Substrate Specificity of the 3-Methylcrotonyl Coenzyme A (CoA) and Geranyl-CoA Carboxylases from
            <i>Pseudomonas aeruginosa</i>

Aguilar, Jean-David; Díaz-Pérez, César; Díaz-Pérez, Alma Laura; Rodríguez‐Zavala, José S.; Nikolau, Basil J.; Campos-Garcı́a, Jesús

doi:10.1128/jb.00454-08

Cited by 21 publications

(24 citation statements)

References 24 publications

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“…Nevertheless, the acyl-CoA carboxylases were distributed in a wide range of bacteria and most often clustered into clades congruent with the accepted main bacterial groups. Moreover, several arguments supported that GCC, MCC and PCC are parts of the acyl-CoA carboxylases: i) GCC, MCC and PCC sequences branched among sequences previously annotated as acyl-CoA carboxylases in our BC and CCT domain phylogenetic trees (Figures 3, 4 and 5); ii) MCCs and monofunctional PCCs were restricted to some proteobacterial groups, supporting the emergence of MCC and PCC functions from an original acyl-CoA carboxylase in a proteobacterial ancestor; iii) the GCC, MCC and PCC sequences shared a common domain architecture with the acyl-CoA carboxylases (Figure 2); iv) some GCC and PCC have been reported to carry out the carboxylation of different substrates, a promiscuity which is characteristic of the acyl-CoA carboxylases [7,30,32]. As a result, our phylogeny-based classification of GCC, MCC and PCC sequences into the acyl-CoA carboxylase group is reliable and strongly supports that these functions are specific adaptations from a promiscuous acyl-CoA carboxylase-like protein according to the metabolic needs of each species, a common process in enzyme evolution [52,53].…”

Section: Discussionmentioning

confidence: 98%

Early evolution of the biotin-dependent carboxylase family

Lombard

Moreira

2011

BMC Evol Biol

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BackgroundBiotin-dependent carboxylases are a diverse family of carboxylating enzymes widespread in the three domains of life, and thus thought to be very ancient. This family includes enzymes that carboxylate acetyl-CoA, propionyl-CoA, methylcrotonyl-CoA, geranyl-CoA, acyl-CoA, pyruvate and urea. They share a common catalytic mechanism involving a biotin carboxylase domain, which fixes a CO2 molecule on a biotin carboxyl carrier peptide, and a carboxyl transferase domain, which transfers the CO2 moiety to the specific substrate of each enzyme. Despite this overall similarity, biotin-dependent carboxylases from the three domains of life carrying their reaction on different substrates adopt very diverse protein domain arrangements. This has made difficult the resolution of their evolutionary history up to now.ResultsTaking advantage of the availability of a large amount of genomic data, we have carried out phylogenomic analyses to get new insights on the ancient evolution of the biotin-dependent carboxylases. This allowed us to infer the set of enzymes present in the last common ancestor of each domain of life and in the last common ancestor of all living organisms (the cenancestor). Our results suggest that the last common archaeal ancestor had two biotin-dependent carboxylases, whereas the last common bacterial ancestor had three. One of these biotin-dependent carboxylases ancestral to Bacteria most likely belonged to a large family, the CoA-bearing-substrate carboxylases, that we define here according to protein domain composition and phylogenetic analysis. Eukaryotes most likely acquired their biotin-dependent carboxylases through the mitochondrial and plastid endosymbioses as well as from other unknown bacterial donors. Finally, phylogenetic analyses support previous suggestions about the existence of an ancient bifunctional biotin-protein ligase bound to a regulatory transcription factor.ConclusionsThe most parsimonious scenario for the early evolution of the biotin-dependent carboxylases, supported by the study of protein domain composition and phylogenomic analyses, entails that the cenancestor possessed two different carboxylases able to carry out the specific carboxylation of pyruvate and the non-specific carboxylation of several CoA-bearing substrates, respectively. These enzymes may have been able to participate in very diverse metabolic pathways in the cenancestor, such as in ancestral versions of fatty acid biosynthesis, anaplerosis, gluconeogenesis and the autotrophic fixation of CO2.

