scholarly journals Differential Substrate Specificity and Kinetic Behavior of Escherichia coli YfdW and Oxalobacter formigenes Formyl Coenzyme A Transferase

2008 ◽  
Vol 190 (7) ◽  
pp. 2556-2564 ◽  
Author(s):  
Cory G. Toyota ◽  
Catrine L. Berthold ◽  
Arnaud Gruez ◽  
Stefán Jónsson ◽  
Ylva Lindqvist ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Substrate Specificity ◽  
Coenzyme A ◽  
Substrate Inhibition ◽  
Kinetic Behavior ◽  
Oxalobacter Formigenes ◽  
Structural Genomic ◽  
E Coli ◽  
Coa Transferase ◽  
Acidic Conditions

ABSTRACT The yfdXWUVE operon appears to encode proteins that enhance the ability of Escherichia coli MG1655 to survive under acidic conditions. Although the molecular mechanisms underlying this phenotypic behavior remain to be elucidated, findings from structural genomic studies have shown that the structure of YfdW, the protein encoded by the yfdW gene, is homologous to that of the enzyme that mediates oxalate catabolism in the obligate anaerobe Oxalobacter formigenes, O. formigenes formyl coenzyme A transferase (FRC). We now report the first detailed examination of the steady-state kinetic behavior and substrate specificity of recombinant, wild-type YfdW. Our studies confirm that YfdW is a formyl coenzyme A (formyl-CoA) transferase, and YfdW appears to be more stringent than the corresponding enzyme (FRC) in Oxalobacter in employing formyl-CoA and oxalate as substrates. We also report the effects of replacing Trp-48 in the FRC active site with the glutamine residue that occupies an equivalent position in the E. coli protein. The results of these experiments show that Trp-48 precludes oxalate binding to a site that mediates substrate inhibition for YfdW. In addition, the replacement of Trp-48 by Gln-48 yields an FRC variant for which oxalate-dependent substrate inhibition is modified to resemble that seen for YfdW. Our findings illustrate the utility of structural homology in assigning enzyme function and raise the question of whether oxalate catabolism takes place in E. coli upon the up-regulation of the yfdXWUVE operon under acidic conditions.

scholarly journals Substrate Specificity of the 3-Methylcrotonyl Coenzyme A (CoA) and Geranyl-CoA Carboxylases from Pseudomonas aeruginosa

2008 ◽  
Vol 190 (14) ◽  
pp. 4888-4893 ◽  
Author(s):  
J. A. Aguilar ◽  
C. Díaz-Pérez ◽  
A. L. Díaz-Pérez ◽  
J. S. Rodríguez-Zavala ◽  
B. J. Nikolau ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Substrate Specificity ◽  
Recombinant Proteins ◽  
Coenzyme A ◽  
Affinity Constant ◽  
Kinetic Behavior ◽  
Sigmoidal Kinetics ◽  
Leucine Catabolism ◽  
Temperature Optima

ABSTRACT Biotin-containing 3-methylcrotonyl coenzyme A (MC-CoA) carboxylase (MCCase) and geranyl-CoA (G-CoA) carboxylase (GCCase) from Pseudomonas aeruginosa were expressed as His-tagged recombinant proteins in Escherichia coli. Both native and recombinant MCCase and GCCase showed pH and temperature optima of 8.5 and 37°C. The apparent K 0.5 (affinity constant for non-Michaelis-Menten kinetics behavior) values of MCCase for MC-CoA, ATP, and bicarbonate were 9.8 μM, 13 μM, and 0.8 μM, respectively. MCCase activity showed sigmoidal kinetics for all the substrates and did not carboxylate G-CoA. In contrast, GCCase catalyzed the carboxylation of both G-CoA and MC-CoA. GCCase also showed sigmoidal kinetic behavior for G-CoA and bicarbonate but showed Michaelis-Menten kinetics for MC-CoA and the cosubstrate ATP. The apparent K 0.5 values of GCCase were 8.8 μM and 1.2 μM for G-CoA and bicarbonate, respectively, and the apparent Km values of GCCase were 10 μM for ATP and 14 μM for MC-CoA. The catalytic efficiencies of GCCase for G-CoA and MC-CoA were 56 and 22, respectively, indicating that G-CoA is preferred over MC-CoA as a substrate. The enzymatic properties of GCCase suggest that it may substitute for MCCase in leucine catabolism and that both the MCCase and GCCase enzymes play important roles in the leucine and acyclic terpene catabolic pathways.

