4QNU

Crystal structure of CmoB bound with Cx-SAM in P21212

Summary for 4QNU

• Entry DOI: 10.2210/pdb4qnu/pdb
• Related: 4QNV 4QNX
• Descriptor: tRNA (mo5U34)-methyltransferase, (2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio] -2-ammoniobutanoate, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: structural genomics, psi-biology, new york structural genomics research consortium, nysgrc, rossmannfold, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 8
• Total formula weight: 300909.19

Authors

Kim, J.,Toro, R.,Bhosle, R.,Almo, S.C.,New York Structural Genomics Research Consortium (NYSGRC) (deposition date: 2014-06-18, release date: 2014-09-17, Last modification date: 2024-02-28)

Primary citation

Kim, J.,Xiao, H.,Koh, J.,Wang, Y.,Bonanno, J.B.,Thomas, K.,Babbitt, P.C.,Brown, S.,Lee, Y.S.,Almo, S.C.
Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification.
Nucleic Acids Res., 43:4602-4613, 2015

PubMed Abstract: Enzyme-mediated modifications at the wobble position of tRNAs are essential for the translation of the genetic code. We report the genetic, biochemical and structural characterization of CmoB, the enzyme that recognizes the unique metabolite carboxy-S-adenosine-L-methionine (Cx-SAM) and catalyzes a carboxymethyl transfer reaction resulting in formation of 5-oxyacetyluridine at the wobble position of tRNAs. CmoB is distinctive in that it is the only known member of the SAM-dependent methyltransferase (SDMT) superfamily that utilizes a naturally occurring SAM analog as the alkyl donor to fulfill a biologically meaningful function. Biochemical and genetic studies define the in vitro and in vivo selectivity for Cx-SAM as alkyl donor over the vastly more abundant SAM. Complementary high-resolution structures of the apo- and Cx-SAM bound CmoB reveal the determinants responsible for this remarkable discrimination. Together, these studies provide mechanistic insight into the enzymatic and non-enzymatic feature of this alkyl transfer reaction which affords the broadened specificity required for tRNAs to recognize multiple synonymous codons.

PubMed: 25855808
DOI: 10.1093/nar/gkv206

Experimental method

X-RAY DIFFRACTION (2.6 Å)