The Escherichia coli YdcF binds S-adenosyl-L-methionine and adopts an alpha/beta fold characteristic of nucleotide-utilizing enzymes

Published

July 1, 2008

Author(s)

Kinlin L. Chao, Kap Lim, C Lehmann, V Doseeva, A J. Howard, Frederick P. Schwarz, Osnat Herzberg

Abstract

The crystal structure of YdcF at a resolution of 0.18 nm reveals a fold of the adenine nucleotide α hydrolase-like family. Following the structural clues, a nucleotide binding screen was carried out employing isothermal titration calorimetry. The following ligands were screened: β-nicotinamide adenine dinucleotide (NAD+), β-nicotinamide adenine dinucleotide phosphate (NADP+), flavin adenine dinucleotide (FAD), adenosine triphosphate (ATP), deoxyadenosine monophosphate (dAMP), and S-adenosyl-L-methionine (AdoMet). Only AdoMET exhibited binding to YdcF with a Kd value of 25 μM and a binding enthalpy of -1.5 + 0.3 kJ mol-1. The dissociation constant is physiologically significant as a survey of the BRENDA database shows that this value is well within the Km values of methyltransferases. Thus, the structure insight, the ligand screening, and the expression profiling suggest that YdcF is an AdoMet-dependent enzyme that plays a role in an anaerobic respiratory pathway.

Citation

Proteins-Structure Function and Bioinformatics

Volume

72

Issue

1

Pub Type

Journals

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Citation

Chao, K. , Lim, K. , Lehmann, C. , Doseeva, V. , Howard, A. , Schwarz, F. and Herzberg, O. (2008), The Escherichia coli YdcF binds S-adenosyl-L-methionine and adopts an alpha/beta fold characteristic of nucleotide-utilizing enzymes, Proteins-Structure Function and Bioinformatics, [online], https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=832211 (Accessed March 26, 2025)