDLINE | ID: mdl-33008397

ABSTRACT

Mycobacterium neoaurum strains can transform phytosterols to 4-androstene-3,17-dione (4-AD), a key intermediate for the synthesis of advanced steroidal medicines. In this work, we presented the complete genome sequence of the M. neoaurum strain HGMS2, which transforms ß-sitosterol to 4-AD. Through genome annotation, a phytosterol-degrading pathway in HGMS2 was predicted and further shown to form a 9,10-secosteroid intermediate by five groups of enzymes. These five groups of enzymes included three cholesterol oxidases (ChoM; group 1: ChoM1, ChoM2 and Hsd), two monooxygenases (Mon; group 2: Mon164 and Mon197), a set of enzymes for side-chain degradation (group 3), one 3-ketosteroid-1,2-dehydrogenase (KstD; group 4: KstD211) and three 3-ketosteroid-9a-hydroxylases (Ksh; group 5: KshA226, KshA395 and KshB122). A gene cluster encoding Mon164, KstD211, KshA226, KshB122 and fatty acid ß-oxidoreductases constituted one integrated metabolic pathway, while genes encoding other key enzymes were sporadically distributed. All key enzymes except those from group 3 were prepared as recombinant proteins and their activities were evaluated, and the proteins exhibited distinct activities compared with enzymes identified from other bacterial species. Importantly, we found that the KstD211 and KshA395 enzymes in the HGMS2 strain retained weak activities and caused the occurrence of two major impurities, i.e., 1,4-androstene-3,17-dione (ADD) and 9-hydroxyl-4-androstene-3,17-dione (9OH-AD) during ß-sitosterol fermentation. The concurrence of these two 4-AD analogs not only lowered 4-AD production yield but also hampered 4-AD purification. HGMS2 has the least number of genes encoding KstD and Ksh enzymes compared with current industrial strains. Therefore, HGMS2 could be a potent strain by which the 4-AD production yield could be enhanced by disabling the KstD211 and KshA395 enzymes. Our work also provides new insight into the engineering of the HGMS2 strain to produce ADD and 9OH-AD for industrial application.


Subject(s)
Androstenedione/biosynthesis , Mycobacteriaceae/enzymology , Mycobacteriaceae/genetics , Phytosterols/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Metabolic Networks and Pathways , Whole Genome Sequencing
7.
Biochem Biophys Res Commun ; 529(3): 548-553, 2020 08 27.
Article in English | MEDLINE | ID: mdl-32736672

ABSTRACT

Using a newly discovered encapsulin from Mycolicibacterium hassiacum, several biocatalysts were packaged in this robust protein cage. The encapsulin was found to be easy to produce as recombinant protein. Elucidation of its crystal structure revealed that it is a spherical protein cage of 60 protomers (diameter of 23 nm) with narrow pores. By developing an effective coexpression and isolation procedure, the effect of packaging a variety of biocatalysts could be evaluated. It was shown that encapsulation results in a significantly higher stability of the biocatalysts. Most of the targeted cofactor-containing biocatalysts remained active in the encapsulin. Due to the restricted diameters of the encapsulin pores (5-9 Å), the protein cage protects the encapsulated enzymes from bulky compounds. The work shows that encapsulins may be valuable tools to tune the properties of biocatalysts such as stability and substrate specificity.


Subject(s)
Bacterial Proteins/metabolism , Enzymes, Immobilized/metabolism , Enzymes/metabolism , Mycobacteriaceae/enzymology , Recombinant Proteins/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/ultrastructure , Biocatalysis , Cryoelectron Microscopy , Crystallography, X-Ray , Enzyme Stability , Enzymes/genetics , Microscopy, Electron, Transmission , Mycobacteriaceae/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/ultrastructure , Substrate Specificity , Temperature
8.
Chembiochem ; 21(20): 2931-2938, 2020 10 15.
Article in English | MEDLINE | ID: mdl-32495977

