Victor Stalon

Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase

Isopentenyl diphosphate:dimethylallyl diphosphate (IPP:DMAPP) isomerase catalyses a crucial activation step in the isoprenoid biosynthesis pathway. This enzyme is responsible for the isomerization of the carbon–carbon double bond of IPP to create the potent electrophile DMAPP. DMAPP then alkylates other molecules, including IPP, to initiate the extraordinary variety of isoprenoid compounds found in nature. The crystal structures of free and metal‐bound Escherichia coli IPP isomerase reveal critical active site features underlying its catalytic mechanism. The enzyme requires one Mn2+ or Mg2+ ion to fold in its active conformation, forming a distorted octahedral metal coordination site composed of three histidines and two glutamates and located in the active site. Two critical residues, C67 and E116, face each other within the active site, close to the metal‐binding site. The structures are compatible with a mechanism in which the cysteine initiates the reaction by protonating the carbon–carbon double bond, with the antarafacial rearrangement ultimately achieved by one of the glutamates involved in the metal coordination sphere. W161 may stabilize the highly reactive carbocation generated during the reaction through quadrupole– charge interaction.

Catalytic Mechanism of Escherichia coli Isopentenyl Diphosphate Isomerase Involves Cys-67, Glu-116, and Tyr-104 as Suggested by Crystal Structures of Complexes with Transition State Analogues and Irreversible Inhibitors

Isopentenyl diphosphate (IPP):dimethylallyl diphosphate (DMAPP) isomerase is a key enzyme in the biosynthesis of isoprenoids. The reaction involves protonation and deprotonation of the isoprenoid unit and proceeds through a carbocationic transition state. Analysis of the crystal structures (2 Å) of complexes ofEscherichia coli IPP·DMAPPs isomerase with a transition state analogue (N,N-dimethyl-2-amino-1-ethyl diphosphate) and a covalently attached irreversible inhibitor (3,4-epoxy-3-methyl-1-butyl diphosphate) indicates that Glu-116, Tyr-104, and Cys-67 are involved in the antarafacial addition/elimination of protons during isomerization. This work provides a new perspective about the mechanism of the reaction.

The occurrence of a catabolic and an anabolic ornithine carbamoyltransferase in Pseudomonas

Abstract The occurrence of two ornithine carbamoyltransferases (carbamoylphosphate: l -ornithine carbamoyltransferase, EC 2.1.3.3) in Pseudomonas is demonstrated by their separation with ammonium sulfate. The two enzymes are distinguished by their activities as a function of pH. On the basis of the regulation of their synthesis, an anabolic function is assigned to one of these enzymes, a catabolic function to the other.

The yggH Gene of Escherichia coli Encodes a tRNA (m7G46) Methyltransferase

We cloned, expressed, and purified the Escherichia coli YggH protein and show that it catalyzes the S-adenosyl-L-methionine-dependent formation of N(7)-methylguanosine at position 46 (m(7)G46) in tRNA. Additionally, we generated an E. coli strain with a disrupted yggH gene and show that the mutant strain lacks tRNA (m(7)G46) methyltransferase activity.

Catabolism of L-arginine by Pseudomonas aeruginosa

Pseudomonas aeruginosa is known to break down arginine by the arginine deiminase pathway. An additional pathway has now been found whereby arginine is converted to putrescine with agmatine and N-carbamoylputrescine as intermediates. The following enzyme activities belonging to this pathway were detected in crude extracts: arginine decarboxylase (EC 4.1.1.19), which catalyses the release of CO2 from arginine to give agmatine; agmatine deiminase (EC 3.5.3.12), which degrades agmatine to N-carbamoylputrescine; and N-carbamoylputrescine amidinohydrolase (EC 3.5.3.-), which then removes the ureido group of carbamoylputrescine. In crude extracts, arginine decarboxylase activity was stimulated by pyridoxal phosphate, Mg2+ and by the products of the catabolic pathway, putrescine and spermidine. Growth of P. aeruginosa on arginine as the sole carbon and nitrogen source markedly increased the activity of arginine decarboxylase. Agmatine and N-carbamoylputrescine induced the synthesis of agmatine deiminase and N-carbamoylputrescine hydrolase. Addition of succinate or citrate to medium containing arginine or agmatine led to repression of the enzymes involved in the arginine decarboxylase pathway. Moreover, the repression of agmatine deiminase and N-carbamoylputrescine hydrolase was further increased when P. aeruginosa was grown in media with agmatine plus glutamine or agmatine plus succinate and ammonia. This suggests that the expression of the agmatine pathway may be regulated by carbon catabolite repression as well as nitrogen catabolite repression.

