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1.
RNA Biol ; 12(4): 435-46, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-25849199

RESUMEN

CCA-adding enzymes are highly specific RNA polymerases that synthesize and maintain the sequence CCA at the tRNA 3'-end. This nucleotide triplet is a prerequisite for tRNAs to be aminoacylated and to participate in protein biosynthesis. During CCA-addition, a set of highly conserved motifs in the catalytic core of these enzymes is responsible for accurate sequential nucleotide incorporation. In the nucleotide binding pocket, three amino acid residues form Watson-Crick-like base pairs to the incoming CTP and ATP. A reorientation of these templating amino acids switches the enzyme's specificity from CTP to ATP recognition. However, the mechanism underlying this essential structural rearrangement is not understood. Here, we show that motif C, whose actual function has not been identified yet, contributes to the switch in nucleotide specificity during polymerization. Biochemical characterization as well as EPR spectroscopy measurements of the human enzyme reveal that mutating the highly conserved amino acid position D139 in this motif interferes with AMP incorporation and affects interdomain movements in the enzyme. We propose a model of action, where motif C forms a flexible spring element modulating the relative orientation of the enzyme's head and body domains to accommodate the growing 3'-end of the tRNA. Furthermore, these conformational transitions initiate the rearranging of the templating amino acids to switch the specificity of the nucleotide binding pocket from CTP to ATP during CCA-synthesis.


Asunto(s)
Dominio Catalítico , Mutación , ARN Nucleotidiltransferasas/química , ARN Nucleotidiltransferasas/metabolismo , ARN de Transferencia/química , Humanos , Simulación del Acoplamiento Molecular , Estructura Terciaria de Proteína , ARN Nucleotidiltransferasas/genética , ARN de Transferencia/metabolismo , Especificidad por Sustrato/genética
2.
Nucleic Acids Res ; 38(13): 4436-47, 2010 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-20348137

RESUMEN

CCA-adding enzymes are polymerases existing in two distinct enzyme classes that both synthesize the C-C-A triplet at tRNA 3'-ends. Class II enzymes (found in bacteria and eukaryotes) carry a flexible loop in their catalytic core required for switching the specificity of the nucleotide binding pocket from CTP- to ATP-recognition. Despite this important function, the loop sequence varies strongly between individual class II CCA-adding enzymes. To investigate whether this loop operates as a discrete functional entity or whether it depends on the sequence context of the enzyme, we introduced reciprocal loop replacements in several enzymes. Surprisingly, many of these replacements are incompatible with enzymatic activity and inhibit ATP-incorporation. A phylogenetic analysis revealed the existence of conserved loop families. Loop replacements within families did not interfere with enzymatic activity, indicating that the loop function depends on a sequence context specific for individual enzyme families. Accordingly, modeling experiments suggest specific interactions of loop positions with important elements of the protein, forming a lever-like structure. Hence, although being part of the enzyme's catalytic core, the loop region follows an extraordinary evolutionary path, independent of other highly conserved catalytic core elements, but depending on specific sequence features in the context of the individual enzymes.


Asunto(s)
ARN Nucleotidiltransferasas/química , Secuencia de Aminoácidos , Bacterias/enzimología , Dominio Catalítico , Secuencia Conservada , Evolución Molecular , Humanos , Modelos Moleculares , Datos de Secuencia Molecular , Filogenia , ARN Nucleotidiltransferasas/clasificación , ARN Nucleotidiltransferasas/metabolismo
3.
J Bacteriol ; 190(19): 6493-500, 2008 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-18658262

RESUMEN

p-Cresol methylhydroxylases (PCMH) from aerobic and facultatively anaerobic bacteria are soluble, periplasmic flavocytochromes that catalyze the first step in biological p-cresol degradation, the hydroxylation of the substrate with water. Recent results suggested that p-cresol degradation in the strictly anaerobic Geobacter metallireducens involves a tightly membrane-bound PCMH complex. In this work, the soluble components of this complex were purified and characterized. The data obtained suggest a molecular mass of 124 +/- 15 kDa and a unique alphaalpha'beta(2) subunit composition, with alpha and alpha' representing isoforms of the flavin adenine dinucleotide (FAD)-containing subunit and beta representing a c-type cytochrome. Fluorescence and mass spectrometric analysis suggested that one FAD was covalently linked to Tyr(394) of the alpha subunit. In contrast, the alpha' subunit did not contain any FAD cofactor and is therefore considered to be catalytically inactive. The UV/visible spectrum was typical for a flavocytochrome with two heme c cofactors and one FAD cofactor. p-Cresol reduced the FAD but only one of the two heme cofactors. PCMH catalyzed both the hydroxylation of p-cresol to p-hydroxybenzyl alcohol and the subsequent oxidation of the latter to p-hydroxybenzaldehyde in the presence of artificial electron acceptors. The very low K(m) values (1.7 and 2.7 microM, respectively) suggest that the in vivo function of PCMH is to oxidize both p-cresol and p-hydroxybenzyl alcohol. The latter was a mixed inhibitor of p-cresol oxidation, with inhibition constants of a K(ic) (competitive inhibition) value of 18 +/- 9 microM and a K(iu) (uncompetitive inhibition) value of 235 +/- 20 microM. A putative functional model for an unusual PCMH enzyme is presented.


Asunto(s)
Proteínas Bacterianas/metabolismo , Geobacter/enzimología , Proteínas de la Membrana/metabolismo , Oxigenasas de Función Mixta/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/aislamiento & purificación , Benzaldehídos/metabolismo , Alcoholes Bencílicos/metabolismo , Dominio Catalítico , Cromatografía en Gel , Cromatografía Líquida de Alta Presión , Cromatografía Liquida , Cresoles/metabolismo , Electroforesis en Gel de Poliacrilamida , Flavina-Adenina Dinucleótido/química , Flavina-Adenina Dinucleótido/metabolismo , Flavoproteínas/química , Flavoproteínas/metabolismo , Geobacter/metabolismo , Hemo/análogos & derivados , Hemo/química , Hemo/metabolismo , Espectrometría de Masas , Proteínas de la Membrana/química , Proteínas de la Membrana/aislamiento & purificación , Oxigenasas de Función Mixta/química , Oxigenasas de Función Mixta/aislamiento & purificación , Peso Molecular , Isoformas de Proteínas/química , Isoformas de Proteínas/metabolismo , Espectrofotometría Ultravioleta
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