2BH2

Crystal Structure of E. coli 5-methyluridine methyltransferase RumA in complex with ribosomal RNA substrate and S-adenosylhomocysteine.

Summary for 2BH2

• Entry DOI: 10.2210/pdb2bh2/pdb
• Related: 1UWV
• Descriptor: 23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA, 23S RIBOSOMAL RNA 1932-1968, S-ADENOSYL-L-HOMOCYSTEINE, ... (5 entities in total)
• Functional Keywords: iron-sulfur cluster, methyltransferase, rna modification, rna processing, transferase, ruma, base flipping, sam, ob-fold, protein-rna complex, base stacking, substrate selectivity, general base, product release, 4fe-4s, metal-binding
• Biological source: ESCHERICHIA COLI; More
• Total number of polymer chains: 4
• Total formula weight: 121464.56

Authors

Lee, T.T.,Agarwalla, S.,Stroud, R.M. (deposition date: 2005-01-06, release date: 2005-03-30, Last modification date: 2024-11-13)

Primary citation

Lee, T.T.,Agarwalla, S.,Stroud, R.M.
A Unique RNA Fold in the Ruma-RNA-Cofactor Ternary Complex Contributes to Substrate Selectivity and Enzymatic Function
Cell(Cambridge,Mass.), 120:599-, 2005

PubMed Abstract: A single base (U1939) within E. coli 23S ribosomal RNA is methylated by its dedicated enzyme, RumA. The structure of RumA/RNA/S-adenosylhomocysteine uncovers the mechanism for achieving unique selectivity. The single-stranded substrate is "refolded" on the enzyme into a compact conformation with six key intra-RNA interactions. The RNA substrate contributes directly to catalysis. In addition to the target base, a second base is "flipped out" from the core loop to stack against the adenine of the cofactor S-adenosylhomocysteine. Nucleotides in permuted sequence order are stacked into the site vacated by the everted target U1939 and compensate for the energetic penalty of base eversion. The 3' hairpin segment of the RNA binds distal to the active site and provides binding energy that contributes to enhanced catalytic efficiency. Active collaboration of RNA in catalysis leads us to conclude that RumA and its substrate RNA may reflect features from the earliest RNA-protein era.

PubMed: 15766524
DOI: 10.1016/J.CELL.2004.12.037

Experimental method

X-RAY DIFFRACTION (2.15 Å)