5VBS

Structural basis for a six letter alphabet including GATCKX

Summary for 5VBS

• Entry DOI: 10.2210/pdb5vbs/pdb
• Descriptor: reverse transcriptase catalytic fragment, DNA (5'-D(*CP*TP*TP*AP*TP*(DX)P*(DX)P*T)-3'), DNA (5'-D(P*AP*(93D)P*(93D)P*AP*TP*AP*AP*G)-3'), ... (4 entities in total)
• Functional Keywords: protein-dna, aegis, unnatural base pair, host-guest system, transferase-dna complex, transferase/dna
• Biological source: Moloney murine leukemia virus (isolate Shinnick) (MoMLV); More
• Cellular location: Gag-Pol polyprotein: Virion . Matrix protein p15: Virion . Capsid protein p30: Virion . Nucleocapsid protein p10-Pol: Virion . Protease: Virion . RNA-binding phosphoprotein p12: Host cytoplasm : P03355
• Total number of polymer chains: 3
• Total formula weight: 34200.00

Authors

Singh, I.,Georgiadis, M.M. (deposition date: 2017-03-30, release date: 2018-03-07, Last modification date: 2023-10-04)

Primary citation

Singh, I.,Kim, M.J.,Molt, R.W.,Hoshika, S.,Benner, S.A.,Georgiadis, M.M.
Structure and Biophysics for a Six Letter DNA Alphabet that Includes Imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-Diaminopyrimidine (K).
ACS Synth Biol, 6:2118-2129, 2017

PubMed Abstract: A goal of synthetic biology is to develop new nucleobases that retain the desirable properties of natural nucleobases at the same time as expanding the genetic alphabet. The nonstandard Watson-Crick pair between imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-diaminopyrimidine (K) does exactly this, pairing via complementary arrangements of hydrogen bonding in these two nucleobases, which do not complement any natural nucleobase. Here, we report the crystal structure of a duplex DNA oligonucleotide in B-form including two consecutive X:K pairs in GATCXK DNA determined as a host-guest complex at 1.75 Å resolution. X:K pairs have significant propeller twist angles, similar to those observed for A:T pairs, and a calculated hydrogen bonding pairing energy that is weaker than that of A:T. Thus, although inclusion of X:K pairs results in a duplex DNA structure that is globally similar to that of an analogous G:C structure, the X:K pairs locally and energetically more closely resemble A:T pairs.

PubMed: 28752992
DOI: 10.1021/acssynbio.7b00150

Experimental method

X-RAY DIFFRACTION (1.749 Å)