ABSTRACT

Comprehensive functional analyses of E-isoprenyl diphosphate synthases (E-IDSs) from nonpathogenic Mycobacterium vanbaalenii have been performed. Mv0992 and Mv1577 represent a nonaprenyl diphosphate (E-C45 ) synthase and a geranylgeranyl diphosphate (E-C20 ) synthase, respectively. Although Mv3536 was identified as an E-C20 synthase using a single enzyme, co-incubation of Mv3536 and Z-IDSs (Mv4662 and Mv3822) strongly suggested it releases an intermediate geranyl diphosphate (E-C10 ) during a continuous condensation reaction. Mv0992 and Mv3536 functions differed from those of the previously reported pathogenic Mycobacterium tuberculosis homologues Rv0562 and Rv2173, respectively. Re-analysis of Rv0562 and Rv2173 demonstrated that their functions were similar to those of Mv0992 and Mv3536 (Rv0562: E-C45 synthase; Rv2173: E-C10-15 synthase). The newly proposed functions of Rv0562 and Rv2173 would be in the biosynthesis of menaquinone and glycosyl carrier lipids essential for growth. Furthermore, a reduced allylic diphosphate could be used as the Z-IDS of the Mv3822 substrate, thereby introducing a potentially novel pathway of cyclic sesquarterpene biosynthesis.


Subject(s)
Alkyl and Aryl Transferases/metabolism , Mycobacteriaceae/enzymology , Mycobacterium tuberculosis/enzymology , Terpenes/metabolism , Alkyl and Aryl Transferases/genetics , Alkyl and Aryl Transferases/isolation & purification , Molecular Structure , Terpenes/chemistry
9.
Appl Microbiol Biotechnol ; 104(7): 2999-3009, 2020 Apr.
Article in English | MEDLINE | ID: mdl-32064550

ABSTRACT

ω-Transaminase (ω-TA) is an attractive alternative to metal catalysts for the stereoselective amination of prochiral ketones. The narrow substrate scope of an R-ω-transaminase from Mycobacterium vanbaalenii (MvTA) limits its application in R-amine synthesis. A fluorescence-based TA activity screening system was developed to extend its substrate scope. The reactions were conducted in microtiter plates (MTPs) and displayed low background interference, high sensitivity (µM magnitude), and a wide dynamic range (ɀ-factor > 0.9). A KnowVolution campaign was performed on this enzyme, and screening ~ 8000 clones with this fluorescence-based screening system resulted in two beneficial substitutions (G68Y and F129A) and three improved variants (M3, M4, and M5). The best variant, MvTA M5 (WT+G68Y+F129A), achieved the highest catalytic efficiency (toward fluorogenic substrate NMA) which was 3.2-fold higher than that of the WT enzyme. MvTA M5 exhibited significantly enhanced activity toward six different prochiral ketones with e.e. > 99% (R). The specific activity of MvTA M5 was more than 100 times higher than that of the WT enzyme toward acetonaphthone (M5: 8.1 U/mg, WT: ~ 0.07 U/mg), and it showed the highest activity on acetonaphthone, p-ethylacetophenone, and phenylacetone.


Subject(s)
High-Throughput Screening Assays/methods , Transaminases/genetics , Transaminases/metabolism , Amines/metabolism , Amino Acid Substitution , Directed Molecular Evolution , Enzyme Stability , Fluorescence , Ketones/metabolism , Kinetics , Mycobacteriaceae/enzymology , Mycobacteriaceae/genetics , Mycobacteriaceae/metabolism , Protein Engineering , Substrate Specificity
10.
Chemistry ; 26(6): 1328-1334, 2020 Jan 27.
Article in English | MEDLINE | ID: mdl-31545545

ABSTRACT

Sulfoxide synthases are non-heme iron enzymes that participate in the biosynthesis of thiohistidines, such as ergothioneine and ovothiol A. The sulfoxide synthase EgtB from Chloracidobacterium thermophilum (CthEgtB) catalyzes oxidative coupling between the side chains of N-α-trimethyl histidine (TMH) and cysteine (Cys) in a reaction that entails complete reduction of molecular oxygen, carbon-sulfur (C-S) and sulfur-oxygen (S-O) bond formation as well as carbon-hydrogen (C-H) bond cleavage. In this report, we show that CthEgtB and other bacterial sulfoxide synthases cannot efficiently accept selenocysteine (SeCys) as a substrate in place of cysteine. In contrast, the sulfoxide synthase from the filamentous fungus Chaetomium thermophilum (CthEgt1) catalyzes C-S and C-Se bond formation at almost equal efficiency. We discuss evidence suggesting that this functional difference between bacterial and fungal sulfoxide synthases emerges from different modes of oxygen activation.


