7JJE

Sarcin-ricin loop with guanosine dithiophosphate residue.

Summary for 7JJE

• Entry DOI: 10.2210/pdb7jje/pdb
• Descriptor: RNA (27-MER) (2 entities in total)
• Functional Keywords: sarcin-ricin loop, rna crystal structure, rna tetraloops, rna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 8778.40

Authors

Pallan, P.S.,Egli, M.,Harp, J.M. (deposition date: 2020-07-25, release date: 2020-12-23, Last modification date: 2023-10-18)

Primary citation

Pallan, P.S.,Lybrand, T.P.,Schlegel, M.K.,Harp, J.M.,Jahns, H.,Manoharan, M.,Egli, M.
Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost.
Biochemistry, 59:4627-4637, 2020

PubMed Abstract: GNRA (N = A, C, G, or U; R = A or G) tetraloops are common RNA secondary structural motifs and feature a phosphate stacked atop a nucleobase. The rRNA sarcin/ricin loop (SRL) is capped by ApGA, and the phosphate p stacks on . We recently found that regiospecific incorporation of a single dithiophosphate (PS2) but not a monothiophosphate (PSO) instead of phosphate in the backbone of RNA aptamers dramatically increases the binding affinity for their targets. In the RNA:thrombin complex, the key contribution to the 1000-fold tighter binding stems from an edge-on contact between PS2 and a phenylalanine ring. Here we investigated the consequences of replacing the SRL phosphate engaged in a face-on interaction with guanine with either PS2 or PSO for stability. We found that PS2···G and p-PSO···G contacts stabilize modified SRLs compared to the parent loop to unexpected levels: up to 6.3 °C in melting temperature and -4.7 kcal/mol in ΔΔ°. Crystal structures demonstrate that the vertical distance to guanine for the closest sulfur is just 0.05 Å longer on average compared to that of oxygen despite the larger van der Waals radius of the former (1.80 Å for S vs 1.52 Å for O). The higher stability is enthalpy-based, and the negative charge as assessed by a neutral methylphosphonate modification plays only a minor role. Quantum mechanical/molecular mechanical calculations are supportive of favorable dispersion attraction interactions by sulfur making the dominant contribution. A stacking interaction between phosphate and guanine (SRL) or uracil (U-turn) is also found in newly classified RNA tetraloop families besides GNRA.

PubMed: 33275419
DOI: 10.1021/acs.biochem.0c00685

Experimental method

X-RAY DIFFRACTION (1.25 Å)