7CTA

Crystal structure of Cx-SAM bound CmoB from Vibrio vulnificus

Summary for 7CTA

• Entry DOI: 10.2210/pdb7cta/pdb
• Descriptor: tRNA U34 carboxymethyltransferase, (2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio] -2-ammoniobutanoate, SULFATE ION, ... (4 entities in total)
• Functional Keywords: carboxymethyl transferase, trna modification, cx-sam, transferase
• Biological source: Vibrio vulnificus MO6-24/O
• Total number of polymer chains: 2
• Total formula weight: 77864.61

Authors

Kim, J.,Jeong, S. (deposition date: 2020-08-18, release date: 2021-03-03, Last modification date: 2023-11-29)

Primary citation

Jeong, S.,Kim, J.
Structural snapshots of CmoB in various states during wobble uridine modification of tRNA.
Biochem.Biophys.Res.Commun., 534:604-609, 2021

PubMed Abstract: CmoB utilizes carboxy-S-adenosyl-l-methionine (CxSAM) to carry out unusual carboxymethyl transfer to form 5-carboxymethoxyuridine (cmoU) of several tRNA species in Gram-negative bacteria. In this report, we present three X-ray crystal structures of CmoB from Vibrio vulnificus representing different states in the course of the reaction pathway; i.e., apo-, substrate-bound, and product-bound forms. Especially, the crystal structure of apo-CmoB unveils a novel open state of the enzyme, capturing unprecedented conformational dynamics around the substrate-binding site. The apo-structure demonstrates that the open conformation favors the release of CxSAM thus representing an inactive form. Our crystal structures of CmoB complexed with CxSAM and S-adenosyl-l-homocysteine (SAH) and combined binding assay results support the proposed mechanism underlying the cofactor selectivity, where CmoB preferentially senses negative charge around amino acid residues Lys-91, Tyr-200, and Arg-315.

PubMed: 33213836
DOI: 10.1016/j.bbrc.2020.11.033

Experimental method

X-RAY DIFFRACTION (2.9 Å)