scholarly journals Application of a Propionyl Coenzyme A Synthetase for Poly(3-Hydroxypropionate-co-3-Hydroxybutyrate) Accumulation in Recombinant Escherichia coli

2000 ◽  
Vol 66 (12) ◽  
pp. 5253-5258 ◽  
Author(s):  
Henry E. Valentin ◽  
Timothy A. Mitsky ◽  
Debbie A. Mahadeo ◽  
Minhtien Tran ◽  
Kenneth J. Gruys
Keyword(s):  
Escherichia Coli ◽  
Coenzyme A ◽  
Ralstonia Eutropha ◽  
Specific Activity ◽  
Biosynthetic Genes ◽  
Acetyl Coa ◽  
Reading Frame ◽  
E Coli ◽  
Coa Transferase ◽  
Serovar Typhimurium

ABSTRACT The genetic operon for propionic acid degradation inSalmonella enterica serovar Typhimurium contains an open reading frame designated prpE which encodes a propionyl coenzyme A (propionyl-CoA) synthetase (A. R. Horswill and J. C. Escalante-Semerena, Microbiology 145:1381–1388, 1999). In this paper we report the cloning of prpE by PCR, its overexpression in Escherichia coli, and the substrate specificity of the enzyme. When propionate was utilized as the substrate for PrpE, a Km of 50 μM and a specific activity of 120 μmol � min−1 � mg−1 were found at the saturating substrate concentration. PrpE also activated acetate, 3-hydroxypropionate (3HP), and butyrate to their corresponding coenzyme A esters but did so much less efficiently than propionate. When prpE was coexpressed with the polyhydroxyalkanoate (PHA) biosynthetic genes from Ralstonia eutropha in recombinant E. coli, a PHA copolymer containing 3HP units accumulated when 3HP was supplied with the growth medium. To compare the utility of acyl-CoA synthetases to that of an acyl-CoA transferase for PHA production, PHA-producing recombinant strains were constructed to coexpress the PHA biosynthetic genes with prpE, with acoE (an acetyl-CoA synthetase gene from R. eutropha [H. Priefert and A. Steinb�chel, J. Bacteriol. 174:6590–6599, 1992]), or with orfZ (an acetyl-CoA:4-hydroxybutyrate-CoA transferase gene from Clostridium propionicum [H. E. Valentin, S. Reiser, and K. J. Gruys, Biotechnol. Bioeng. 67:291–299, 2000]). Of the three enzymes, PrpE and OrfZ enabled similar levels of 3HP incorporation into PHA, whereas AcoE was significantly less effective in this capacity.

scholarly journals 3-oxo acid coenzyme A-transferase in normal and diabetic rat muscle

1976 ◽  
Vol 158 (2) ◽  
pp. 509-512 ◽  
Author(s):  
A Fenselau ◽  
K Wallis
Keyword(s):  
Skeletal Muscle ◽  
Coenzyme A ◽  
Substrate Inhibition ◽  
Diabetic Rats ◽  
Diabetic Rat ◽  
Functional Parameters ◽  
Rat Muscle ◽  
Coa Transferase ◽  
Normal Rat ◽  
Streptozotocin Diabetic Rats

The amounts of succinyl-CoA--3-oxo acid CoA-transferase (EC 2.8.3.5) decrease progressively in skeletal muscle in streptozotocin-diabetic rats, reaching after 10 days about 50% of the value in normal rat muscle. Electrofocusing studies indicate the occurrence of partial proteolysis of the enzyme in diabetic muscle. However, several functional parameters relating to acetoacetate utilization, including substrate inhibition, are quite similar for muscle transferase preparations from normal and diseased rats. The development of pathological ketoacidosis is discussed in the light of these observations.

scholarly journals Tyrosine phosphorylation-dependent localization of TmaR that controls activity of a major bacterial sugar regulator by polar sequestration

