Molecular and crystal structure of the tRNA minor constituent dihydrouridine

Suck, Dietrich; Zechmeister, K.

doi:10.1107/s056774087200281x

Cited by 42 publications

(20 citation statements)

References 6 publications

(7 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The heterocycle exists in the diketo form; C(2)-S and C(4)-O(4) both have double-bond character. Bond distances and angles in the base are comparable with those found in 5,6-dihydrouridine (Suck, Saenger & Zechmeister, 1972).…”

Section: 6-dihydro-2-thiouracil Residuesupporting

confidence: 67%

The molecular and crystal structure of 5,6-dihydro-2-thiouridine, C9H14N2O5S

Kojić‐Prodić¹,

Liminga²,

Šljukić³

et al. 1974

Acta Crystallogr Sect B

View full text Add to dashboard Cite

5,6-Dihydro-2-thiouridine crystallizes in the space group P2~ with a= 15-330, b=7.517, c=5.070 A,, fl = 107.89 °, Z= 2. The structure was solved by direct methods and refined by the full-matrix least-squares technique to R 0.098. Because of the saturated C(5)-C(6) bond, the nucleobase is not planar. The ribose moiety has C(3')-endo conformation and the nucleoside molecule exhibits the usual anti conformation. The thiouridine molecules are connected by hydrogen bonds between sugar-sugar and base-base residues to form a three-dimensional network. There is no base stacking.

show abstract

Section: 6-dihydro-2-thiouracil Residuesupporting

confidence: 67%

The molecular and crystal structure of 5,6-dihydro-2-thiouridine, C9H14N2O5S

Kojić‐Prodić¹,

Liminga²,

Šljukić³

et al. 1974

Acta Crystallogr Sect B

View full text Add to dashboard Cite

show abstract

“…It is difficult to form any general conclusions about the differences in molecular dimensions because of several factors: the conjugation of the lone electron pair on N(1) with C(2)=O,S(2) or with C(5)-C(6), electron delocalization of different sorts, and hydrogenbonding. But a remarkable shortening of N(1)-C(2) in saturated pyrimidines was observed in 5,6-dihydro-2-thiouracil (1-317/~), 5,6-dihydrouracil (1.335 A) (Rohrer & Sundaralingam, 1970), 5,6-dihydrouridine, molecules A and B (1.356/~, 1.351/k) (Suck, Saenger & Zechmeister, 1972) and 5,6-dihydro-2,4-dithiouridine (1.331/~) (Koji6-Prodi6, Kvick & Ru~i6-Toro~, 1976). The C(5)-C(6) distance of 1.474 (5)/k is significantly shorter than the sp 3 single bond value of 1.533/~ (Bartell, 1959).…”

Section: Description and Discussion Of The Structurementioning

confidence: 99%

The crystal and molecular structure of 5,6-dihydro-2-thiouracil, C4H6N2OS

Kojić‐Prodić¹,

Ružić‐Toroš²,

Coffou³

1976

Acta Crystallogr Sect B

View full text Add to dashboard Cite

“…Sequence locations of dihydrouridine in isoaccepting tRNAs of the four organisms studied are not known but are presumably mainly within positions 14 to 21 of the D loop, a generally conserved modification pattern in bacterial tRNAs (19,46). The uniquely nonplanar base of dihydrouridine which results from the absence of a C-5 C-6 double bond resists stacking (49,51), normally a common mechanism of stabilization in RNA. In addition, recent nuclear magnetic resonance studies of dihydrouridine 3Ј-monophosphate and the oligonucleotide ApDpA indicate that dihydrouridine is unusual in that the C-2Ј-endo sugar conformation (the principal conformer of DNA) is favored and that this effect is propagated to the 5Ј-neighboring residue in the oligonucleotide (10).…”

Section: Discussionmentioning

confidence: 99%

Posttranscriptional modification of tRNA in psychrophilic bacteria

et al. 1997

View full text Add to dashboard Cite

Posttranscriptional modification in tRNA is known to play a multiplicity of functional roles, including maintenance of tertiary structure and cellular adaptation to environmental factors such as temperature. Nucleoside modification has been studied in unfractionated tRNA from three psychrophilic bacteria (ANT-300 and Vibrio sp. strains 5710 and 29-6) and one psychrotrophic bacterium (Lactobacillus bavaricus). Based on analysis of total enzymatic hydrolysates by liquid chromatography-mass spectrometry, unprecedented low amounts of modification were found in the psychrophiles, particularly from the standpoint of structural diversity of modifications observed. Thirteen to 15 different forms of posttranscriptional modification were found in the psychrophiles, and 10 were found in L. bavaricus, compared with approximately 29 known to occur in bacterial mesophiles and 24 to 31 known to occur in the archaeal hyperthermophiles. The four most abundant modified nucleosides in tRNA from each organism were dihydrouridine, pseudouridine, 7-methylguanosine, and 5-methyluridine. The molar abundances of the latter three nucleosides were comparable to those found in tRNA from Escherichia coli. By contrast, the high levels of dihydrouridine observed in all three psychrophiles are unprecedented for any organism in any of the three phylogenetic domains. tRNA from these organisms contains 40 to 70% more dihydrouridine, on average, than that of the mesophile E. coli or the psychrotroph L. bavaricus. This finding supports the concept that a functional role for dihydrouridine is in maintenance of conformational flexibility of RNA, especially important to organisms growing under conditions where the dynamics of thermal motion are severely compromised. This is in contrast to the role of modifications contained in RNA from thermophiles, which is to reduce regional RNA flexibility and provide structural stability to RNA for adaptation to high temperature.The structural diversity (31) and multiplicity of roles played by posttranscriptional modification in RNA, particularly tRNA (3, 4, 59), has been clearly established. Despite the fact that 80 different modified nucleosides are presently known (8) to occur in tRNA from organisms representing all three phylogenetic domains (31), nearly all knowledge of posttranscriptional modification in RNA is derived from studies of mesophiles and thermophiles. Of 521 reported tRNA sequences (46), the only apparent exception is the initiator tRNA from the arthropod Euphausia sperba, which inhabits the Antarctic Sea (52). We are unaware of previous investigations reporting modification in tRNA from any psychrophilic microorganism, despite the fact that greater than 80% of the biosphere is characterized by temperatures below 5ЊC. Nevertheless, interest in these organisms and their biotechnological potential has increased substantially in recent years (25, 32), and they represent a fundamentally important but understudied segment of the biosphere. Psychrophilic microorganisms have an optimum temperature for g...

show abstract

Molecular and crystal structure of the tRNA minor constituent dihydrouridine

Cited by 42 publications

References 6 publications

The molecular and crystal structure of 5,6-dihydro-2-thiouridine, C9H14N2O5S

The molecular and crystal structure of 5,6-dihydro-2-thiouridine, C9H14N2O5S

The crystal and molecular structure of 5,6-dihydro-2-thiouracil, C4H6N2OS

Posttranscriptional modification of tRNA in psychrophilic bacteria

Contact Info

Product

Resources

About