Lysidine (nucleoside)

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Lysidine (nucleoside)
Lysidine.svg
Names
IUPAC name
2-Amino-6-[4-amino-1-(3,4-dihydroxy-5-hydroxymethyloxolan-2-yl)-1H-pyrimidin-2-ylideneamino]hexanoic acid
Other names
4-Amino-2-(N(6)-lysino)-1-ribofuranosylpyrimidine, 2-lysyl-cytidine
Identifiers
3D model (JSmol)
ChemSpider
PubChem CID
  • InChI=1S/C15H25N5O6/c16-8(14(24)25)3-1-2-5-18-15-19-10(17)4-6-20(15)13-12(23)11(22)9(7-21)26-13/h4,6,8-9,11-13,21-23H,1-3,5,7,16H2,(H,24,25)(H2,17,18,19)/t8-,9+,11+,12+,13+/m0/s1
    Key: MDWUIKMWKDMPDE-IINAIABHSA-N
  • OC[C@H]1O[C@@H](N2C=CC(N)=N/C2=N\CCCC[C@H](N)C(O)=O)[C@H](O)[C@@H]1O
Properties
C15H25N5O6
Molar mass 371.39 g/mol
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
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Lysidine is an uncommon nucleoside, rarely seen outside of tRNA. It is a derivative of cytidine in which the carbonyl is replaced by the amino acid lysine. The first position, i.e. the wobble base, in the anti-codon of the eubacterial isoleucine-specific tRNA pertaining to the AUA codon is typically changed from a cytidine which would pair with guanosine to a lysidine which will base pair with adenosine. Lysidine improves translation fidelity because uridine cannot be used at this position even though it is a conventional partner for adenosine since it will also "wobble base pair" with guanosine. [1] [2] Lysidine is denoted as L [3] or k2C [4] (lysine bound to C2 atom of cytidine).

Hydrogen bonding (arrows) in the lysidine (L) and adenosine (A) base pair, compared against the cytidine (C) and guanosine (G) base pair. Lysidine A.png
Hydrogen bonding (arrows) in the lysidine (L) and adenosine (A) base pair, compared against the cytidine (C) and guanosine (G) base pair.

References

  1. ↑ Nakanishi, Kotaro; Fukai, Shuya; Ikeuchi, Yoshiho; Soma, Akiko; Sekine, Yasuhiko; Suzuki, Tsutomu; Nureki, Osamu (24 May 2005). "Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain". Proceedings of the National Academy of Sciences of the United States of America. 102 (21): 7487–7492. Bibcode:2005PNAS..102.7487N. doi: 10.1073/pnas.0501003102 . PMC   1140429 . PMID   15894617.
  2. ↑ Salowe, Scott P.; Wiltsie, Judyann; Hawkins, Julio C.; Sonatore, Lisa M. (April 2009). "The Catalytic Flexibility of tRNAIle-lysidine Synthetase Can Generate Alternative tRNA Substrates for Isoleucyl-tRNA Synthetase". Journal of Biological Chemistry. 284 (15): 9656–9662. doi: 10.1074/jbc.M809013200 . PMC   2665086 . PMID   19233850.
  3. ↑ Nakanishi, Kotaro; Bonnefond, Luc; Kimura, Satoshi; Suzuki, Tsutomu; Ishitani, Ryuichiro; Nureki, Osamu (October 2009). "Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase". Nature. 461 (7267): 1144–1148. Bibcode:2009Natur.461.1144N. doi:10.1038/nature08474. PMID   19847269. S2CID   4426738.
  4. ↑ Sonawane, Kailas D.; Tewari, Ravindra (19 September 2008). "Conformational Preferences of Hypermodified Nucleoside Lysidine (k2C) Occurring at 'Wobble' Position in Anticodon Loop of tRNAIle". Nucleosides, Nucleotides & Nucleic Acids. 27 (10–11): 1158–1174. doi:10.1080/15257770802341475. PMID   18788046. S2CID   25220901.
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