Subject(s)
Acidobacteria/enzymology , Bacterial Proteins/antagonists & inhibitors , Fungal Proteins/antagonists & inhibitors , Selenocysteine/chemistry , Bacterial Proteins/metabolism , Binding Sites , Binding, Competitive , Biocatalysis , Catalytic Domain , Cysteine Dioxygenase/antagonists & inhibitors , Cysteine Dioxygenase/metabolism , Ergothioneine/chemistry , Ergothioneine/metabolism , Fungal Proteins/metabolism , Kinetics , Molecular Dynamics Simulation , Mycobacteriaceae/enzymology , Selenocysteine/metabolism
11.
Bioorg Med Chem Lett ; 30(2): 126792, 2020 01 15.
Article in English | MEDLINE | ID: mdl-31757668

ABSTRACT

Inosine-5'-monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme involved in nucleotide biosynthesis. Because of its critical role in purine biosynthesis, IMPDH is a drug design target for immunosuppressive, anticancer, antiviral and antimicrobial chemotherapy. In this study, we use mass spectrometry and X-ray crystallography to show that the inhibitor 6-Cl-purine ribotide forms a covalent adduct with the Cys-341 residue of Mycobacterium thermoresistibile IMPDH.


Subject(s)
Bacterial Proteins/antagonists & inhibitors , Enzyme Inhibitors/chemistry , IMP Dehydrogenase/antagonists & inhibitors , Mycobacteriaceae/enzymology , Bacterial Proteins/metabolism , Binding Sites , Crystallography, X-Ray , Drug Design , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/metabolism , IMP Dehydrogenase/metabolism , Molecular Dynamics Simulation , Protein Structure, Tertiary , Purine Nucleotides/chemical synthesis , Purine Nucleotides/chemistry , Purine Nucleotides/metabolism
12.
mBio ; 10(6)2019 11 26.
Article in English | MEDLINE | ID: mdl-31772052

ABSTRACT

Trehalose is an essential disaccharide for mycobacteria and a key constituent of several cell wall glycolipids with fundamental roles in pathogenesis. Mycobacteria possess two pathways for trehalose biosynthesis. However, only the OtsAB pathway was found to be essential in Mycobacterium tuberculosis, with marked growth and virulence defects of OtsA mutants and strict essentiality of OtsB2. Here, we report the first mycobacterial OtsA structures from Mycobacterium thermoresistibile in both apo and ligand-bound forms. Structural information reveals three key residues in the mechanism of substrate preference that were further confirmed by site-directed mutagenesis. Additionally, we identify 2-oxoglutarate and 2-phosphoglycerate as allosteric regulators of OtsA. The structural analysis in this work strongly contributed to define the mechanisms for feedback inhibition, show different conformational states of the enzyme, and map a new allosteric site.IMPORTANCE Mycobacterial infections are a significant source of mortality worldwide, causing millions of deaths annually. Trehalose is a multipurpose disaccharide that plays a fundamental structural role in these organisms as a component of mycolic acids, a molecular hallmark of the cell envelope of mycobacteria. Here, we describe the first mycobacterial OtsA structures. We show mechanisms of substrate preference and show that OtsA is regulated allosterically by 2-oxoglutarate and 2-phosphoglycerate at an interfacial site. These results identify a new allosteric site and provide insight on the regulation of trehalose synthesis through the OtsAB pathway in mycobacteria.


Subject(s)
Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Glucosyltransferases/chemistry , Glucosyltransferases/metabolism , Glyceric Acids/metabolism , Ketoglutaric Acids/metabolism , Mycobacteriaceae/enzymology , Allosteric Regulation , Bacterial Proteins/genetics , Gene Expression Regulation, Bacterial , Gene Expression Regulation, Enzymologic , Glucosyltransferases/genetics , Mycobacteriaceae/genetics , Mycobacteriaceae/metabolism , Substrate Specificity , Trehalose/metabolism
13.
Biochem Biophys Res Commun ; 517(3): 399-406, 2019 09 24.
Article in English | MEDLINE | ID: mdl-31378370

ABSTRACT

Mycobacterium smegmatis is a good model for studying the physiology and pathogenesis of Mycobacterium tuberculosis due to its genetic similarity. As methionine biosynthesis exists only in microorganisms, the enzymes involved in methionine biosynthesis can be a potential target for novel antibiotics. Homoserine O-acetyltransferase from M. smegmatis (MsHAT) catalyzes the transfer of acetyl-group from acetyl-CoA to homoserine. To investigate the molecular mechanism of MsHAT, we determined its crystal structure in apo-form and in complex with either CoA or homoserine and revealed the substrate binding mode of MsHAT. A structural comparison of MsHAT with other HATs suggests that the conformation of the α5 to α6 region might influence the shape of the dimer. In addition, the active site entrance shows an open or closed conformation and might determine the substrate binding affinity of HATs.


