Mobile loop dynamics in adenosyltransferase control binding and reactivity of coenzyme B ₁₂

Abstract

Cobalamin is a complex organometallic cofactor that is processed and targeted via a network of chaperones to its dependent enzymes. AdoCbl (5′-deoxyadenosylcobalamin) is synthesized from cob(II)alamin in a reductive adenosylation reaction catalyzed by adenosyltransferase (ATR), which also serves as an escort, delivering AdoCbl to methylmalonyl-CoA mutase (MCM). The mechanism by which ATR signals that its cofactor cargo is ready (AdoCbl) or not [cob(II)alamin] for transfer to MCM, is not known. In this study, we have obtained crystallographic snapshots that reveal ligand-induced ordering of the N terminus ofMycobacterium tuberculosisATR, which organizes a dynamic cobalamin binding site and exerts exquisite control over coordination geometry, reactivity, and solvent accessibility. Cob(II)alamin binds with its dimethylbenzimidazole tail splayed into a side pocket and its corrin ring buried. The cosubstrate, ATP, enforces a four-coordinate cob(II)alamin geometry, facilitating the unfavorable reduction to cob(I)alamin. The binding mode for AdoCbl is notably different from that of cob(II)alamin, with the dimethylbenzimidazole tail tucked under the corrin ring, displacing the N terminus of ATR, which is disordered. In this solvent-exposed conformation, AdoCbl undergoes facile transfer to MCM. The importance of the tail in cofactor handover from ATR to MCM is revealed by the failure of 5′-deoxyadenosylcobinamide, lacking the tail, to transfer. In the absence of MCM, ATR induces a sacrificial cobalt–carbon bond homolysis reaction in an unusual reversal of the heterolytic chemistry that was deployed to make the same bond. The data support an important role for the dimethylbenzimidazole tail in moving the cobalamin cofactor between active sites.

Patient mutations in human ATP:cob(I)alamin adenosyltransferase differentially affect its catalytic versus chaperone functions

“…In this structure, a complete ordering of loops, except for the first 50 residues, was observed. As seen previously ( 16 ), ATP induced ordering of residues 68 to 80 into a β-hairpin, forming the roof of the active site ( Fig. 6 B ).…”

“…The base in the base-on form of cobalamin refers specifically to DMB. Crystallographic snapshots of the homologous ATR from Mycobacterium tuberculosis have revealed the importance of protein and cofactor tail dynamics in controlling cofactor coordination and reactivity ( 16 ). In the presence of ATP and cob(II)alamin, the N-terminus of ATR becomes ordered, forming a cup shaped structure that forces the DMB tail into a side pocket.…”

Redox-Linked Coordination Chemistry Directs Vitamin B12 Trafficking

“…Sci. U. S. A.20201173041230422 LiZ.MascarenhasR.TwahirU.…”

Spectrum and characterization of bi-allelic variants in MMAB causing cblB-type methylmalonic aciduria

“…Extensive biochemical characterization of bacterial PduO-type adenosyltransferases, a class to which MMAB also belongs, has illustrated their unique reaction mechanism (Johnson et al 2004;Mera et al 2007;Padovani et al 2008;St. Maurice et al 2008;Padovani and Banerjee 2009;Park et al 2012;Mascarenhas et al 2020). These studies have demonstrated that ATP binds to one of three potential active-sites, each occurring at the homotrimer subunit interfaces, following which cobalamin binds to the same site in the base-off state.…”