Crystal structure determination and dynamic studies of Mycobacterium tuberculosis Cytidine deaminase in complex with products

Sánchez-Quitian, Zilpa Adriana; Timmers, Luís Fernando S. M.; Caceres, Rafael Andrade; Rehm, Jacqueline Gonçalves; Thompson, Claudia Elizabeth; Basso, Luiz Augusto; Azevedo, Walter Filgueira de; Santos, Daniel Silas Veras dos

doi:10.1016/j.abb.2011.01.022

Cited by 7 publications

(11 citation statements)

References 23 publications

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“…The pH optimum was similar and amounted to pH 3.5 for the native protein, and 4.0 for an enzyme expressed in P. pastoris. It was suggested that the recombinant protein was inhibited by succinate and by citrate in a competitive and uncompetitive manner, respectively (Moussatche et al, 2011). It was also demonstrated that bacterial oxalate decarboxylase from B. subtilis can be converted into an oxidase by mutation in the active site of the enzyme (Burrell et al, 2007).…”

Section: Discussionmentioning

confidence: 99%

“…Currently, only three oxalate oxidases of basidiomycete fungi have been described -an enzyme from Tilletia contraversa (Vaisey et al, 1961), the best characterised so far enzyme from Ceriporiopsis subvermispora (Aguilar et al, 1999), and an enzyme produced by Abortiporus biennis (Grąz et al, 2009). The enzyme from C. subvermispora was also expressed in Pichia pastoris and characterised as Mn(II)-containing bicupin protein sharing homology with bicupin microbial oxalate decarboxylase (Moussatche et al, 2011). Oxalate oxidase decomposes oxalic acid to carbon dioxide and hydrogen peroxide.…”

Section: Introductionmentioning

confidence: 99%

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Oxalic acid degradation by a novel fungal oxalate oxidase from Abortiporus biennis

Grąz¹,

Rachwał²,

Zan³

et al. 2016

Acta Biochim Pol

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Oxalate oxidase was identified in mycelial extracts of a basidiomycete Abortiporus biennis strain. Intracellular enzyme activity was detected only after prior lowering of the pH value of the fungal cultures by using oxalic or hydrochloric acids. This enzyme was purified using size exclusion chromatography (Sephadex G-25) and ion-exchange chromatography (DEAE-Sepharose). This enzyme exhibited optimum activity at pH 2 when incubated at 40°C, and the optimum temperature was established at 60°C. Among the tested organic acids, this enzyme exhibited specificity only towards oxalic acid. Molecular mass was calculated as 58 kDa. The values of Km for oxalate and Vmax for the enzyme reaction were 0.015 M and 30 mmol min(-1), respectively.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Oxalic acid degradation by a novel fungal oxalate oxidase from Abortiporus biennis

Grąz¹,

Rachwał²,

Zan³

et al. 2016

Acta Biochim Pol

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“…8,9 The proton and the hydroxyl anion add to, respectively, the N3 and the C4 atoms of the N3]C4 double bond of cytidine to form a tetrahedral intermediate in the rst step. [18][19][20][21] In previous pH-rate prole studies of MtCDA, protonation of a single ionizable group with an apparent pK a value of 4.3 (AE1) reduced the catalytic activity and protonation of a group with apparent pK a of 4.7 (AE0.7) appeared to be involved in cytidine binding. 8,9 Hydrogen bonding plays an important role in transition state stabilization for E. coli CDA, and the carboxymethyl group of Glu104 appears to minimize the activation barrier for deamination, not only by stabilizing the altered substrate in the transition state but also by destabilizing the enzyme-substrate and enzyme-product complexes.…”

Section: Introductionmentioning

confidence: 94%

“…7 The proposed mechanism of catalysis for Escherichia coli CDA includes a zinc atom in the active site that activates a water molecule to form a hydroxide ion and H + by heterolytic bond cleavage. 20 The human CDA region involved in substrate binding contains the residues 32 18,19,21 Conserved residues in tetrameric CDA enzyme involved in catalysis are 65 CAERTA 70 for human CDA, 53 CAERTA 58 for B. subtilis CDA, and 56 CAECAV 61 for MtCDA. In the second step, uridine is produced with the release of ammonia.…”