Subject(s)
Acetyl Coenzyme A/chemistry , Acetyltransferases/chemistry , Apoproteins/chemistry , Bacterial Proteins/chemistry , Homoserine/chemistry , Mycobacterium smegmatis/chemistry , Acetyl Coenzyme A/metabolism , Acetyltransferases/genetics , Acetyltransferases/metabolism , Amino Acid Sequence , Apoproteins/genetics , Apoproteins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Catalytic Domain , Cloning, Molecular , Crystallography, X-Ray , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Haemophilus influenzae/chemistry , Haemophilus influenzae/enzymology , Haemophilus influenzae/genetics , Homoserine/metabolism , Kinetics , Leptospira interrogans/chemistry , Leptospira interrogans/enzymology , Leptospira interrogans/genetics , Models, Molecular , Mycobacteriaceae/chemistry , Mycobacteriaceae/enzymology , Mycobacteriaceae/genetics , Mycobacterium abscessus/chemistry , Mycobacterium abscessus/enzymology , Mycobacterium abscessus/genetics , Mycobacterium smegmatis/enzymology , Mycobacterium smegmatis/genetics , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Protein Multimerization , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Alignment , Sequence Homology, Amino Acid , Substrate Specificity
14.
PLoS One ; 6(1): e15228, 2011 Jan 11.
Article in English | MEDLINE | ID: mdl-21264299

ABSTRACT

Dephosphocoenzyme A kinase performs the transfer of the γ-phosphate of ATP to dephosphocoenzyme A, catalyzing the last step of coenzyme A biosynthesis. This enzyme belongs to the P-loop-containing NTP hydrolase superfamily, all members of which posses a three domain topology consisting of a CoA domain that binds the acceptor substrate, the nucleotide binding domain and the lid domain. Differences in the enzymatic organization and regulation between the human and mycobacterial counterparts, have pointed out the tubercular CoaE as a high confidence drug target (HAMAP database). Unfortunately the absence of a three-dimensional crystal structure of the enzyme, either alone or complexed with either of its substrates/regulators, leaves both the reaction mechanism unidentified and the chief players involved in substrate binding, stabilization and catalysis unknown. Based on homology modeling and sequence analysis, we chose residues in the three functional domains of the enzyme to assess their contributions to ligand binding and catalysis using site-directed mutagenesis. Systematically mutating the residues from the P-loop and the nucleotide-binding site identified Lys14 and Arg140 in ATP binding and the stabilization of the phosphoryl intermediate during the phosphotransfer reaction. Mutagenesis of Asp32 and Arg140 showed catalytic efficiencies less than 5-10% of the wild type, indicating the pivotal roles played by these residues in catalysis. Non-conservative substitution of the Leu114 residue identifies this leucine as the critical residue from the hydrophobic cleft involved in leading substrate, DCoA binding. We show that the mycobacterial enzyme requires the Mg(2+) for its catalytic activity. The binding energetics of the interactions of the mutant enzymes with the substrates were characterized in terms of their enthalpic and entropic contributions by ITC, providing a complete picture of the effects of the mutations on activity. The properties of mutants defective in substrate recognition were consistent with the ordered sequential mechanism of substrate addition for CoaE.


Subject(s)
Mutagenesis, Site-Directed , Mycobacteriaceae/enzymology , Phosphotransferases (Alcohol Group Acceptor)/genetics , Bacterial Proteins , Catalysis , Humans , Protein Binding , Substrate Specificity/genetics , Thermodynamics
15.
Protein Sci ; 16(9): 1896-904, 2007 Sep.
Article in English | MEDLINE | ID: mdl-17660248