L-Arginine Utilization by Pseudomonas Species

The utilization of arginine was studied in several different Pseudomonas species. The arginine decarboxylase and agmatine deiminase pathways were found to be characteristic of Pseudomonas species of group I as defined by Palleroni et al. (1974). Pseudomonas putida strains had three distinct arginine catabolic pathways initiated by arginine decarboxylase, arginine deiminase and arginine oxidase, respectively. The two former routes were also present in P. fluorescens and P. mendocina and in P. aeruginosa which also used arginine by a further unknown pathway. None of these pathways occurred in P. cepacia strains; agmatine catabolism seemed to follow an unusual route involving guanidinobutyrate as intermediate.

The specialization of the two ornithine carbamoyltransferases of Pseudomonas

Abstract The two ornithine carbamoyltransferases (carbamoylphosphate: l -ornithine carbamoyltransferase, EC 2.1.3.3) of Pseudomonas are integrated into different metabolic sequences. This integration appears both in their regulation and in their activities. In Pseudomonas IRC 204, the catabolic ornithine carbamoyltransferase is subject to catabolite repression in the same way as arginine deiminase ( l -arginine iminohydrolase, EC 3.5.3.6) and carbamate kinase (ATP: carbamate phosphotransferase, EC 2.7.2.2). The catabolic ornithine carbamoyltransferase in vivo, has little or no biosynthetic function. The anabolic ornithine carbamoyltransferase, unlike other similar enzymes, is unable to perform the catabolic phosphorolysis.

Arginine degradation in Pseudomonas aeruginosa mutants blocked in two arginine catabolic pathways.

SummaryPseudomonas aeruginosa mutants defective in agmatine utilization (agu) were isolated. The genes encoding agmatine deiminase (aguA) and N-carbamoylputrescine amidinohydrolase (aguB) were 98% cotransducible and mapped between gpu and ser-3 in the 30 min region of the chromosome. Constructed agu arc double mutants (blocked in the arginine decarboxylase and arginine deiminase pathways) used arginine efficiently as the sole carbon and nitrogen source. This suggests the existence of a further arginine catabolic pathway in P. aeruginosa. The mapping data of this study confirm that in P. aeruginosa the chromosomal genes with catabolic functions do not show supraoperonic clustering as found in P. putida.

Catabolism of arginine, citrulline and ornithine by Pseudomonas and related bacteria.

The distribution of the arginine succinyltransferase pathway was examined in representative strains of Pseudomonas and related bacteria able to use arginine as the sole carbon and nitrogen source for growth. The arginine succinyltransferase pathway was induced in arginine-grown cells. The accumulation of succinylornithine following in vivo inhibition of succinylornithine transaminase activity by aminooxyacetic acid showed that this pathway is responsible for the dissimilation of the carbon skeleton of arginine. Catabolism of citrulline as a carbon source was restricted to relatively few of the organisms tested. In P. putida, P. cepacia and P. indigofera, ornithine was the main product of citrulline degradation. In most strains which possessed the arginine succinyltransferase pathway, the first step of ornithine utilization as a carbon source was the conversion of ornithine into succinylornithine through an ornithine succinyltransferase. However P. cepacia and P. putida used ornithine by a pathway which proceeded via proline as an intermediate and involved an ornithine cyclase activity.

Isolation and characterization of Pseudomonas putida mutants affected in arginine, ornithine and citrulline catabolism: function of the arginine oxidase and arginine succinyltransferase pathways

Pseudomonas putida mutants impaired in the utilization of arginine are affected in either the arginine succinyltransferase pathway, the arginine oxidase route, or both. However, mutants affected in one of the pathways still grow on arginine as sole carbon source. Analysis of the products excreted by both wild-type and mutant strains suggests that arginine is mainly channelled by the oxidase route. Proline non-utilizing mutants are also affected in ornithine utilization, confirming the role of proline as an intermediate in ornithine catabolism. Mutants affected in ornithine cyclodeaminase activity still grow on proline and become unable to use ornithine. Both proline non-utilizing mutants and ornithine-cyclodeaminase-minus mutants are unable to use citrulline. These results, together with induction of ornithine cyclodeaminase when wild-type P. putida is grown on citrulline, indicate that utilization of citrulline as a carbon source proceeds via proline with ornithine as an intermediate. Thus in P. putida, the aerobic catabolism of arginine on the one hand and citrulline and ornithine on the other proceed by quite different metabolic segments.