2020 ◽  
Vol 118 (2) ◽  
pp. e2016017118
Author(s):  
Tamar Szoke ◽  
Nitsan Albocher ◽  
Sutharsan Govindarajan ◽  
Anat Nussbaum-Shochat ◽  
Orna Amster-Choder
Keyword(s):  
Escherichia Coli ◽  
Sugar Uptake ◽  
Dependent Manner ◽  
Tyrosine Residue ◽  
Sugar Consumption ◽  
E Coli ◽  
Acidic Conditions ◽  
Enzyme I ◽  
Uptake And Metabolism ◽  
Protein Enzyme

The poles of Escherichia coli cells are emerging as hubs for major sensory systems, but the polar determinants that allocate their components to the pole are largely unknown. Here, we describe the discovery of a previously unannotated protein, TmaR, which localizes to the E. coli cell pole when phosphorylated on a tyrosine residue. TmaR is shown here to control the subcellular localization and activity of the general PTS protein Enzyme I (EI) by binding and polar sequestration of EI, thus regulating sugar uptake and metabolism. Depletion or overexpression of TmaR results in EI release from the pole or enhanced recruitment to the pole, which leads to increasing or decreasing the rate of sugar consumption, respectively. Notably, phosphorylation of TmaR is required to release EI and enable its activity. Like TmaR, the ability of EI to be recruited to the pole depends on phosphorylation of one of its tyrosines. In addition to hyperactivity in sugar consumption, the absence of TmaR also leads to detrimental effects on the ability of cells to survive in mild acidic conditions. Our results suggest that this survival defect, which is sugar- and EI-dependent, reflects the difficulty of cells lacking TmaR to enter stationary phase. Our study identifies TmaR as the first, to our knowledge, E. coli protein reported to localize in a tyrosine-dependent manner and to control the activity of other proteins by their polar sequestration and release.

scholarly journals Family Shuffling of Expandase Genes To Enhance Substrate Specificity for Penicillin G

2004 ◽  
Vol 70 (10) ◽  
pp. 6257-6263 ◽  
Author(s):  
Jyh-Shing Hsu ◽  
Yunn-Bor Yang ◽  
Chan-Hui Deng ◽  
Chia-Li Wei ◽  
Shwu-Huey Liaw ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Substrate Specificity ◽  
Kinetic Parameters ◽  
Substrate Inhibition ◽  
Fold Increase ◽  
Streptomyces Clavuligerus ◽  
Penicillin G ◽  
Dna Shuffling ◽  
Homologous Genes ◽  
Family Shuffling

ABSTRACT Deacetoxycephalosporin C synthase (expandase) from Streptomyces clavuligerus, encoded by cefE, is an important industrial enzyme for the production of 7-aminodeacetoxycephalosporanic acid from penicillin G. To improve the substrate specificity for penicillin G, eight cefE-homologous genes were directly evolved by using the DNA shuffling technique. After the first round of shuffling and screening, using an Escherichia coli ESS bioassay, four chimeras with higher activity were subjected to a second round. Subsequently, 20 clones were found with significantly enhanced activity. The kinetic parameters of two isolates that lack substrate inhibition showed 8.5- and 118-fold increases in the k cat/Km ratio compared to the S. clavuligerus expandase. The evolved enzyme with the 118-fold increase is the most active obtained to date anywhere. Our shuffling results also indicate the remarkable plasticity of the expandase, suggesting that more-active chimeras might be achievable with further rounds.

scholarly journals Engineered Synthetic Pathway for Isopropanol Production in Escherichia coli

2007 ◽  
Vol 73 (24) ◽  
pp. 7814-7818 ◽  
Author(s):  
T. Hanai ◽  
S. Atsumi ◽  
J. C. Liao
Keyword(s):  
Escherichia Coli ◽  
Secondary Alcohol ◽  
Clostridium Beijerinckii ◽  
Synthetic Pathway ◽  
E Coli ◽  
Coa Transferase ◽  
Secondary Alcohol Dehydrogenase ◽  
Acetoacetate Decarboxylase ◽  
Shake Flasks ◽  
K 12

