The nickel-sirohydrochlorin formation mechanism of the ancestral class II chelatase CfbA in coenzyme F430 biosynthesis

Abstract

The class II chelatase CfbA catalyzes Ni2+insertion into sirohydrochlorin (SHC) to yield the product nickel-sirohydrochlorin (Ni-SHC) during coenzyme F430 biosynthesis. CfbA is an important ancestor of all the class II chelatase family of enzymes, including SirB and CbiK/CbiX, functioning not only as a nickel-chelatase, but also as a cobalt-chelatasein vitro. Thus, CfbA is a key enzyme in terms of diversity and evolution of the chelatases catalyzing formation of metal-SHC-type of cofactors. However, the reaction mechanism of CfbA with Ni2+and Co2+remains elusive. To understand the structural basis of the underlying mechanisms and evolutionary aspects of the class II chelatases, X-ray crystal structures ofMethanocaldococcus jannaschiiwild-type CfbA with various ligands, including SHC, Ni2+, Ni-SHC, and Co2+were determined. Further, X-ray crystallographic snapshot analysis captured a unique Ni2+-SHC-His intermediate complex and Co-SHC-bound CfbA, which resulted from a more rapid chelatase reaction for Co2+than Ni2+. Meanwhile, anin vitroactivity assay confirmed the different reaction rates for Ni2+and Co2+by CfbA. Based on these structural and functional analyses, the following substrate-SHC-assisted Ni2+insertion catalytic mechanism was proposed: Ni2+insertion to SHC is promoted by the support of an acetate side chain of SHC.