Steve Ealick's Research Group

Clostridium botulinum BcmB

PDB file:



Clostridium botulinum BcmB is a member of the 2´-deoxynucleoside ribosyltransferase (NDT) superfamily, which includes purine deoxyribosyltransferase (PTD) and nucleoside 2-deoxyribosyltransferase (NDRT) that we previously studied. Similarly to MilB with which it has a 47% sequence identity, BcmB shows cytidine 5´-monophosphate (CMP) hydrolase activity, but is used for the production of the 5-hydroxymethylcytosine precursor for the biosynthesis of bacimethrin, a thiamin antimetabolite found in C. botulinum.

There are three protein chains in the BcmB asymmetric unit. The protomer has the same basic α/β fold as MilB with parallel β-strands flanked by α-helices.

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Chains A and B form a dimer by twofold noncrystallographic symmetry as does Chain C with an equivalent C associated by twofold crystallographic symmetry. The biologically relevent form of the dimer was confirmed by size exclusion chromatography.

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A comparison of the active sites of MilB (green, with CMP) and BcmB (blue) is shown at the right. Unlike other NDT family members, MilB and BcmB family members that prefer 2´-ribosyl groups have a critical phenylalanine (Phe6 in BcmB and Phe17 in MilB) positioned in the active site. Mutation of this phenylalanine residue to tyrosine results in a 1000-fold reversal of substrate specificity from CMP to deoxy CMP.


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Sikowitz MD, Cooper LE, Begley TP, Kaminski PA, and Ealick SE. Reversal of Substrate Specificity of CMP N-glycosidase to dCMP. Biochemistry 52:4037–4047 (2013). PubMed

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