ABSTRACT A synthetic pathway was engineered in Escherichia coli to produce isopropanol by expressing various combinations of genes from Clostridium acetobutylicum ATCC 824, E. coli K-12 MG1655, Clostridium beijerinckii NRRL B593, and Thermoanaerobacter brockii HTD4. The strain with the combination of C. acetobutylicum thl (acetyl-coenzyme A [CoA] acetyltransferase), E. coli atoAD (acetoacetyl-CoA transferase), C. acetobutylicum adc (acetoacetate decarboxylase), and C. beijerinckii adh (secondary alcohol dehydrogenase) achieved the highest titer. This strain produced 81.6 mM isopropanol in shake flasks with a yield of 43.5% (mol/mol) in the production phase. To our knowledge, this work is the first to produce isopropanol in E. coli, and the titer exceeded that from the native producers.

scholarly journals Analysis of crystalline and solution states of ligand-free spermidine N-acetyltransferase (SpeG) from Escherichia coli

2019 ◽  
Vol 75 (6) ◽  
pp. 545-553 ◽  
Author(s):  
Ekaterina V. Filippova ◽  
Steven Weigand ◽  
Olga Kiryukhina ◽  
Alan J. Wolfe ◽  
Wayne F. Anderson
Keyword(s):  
Escherichia Coli ◽  
Vibrio Cholerae ◽  
Crystal Structures ◽  
Coenzyme A ◽  
Amino Group ◽  
Acetyl Coenzyme A ◽  
E Coli ◽  
Ligand Free ◽  
Acetyl Group ◽  
Terminal Amino

Spermidine N-acetyltransferase (SpeG) transfers an acetyl group from acetyl-coenzyme A to an N-terminal amino group of intracellular spermidine. This acetylation inactivates spermidine, reducing the polyamine toxicity that tends to occur under certain chemical and physical stresses. The structure of the SpeG protein from Vibrio cholerae has been characterized: while the monomer possesses a structural fold similar to those of other Gcn5-related N-acetyltransferase superfamily members, its dodecameric structure remains exceptional. In this paper, structural analyses of SpeG isolated from Escherichia coli are described. Like V. cholerae SpeG, E. coli SpeG forms dodecamers, as revealed by two crystal structures of the ligand-free E. coli SpeG dodecamer determined at 1.75 and 2.9 Å resolution. Although both V. cholerae SpeG and E. coli SpeG can adopt an asymmetric open dodecameric state, solution analysis showed that the oligomeric composition of ligand-free E. coli SpeG differs from that of ligand-free V. cholerae SpeG. Based on these data, it is proposed that the equilibrium balance of SpeG oligomers in the absence of ligands differs from one species to another and thus might be important for SpeG function.

scholarly journals Properties of Succinyl-Coenzyme A:l-Malate Coenzyme A Transferase and Its Role in the Autotrophic 3-Hydroxypropionate Cycle of Chloroflexus aurantiacus

2006 ◽  
Vol 188 (7) ◽  
pp. 2646-2655 ◽  
Author(s):  
Silke Friedmann ◽  
Astrid Steindorf ◽  
Birgit E. Alber ◽  
Georg Fuchs
Keyword(s):  
Escherichia Coli ◽  
Coenzyme A ◽  
Chloroflexus Aurantiacus ◽  
Class Iii ◽  
Terminal Amino Acid ◽  
Acetyl Coa ◽  
Acetyl Coenzyme A ◽  
Coa Transferase ◽  
Terminal Amino ◽  
Terminal Amino Acid Sequence

ABSTRACT The 3-hydroxypropionate cycle has been proposed to operate as the autotrophic CO2 fixation pathway in the phototrophic bacterium Chloroflexus aurantiacus. In this pathway, acetyl coenzyme A (acetyl-CoA) and two bicarbonate molecules are converted to malate. Acetyl-CoA is regenerated from malyl-CoA by l-malyl-CoA lyase. The enzyme forming malyl-CoA, succinyl-CoA:l-malate coenzyme A transferase, was purified. Based on the N-terminal amino acid sequence of its two subunits, the corresponding genes were identified on a gene cluster which also contains the gene for l-malyl-CoA lyase, the subsequent enzyme in the pathway. Both enzymes were severalfold up-regulated under autotrophic conditions, which is in line with their proposed function in CO2 fixation. The two CoA transferase genes were cloned and heterologously expressed in Escherichia coli, and the recombinant enzyme was purified and studied. Succinyl-CoA:l-malate CoA transferase forms a large (αβ)n complex consisting of 46- and 44-kDa subunits and catalyzes the reversible reaction succinyl-CoA + l-malate → succinate + l-malyl-CoA. It is specific for succinyl-CoA as the CoA donor but accepts l-citramalate instead of l-malate as the CoA acceptor; the corresponding d-stereoisomers are not accepted. The enzyme is a member of the class III of the CoA transferase family. The demonstration of the missing CoA transferase closes the last gap in the proposed 3-hydroxypropionate cycle.