ABSTRACT

Mycobacterium leprae protein ML2640c belongs to a large family of conserved hypothetical proteins predominantly found in mycobacteria, some of them predicted as putative S-adenosylmethionine (AdoMet)-dependent methyltransferases (MTase). As part of a Structural Genomics initiative on conserved hypothetical proteins in pathogenic mycobacteria, we have determined the structure of ML2640c in two distinct crystal forms. As expected, ML2640c has a typical MTase core domain and binds the methyl donor substrate AdoMet in a manner consistent with other known members of this structural family. The putative acceptor substrate-binding site of ML2640c is a large internal cavity, mostly lined by aromatic and aliphatic side-chain residues, suggesting that a lipid-like molecule might be targeted for catalysis. A flap segment (residues 222-256), which isolates the binding site from the bulk solvent and is highly mobile in the crystal structures, could serve as a gateway to allow substrate entry and product release. The multiple sequence alignment of ML2640c-like proteins revealed that the central alpha/beta core and the AdoMet-binding site are very well conserved within the family. However, the amino acid positions defining the binding site for the acceptor substrate display a higher variability, suggestive of distinct acceptor substrate specificities. The ML2640c crystal structures offer the first structural glimpses at this important family of mycobacterial proteins and lend strong support to their functional assignment as AdoMet-dependent methyltransferases.


Subject(s)
Methyltransferases/chemistry , Mycobacteriaceae/enzymology , Mycobacterium leprae/enzymology , S-Adenosylmethionine/chemistry , Amino Acid Sequence , Binding Sites , Computational Biology/methods , Crystallography, X-Ray , Databases, Protein , Methyltransferases/genetics , Methyltransferases/metabolism , Models, Molecular , Molecular Sequence Data , Mycobacteriaceae/genetics , Mycobacterium leprae/genetics , Protein Binding , Protein Structure, Secondary , Protein Structure, Tertiary , Sequence Homology, Amino Acid , Static Electricity , Substrate Specificity
16.
Antonie Van Leeuwenhoek ; 87(3): 221-32, 2005 Apr.
Article in English | MEDLINE | ID: mdl-15803388

ABSTRACT

The nitrile metabolising strains AJ270, AJ300 and AJ115 were isolated from the same location. The strains have very similar nitrile metabolising profiles. Sequencing of the 16S rRNA gene indicates that strains AJ270 and AJ300 are novel strains of Rhodococcus erythropolis while strain AJ115 is a novel Microbacterium strain very closely related to Microbacterium oxydans and Microbacterium liquefaciens. Analysis of the structure of the nitrile hydratase/amidase gene clusters in the three strains indicates that this region is identical in these strains and that this structure is different to other nitrile hydratase/amidase gene clusters. The major difference seen is the insertion of a complete copy of the insertion sequence IS1166 in the nhr2 gene. This copy of IS1166 generates a 10 bp direct duplication at the point of insertion and has one ORF encoding a protein of 434 amino acids, with 98% homology to the transposase of IS666 from Mycobacterium avium. A gene oxd, encoding aldoxime dehydratase is found upstream of the nitrile hydratase gene cluster and an open reading frame encoding a protein with homology to GlnQ type ABC transporters is found downstream of the nitrile hydratase/amidase genes. The identity of the nitrile hydratase/amidase gene clusters in the three strains suggests horizontal gene transfer of this region. Analysis of the strains for both linear and circular plasmids indicates that both are present in the strains but hybridisation studies indicate that the nitrile hydratase/amidase gene cluster is chromosomally located. The nitrile hydratase/amidase enzymes of strain AJ270 are inducible with acetonitrile or acetamide. Interestingly although a number of Fe-type nitrile hydratases have been shown to be photosensitive, the enzyme from strain AJ270 is not.


Subject(s)
Evolution, Molecular , Gene Transfer, Horizontal , Genes, Bacterial , Hydro-Lyases/genetics , Mycobacteriaceae/genetics , Rhodococcus/genetics , ATP-Binding Cassette Transporters/genetics , Amino Acid Sequence , Base Sequence , Chromosomes, Bacterial/genetics , DNA Transposable Elements , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Gene Order , Hydro-Lyases/metabolism , Molecular Sequence Data , Multigene Family , Mycobacteriaceae/enzymology , Mycobacteriaceae/isolation & purification , Open Reading Frames , Phylogeny , Plasmids/genetics , Polymerase Chain Reaction , Repetitive Sequences, Nucleic Acid/genetics , Rhodococcus/enzymology , Rhodococcus/isolation & purification , Sequence Alignment , Sequence Homology , Transposases/genetics
17.
J Bacteriol ; 187(4): 1369-76, 2005 Feb.
Article in English | MEDLINE | ID: mdl-15687201