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Section: Discussionmentioning

confidence: 98%

Early evolution of the biotin-dependent carboxylase family

Lombard

Moreira

2011

BMC Evol Biol

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“…3) [61]. In Pseudomonas organisms, MCC is required for the metabolism of acyclic terpenoids [14,208–212]. In Arabidopsis , MCC activity is required for seed development and germination [213].…”

Section: -Methylcrotonyl-coa Carboxylase (Mcc)mentioning

confidence: 99%

“…Human MCC has been expressed and purified from the baculovirus system in the active form [216]. It demonstrated hyperbolic kinetics with ATP and 3-methylcrotonyl-CoA, while the Pseudomonas MCC showed sigmoidal kinetics toward ATP [212]. …”

Section: -Methylcrotonyl-coa Carboxylase (Mcc)mentioning

confidence: 99%

Structure and function of biotin-dependent carboxylases

Tong

2012

Cell. Mol. Life Sci.

373

338

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Biotin-dependent carboxylases include acetyl-CoA carboxylase (ACC), propionyl-CoA carboxylase (PCC), 3-methylcrotonyl-CoA carboxylase (MCC), geranyl-CoA carboxylase (GCC), pyruvate carboxylase (PC), and urea carboxylase (UC). They contain biotin carboxylase (BC), carboxyltransferase (CT) and biotin-carboxyl carrier protein (BCCP) components. These enzymes are widely distributed in nature and have important functions in fatty acid metabolism, amino acid metabolism, carbohydrate metabolism, polyketide biosynthesis, urea utilization, and other cellular processes. ACCs are also attractive targets for drug discovery against type 2 diabetes, obesity, cancer, microbial infections, and other diseases, and the plastid ACC of grasses is the target of action of three classes of commercial herbicides. Deficiencies in the activities of PCC, MCC or PC are linked to serious diseases in humans. Our understanding of these enzymes has been greatly enhanced over the past few years by the crystal structures of the holoenzymes of PCC, MCC, PC, and UC. The structures reveal unanticipated features in the architectures of the holoenzymes, including the presence of previously unrecognized domains, and provide a molecular basis for understanding their catalytic mechanism as well as the large collection of disease-causing mutations in PCC, MCC and PC. This review will summarize the recent advances in our knowledge on the structure and function of these important metabolic enzymes.

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“…However, in contrast to other acyl-CoA esters, which are usually carboxylated at the ␣ position, the CO 2 group is in this case introduced at the ␥ position (50,52,59). Recently, the genes encoding geranoyl-CoA carboxylase, a homolog of 3-methylcrotonyl-CoA carboxylase, were identified and functionally assigned (4,63). Geranoyl-CoA carboxylase is involved in the degradation of branched iosoprenoids (acylic terpenes) and also employs ␥-carboxylation to overcome incomplete ␤-oxidation (50,51).…”

Section: Carboxylases In Assimilatory Pathwaysmentioning

confidence: 99%

Carboxylases in Natural and Synthetic Microbial Pathways

Erb

2011

Appl Environ Microbiol

183

165

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Carboxylases are among the most important enzymes in the biosphere, because they catalyze a key reaction in the global carbon cycle: the fixation of inorganic carbon (CO 2 ). This minireview discusses the physiological roles of carboxylases in different microbial pathways that range from autotrophy, carbon assimilation, and anaplerosis to biosynthetic and redox-balancing functions. In addition, the current and possible future uses of carboxylation reactions in synthetic biology are discussed. Such uses include the possible transformation of the greenhouse gas carbon dioxide into value-added compounds and the production of novel antibiotics.

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

Abstract: Biotin-containing 3-methylcrotonyl coenzyme A (MC-CoA

Cited by 21 publications

References 24 publications

Early evolution of the biotin-dependent carboxylase family

Early evolution of the biotin-dependent carboxylase family

Structure and function of biotin-dependent carboxylases

Carboxylases in Natural and Synthetic Microbial Pathways

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