scholarly journals Oxalate-Degrading Activity in Bifidobacterium animalis subsp. lactis: Impact of Acidic Conditions on the Transcriptional Levels of the Oxalyl Coenzyme A (CoA) Decarboxylase and Formyl-CoA Transferase Genes

2010 ◽  
Vol 76 (16) ◽  
pp. 5609-5620 ◽  
Author(s):  
Silvia Turroni ◽  
Claudia Bendazzoli ◽  
Samuele C. F. Dipalo ◽  
Marco Candela ◽  
Beatrice Vitali ◽  
...  
Keyword(s):  
Coenzyme A ◽  
Genomic Library ◽  
Open Reading Frames ◽  
Transcriptional Analysis ◽  
Bifidobacterium Animalis ◽  
Reverse Transcription Pcr ◽  
Coa Transferase ◽  
Degrading Bacteria ◽  
Key Enzyme ◽  
Acidic Conditions

ABSTRACT Oxalic acid occurs extensively in nature and plays diverse roles, especially in pathological processes. Due to its highly oxidizing effects, hyperabsorption or abnormal synthesis of oxalate can cause serious acute disorders in mammals and can be lethal in extreme cases. Intestinal oxalate-degrading bacteria could therefore be pivotal in maintaining oxalate homeostasis and reducing the risk of kidney stone development. In this study, the oxalate-degrading activities of 14 bifidobacterial strains were measured by a capillary electrophoresis technique. The oxc gene, encoding oxalyl-coenzyme A (CoA) decarboxylase, a key enzyme in oxalate catabolism, was isolated by probing a genomic library of Bifidobacterium animalis subsp. lactis BI07, which was one of the most active strains in the preliminary screening. The genetic and transcriptional organization of oxc flanking regions was determined, unraveling the presence of two other independently transcribed open reading frames, potentially responsible for the ability of B. animalis subsp. lactis to degrade oxalate. pH-controlled batch fermentations revealed that acidic conditions were a prerequisite for a significant oxalate degradation rate, which dramatically increased in cells first adapted to subinhibitory concentrations of oxalate and then exposed to pH 4.5. Oxalate-preadapted cells also showed a strong induction of the genes potentially involved in oxalate catabolism, as demonstrated by a transcriptional analysis using quantitative real-time reverse transcription-PCR. These findings provide new insights into the characterization of oxalate-degrading probiotic bacteria and may support the use of B. animalis subsp. lactis as a promising adjunct for the prophylaxis and management of oxalate-related kidney disease.

scholarly journals Enzymic synthesis of N-acetyl-l-phenylalanine in Escherichia coli K12

1971 ◽  
Vol 124 (5) ◽  
pp. 905-913 ◽  
Author(s):  
R. V. Krishna ◽  
P. R. Krishnaswamy ◽  
D. Rajagopal Rao
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Substrate Specificity ◽  
Acetyl Coa ◽  
Ph Optimum ◽  
E Coli ◽  
Enzymic Synthesis ◽  
Escherichia Coli K12

1. Cell-free extracts of Escherichia coli K12 catalyse the synthesis of N-acetyl-l-phenylalanine from acetyl-CoA and l-phenylalanine. 2. The acetyl-CoA–l-phenylalanine α-N-acetyltransferase was purified 160-fold from cell-free extracts. 3. The enzyme has a pH optimum of 8 and catalyses the acetylation of l-phenylalanine. Other l-amino acids such as histidine and alanine are acetylated at slower rates. 4. A transacylase was also purified from E. coli extracts and its substrate specificity studied. 5. The properties of both these enzymes were compared with those of other known amino acid acetyltransferases and transacylases.

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