Abstract of the PDB Structure's related Publication:
Post-transcriptional base modifications are important to the maturation process of transfer RNAs (tRNAs). Certain modifications are abundant and present at several positions in tRNA as for example the dihydrouridine, a modified base found in the three domains of life. Even though the function of dihydrourine is not well understood, its high content in tRNAs from psychrophilic bacteria or cancer cells obviously emphasizes a central role in cell adaptation. The reduction of uridine to dihydrouridine is catalyzed by a large family of flavoenzymes named dihydrouridine synthases (Dus). Prokaryotes have three Dus (A, B and C) wherein DusB is considered as an ancestral protein from which the two others derived via gene duplications. Here, we unequivocally established the complete substrate specificities of the three Escherichia coli Dus and solved the crystal structure of DusB, enabling for the first time an exhaustive structural comparison between these bacterial flavoenzymes. Based on our results, we propose an evolutionary scenario explaining how substrate specificities has been diversified from a single structural fold.
Dihydrouridine synthases are a conserved enzyme family that is encoded by the orthologous COG0042 gene family (Kasprzak et al. 2012 ). Dihydrouridine (D) is a post-transcriptionally modified pyrimidine nucleoside. D results from the reduction of C5,6-double bond of a uridine residue in RNA transcripts (Kasprzak et al. 2012 ) that brings to the addition of two hydrogen atoms C6 and C5. With the absence of the double bond, dihydrouridine is believed to decrease region stability, promoting dynamic motion and accommodating loop structure. D is generated post-transcriptionally by Dus enzymes and it is found in different positions of tRNAs. In E.coli, tRNA dihydrouridine synthase B synthase catalyzes the synthesis of 5,6-dihydro uridine (D) via the reduction of C5,6. It is responsible for half of the wild-cellular tRNA modifications (Bishop et al. 2002 ).DusB and DusC enzymes together introduce all D at positions 16, 17, 20, and 20a in all tRNAs, but it is not known which of them modifies which base and in which tRNA. FMN is the cofactor for the reduction reaction. It has been observed to modify position 20 of tRNAIni.