ABSTRACT

The wax ester synthase/acyl coenzyme A (acyl-CoA):diacylglycerol acyltransferase (WS/DGAT) catalyzes the final steps in triacylglycerol (TAG) and wax ester (WE) biosynthesis in the gram-negative bacterium Acinetobacter sp. strain ADP1. It constitutes a novel class of acyltransferases which is fundamentally different from acyltransferases involved in TAG and WE synthesis in eukaryotes. The enzyme was purified by a three-step purification protocol to apparent homogeneity from the soluble fraction of recombinant Escherichia coli Rosetta (DE3)pLysS (pET23a::atfA). Purified WS/DGAT revealed a remarkably low substrate specificity, accepting a broad range of various substances as alternative acceptor molecules. Besides having DGAT and WS activity, the enzyme possesses acyl-CoA:monoacylglycerol acyltransferase (MGAT) activity. The sn-1 and sn-3 positions of acylglycerols are accepted with higher specificity than the sn-2 position. Linear alcohols ranging from ethanol to triacontanol are efficiently acylated by the enzyme, which exhibits highest specificities towards medium-chain-length alcohols. The acylation of cyclic and aromatic alcohols, such as cyclohexanol or phenylethanol, further underlines the unspecific character of this enzyme. The broad range of possible substrates may lead to biotechnological production of interesting wax ester derivatives. Determination of the native molecular weight revealed organization as a homodimer. The large number of WS/DGAT-homologous genes identified in pathogenic mycobacteria and their possible importance for the pathogenesis and latency of these bacteria makes the purified WS/DGAT from Acinetobacter sp. strain ADP1 a valuable model for studying this group of proteins in pathogenic mycobacteria.


Subject(s)
Acinetobacter/enzymology , Acyltransferases/isolation & purification , Acyltransferases/metabolism , Acinetobacter/chemistry , Acyltransferases/genetics , Alcohols/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/isolation & purification , Bacterial Proteins/metabolism , Cytoplasm/chemistry , Cytoplasm/enzymology , Diacylglycerol O-Acyltransferase , Dimerization , Escherichia coli/genetics , Escherichia coli/metabolism , Molecular Weight , Mycobacteriaceae/enzymology , Mycobacteriaceae/genetics , Mycobacteriaceae/pathogenicity , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Substrate Specificity , Triglycerides/biosynthesis , Waxes/metabolism
18.
Res Microbiol ; 141(5): 551-61, 1990 Jun.
Article in English | MEDLINE | ID: mdl-2218060

ABSTRACT

Cell-free extracts of various strains belonging to Mycobacterium paratuberculosis (Ptb) and "wood-pigeon" (WP) mycobacteria were compared by polyacrylamide gel electrophoresis and the various protein bands obtained were tested for peroxidase enzyme activity. One strain of Mycobacterium avium served as a control. Bacterial extracts were also analysed by crossed immunoelectrophoresis (CRIEP) and fused rocket immunoelectrophoresis (FRIEP) using antisera raised in rabbit against M. paratuberculosis and WP mycobacteria. The immunoprecipitates obtained both in CRIEP and FRIEP plates were subsequently stained for selective peroxidase enzyme staining. Our results showed that, although Ptb and WP mycobacteria shared common peroxidase isoenzymes and antigens, they also had specific immunoprecipitates showing the differences between the two groups of bacteria.


Subject(s)
Mycobacteriaceae/classification , Mycobacterium/classification , Peroxidases/analysis , Electrophoresis, Polyacrylamide Gel , Immunoelectrophoresis , In Vitro Techniques , Isoenzymes/analysis , Mycobacteriaceae/enzymology , Mycobacteriaceae/immunology , Mycobacterium/enzymology , Mycobacterium/immunology
19.
J Bacteriol ; 171(12): 6873-7, 1989 Dec.
Article in English | MEDLINE | ID: mdl-2592353

ABSTRACT

The ability of nitrogenase-containing Frankia sp. strain CpI1 vesicles to regrow vegetative hyphae is demonstrated. Vesicles attached to hyphae in N2-fixing CpI1 cultures and sucrose gradient-isolated vesicles exhibited hyphal outgrowths when incubated in certain defined liquid media. Single or multiple hyphal extensions grew out from the vesicles.


Subject(s)
Mycobacteriaceae/growth & development , Organelles/ultrastructure , Mycobacteriaceae/cytology , Mycobacteriaceae/enzymology , Nitrogen Fixation
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