4LGT
Crystal structure of the catalytic domain of RluB in complex with a 21-nucleotide RNA substrate
Summary for 4LGT
| Entry DOI | 10.2210/pdb4lgt/pdb |
| Related | 4LAB |
| Descriptor | Ribosomal large subunit pseudouridine synthase B, stem-loop of 23S rRNA (3 entities in total) |
| Functional Keywords | beta sheet alpha-beta protein, rrna modification peudouridine synthase, e. coli ribosomal rna, isomerase-rna complex, isomerase/rna |
| Biological source | Escherichia coli More |
| Total number of polymer chains | 4 |
| Total formula weight | 70857.47 |
| Authors | Czudnochowski, N.,Finer-Moore, J.S.,Stroud, R.M. (deposition date: 2013-06-28, release date: 2013-11-20, Last modification date: 2023-12-06) |
| Primary citation | Czudnochowski, N.,Ashley, G.W.,Santi, D.V.,Alian, A.,Finer-Moore, J.,Stroud, R.M. The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs. Nucleic Acids Res., 42:2037-2048, 2014 Cited by PubMed Abstract: RluB catalyses the modification of U2605 to pseudouridine (Ψ) in a stem-loop at the peptidyl transferase center of Escherichia coli 23S rRNA. The homolog RluF is specific to the adjacent nucleotide in the stem, U2604. The 1.3 Å resolution crystal structure of the complex between the catalytic domain of RluB and the isolated substrate stem-loop, in which the target uridine is substituted by 5-fluorouridine (5-FU), reveals a covalent bond between the isomerized target base and tyrosine 140. The structure is compared with the catalytic domain alone determined at 2.5 Å resolution. The RluB-bound stem-loop has essentially the same secondary structure as in the ribosome, with a bulge at A2602, but with 5-FU2605 flipped into the active site. We showed earlier that RluF induced a frame-shift of the RNA, moving A2602 into the stem and translating its target, U2604, into the active site. A hydrogen-bonding network stabilizes the bulge in the RluB-RNA but is not conserved in RluF and so RluF cannot stabilize the bulge. On the basis of the covalent bond between enzyme and isomerized 5-FU we propose a Michael addition mechanism for pseudouridine formation that is consistent with all experimental data. PubMed: 24214967DOI: 10.1093/nar/gkt1050 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.3 Å) |
Structure validation
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