Crystal Structure of S-adenosyl-L-homocysteine Hydrolase from Cytophaga hutchinsonii, a Case of Combination of Crystallographic and Non-crystallographic Symmetry

The majority of living organisms utilize S-adenosyl-L-homocysteine hydrolase (SAHase) as a key regulator of cellular methylation reactions. The unusual evolution history of SAHase genes is reflected in the phylogeny of these proteins, which are grouped into two major domains: mainly archaeal and eukaryotic/bacterial. Such a phylogeny is in contradiction to the three-domain topology of the tree of life, commonly based on 16S rRNA sequences. Within the latter domain, SAHases are classified as eukaryotic-only or bacterial-only clades depending on their origin and sequence peculiarities. A rare exception in this classification is SAHase from a cellulose-utilizing soil bacterium Cytophaga hutchinsonii (ChSAHase), as the phylogenetic analyses indicate that ChSAHase belongs to the animal clade. Here, the P2(1)2(1)2 crystal structure of recombinant ChSAHase in ternary complex with the oxidized form of the NAD(+) cofactor and a reaction product/substrate (adenosine) is presented. Additionally, a sodium cation was identified in close proximity of the active site. The crystal contains two translational NCS-related intimate dimers of ChSAHase subunits in the asymmetric unit. Two complete tetrameric enzyme molecules are generated from these dimers within the crystal lattice through the operation of crystallographic twofold axes in the z direction.