2CD3

Refinement of RNase P P4 stemloop structure using residual dipolar coupling data - C70U mutant

Summary for 2CD3

• Entry DOI: 10.2210/pdb2cd3/pdb
• Related: 2CD1 2CD5 2CD6
• Descriptor: 5'-R(*GP*GP*AP*AP*GP*UP*UP*CP*GP*GP *UP*CP*UP*UP*CP*GP*GP*AP*CP*CP*GP*GP*CP*UP*UP*CP*C)-3' (1 entity in total)
• Functional Keywords: nucleic acid, c70u mutant, metal binding site, p4 stem, ribonuclease p, ribonucleic acid, ribozyme, transfer rna processing
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 1
• Total formula weight: 8634.13

Authors

Schmitz, M. (deposition date: 2006-01-19, release date: 2007-05-01, Last modification date: 2024-05-15)

Primary citation

Solution Structure and Metal-Ion Binding of the P4 Element from Bacterial Rnase P RNA
RNA, 6:1212-, 2000

PubMed Abstract: We determined the solution structure of two 27-nt RNA hairpins and their complexes with cobalt(III)-hexammine (Co(NH3)3+(6)) by NMR spectroscopy. The RNA hairpins used in this study are the P4 region from Escherichia coli RNase P RNA and a C-to-U mutant that confers altered divalent metal-ion specificity (Ca2+ replaces Mg2+) for catalytic activity of this ribozyme. Co(NH3)3+(6) is a useful spectroscopic probe for Mg(H2O)2+(6)-binding sites because both complexes have octahedral symmetry and have similar radii. The thermodynamics of binding to both RNA hairpins was studied using chemical shift changes upon titration with Mg2+, Ca2+, and Co(NH3)3+(6). We found that the equilibrium binding constants for each of the metal ions was essentially unchanged when the P4 model RNA hairpin was mutated, although the NMR structures show that the RNA hairpins adopt different conformations. In the C-to-U mutant a C.G base pair is replaced by U.G, and the conserved bulged uridine in the P4 wild-type stem shifts in the 3' direction by 1 nt. Intermolecular NOE cross-peaks between Co(NH3)3+(6) and RNA protons were used to locate the site of Co(NH3)3+(6) binding to both RNA hairpins. The metal ion binds in the major groove near a bulge loop, but is shifted 5' by more than 1 bp in the mutant. The change of the metal-ion binding site provides a possible explanation for changes in catalytic activity of the mutant RNase P in the presence of Ca2+.

PubMed: 10999599
DOI: 10.1017/S1355838200000881

Experimental method

SOLUTION NMR