Section: Introductionmentioning

confidence: 99%

Functional and structural evidence for the catalytic role played by glutamate-47 residue in the mode of action of Mycobacterium tuberculosis cytidine deaminase

et al. 2015

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Strategies to combat tuberculosis (TB) are needed to kill drug-resistant strains and be effective against latent Mycobacterium tuberculosis, the causative agent of TB. Cytidine deaminase (CDA) catalyzes the hydrolytic deamination of cytidine to uridine, and belongs to the pyrimidine salvage pathway. The CDA from M. tuberculosis (MtCDA) is a target for the development of drugs against TB because it may be involved in latency mechanisms. The role of the conserved glutamate-47 (E47) residue was evaluated by construction of five mutant proteins (E47A, E47D, E47L, E47H, and E47Q). Mutants E47A and E47H were expressed in the insoluble fraction, whereas E47D, E47L and E47Q were soluble and purified. The E47D, E47L and E47Q mutants contained 1 mol of Zn 2+ per mol of protein subunit. These mutations had no effect on the oligomerization state of MtCDA. Steady-state kinetic results showed that K M values for the E47D and E47Q mutants were not significantly altered, whereas there was a decrease in k cat values of 37-fold for E47D and 19-fold for E47Q mutant. No activity could be detected for E47L mutant. No k cat and k cat /K M dependence on pH values ranging from 4.0 to 11 were observed for E47D mutant from pHrate profiles. A catalytic role was proposed for the g-carboxyl group of E47, and its likely involvement in the stabilization of the transition state was suggested. Structural comparisons between E47D and E47Q mutants with the apo and holo forms of wild-type MtCDA reveal subtle differences that support this proposal.

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“…Cytidine deaminase (cdd; Rv3315c) catalyzes the Zn 2+ -dependent hydrolytic deamination of cytidine or 2′-deoxycytidine to uridine or 2′-deoxyuridine, respectively (73,74). Located downstream of cdd, on an operon, is the gene encoding thymidine phosphorylase (deoA; Rv3314c), another pyrimidine salvage enzyme, which catalyzes the reversible hydrolysis of thymidine to D-2deoxyribose-1-phosphate and thymine.…”

Section: Pyrimidine Salvagementioning

confidence: 99%

Nucleotide Metabolism and DNA Replication

2014

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The development and application of a highly versatile suite of tools for mycobacterial genetics, coupled with widespread use of "omics" approaches to elucidate the structure, function, and regulation of mycobacterial proteins, has led to spectacular advances in our understanding of the metabolism and physiology of mycobacteria. In this article, we provide an update on nucleotide metabolism and DNA replication in mycobacteria, highlighting key findings from the past 10 to 15 years. In the first section, we focus on nucleotide metabolism, ranging from the biosynthesis, salvage, and interconversion of purine and pyrimidine ribonucleotides to the formation of deoxyribonucleotides. The second part of the article is devoted to DNA replication, with a focus on replication initiation and elongation, as well as DNA unwinding. We provide an overview of replication fidelity and mutation rates in mycobacteria and summarize evidence suggesting that DNA replication occurs during states of low metabolic activity, and conclude by suggesting directions for future research to address key outstanding questions. Although this article focuses primarily on observations from Mycobacterium tuberculosis, it is interspersed, where appropriate, with insights from, and comparisons with, other mycobacterial species as well as better characterized bacterial models such as Escherichia coli. Finally, a common theme underlying almost all studies of mycobacterial metabolism is the potential to identify and validate functions or pathways that can be exploited for tuberculosis drug discovery. In this context, we have specifically highlighted those processes in mycobacterial DNA replication that might satisfy this critical requirement.

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Crystal structure determination and dynamic studies of Mycobacterium tuberculosis Cytidine deaminase in complex with products

Cited by 7 publications

References 23 publications

Oxalic acid degradation by a novel fungal oxalate oxidase from Abortiporus biennis

Oxalic acid degradation by a novel fungal oxalate oxidase from Abortiporus biennis

Functional and structural evidence for the catalytic role played by glutamate-47 residue in the mode of action of Mycobacterium tuberculosis cytidine deaminase

Nucleotide Metabolism and DNA Replication

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