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

Abstract

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 P21212 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.

Biological Catalysis and Information Storage Have Relied on N-Glycosyl Derivatives of β-D-Ribofuranose since the Origins of Life

“…The bond may affect alkaline metal ions [156], mainly Na + and K + or a number of transition metal cations, such as Zn 2+ , Mn 2+ , Fe 2+ and others [157][158][159]. Moreover, activities of these enzymes can be regulated by using the coordination of both alkaline and transition metal cations in the active site area, as observed for pyruvate kinases [160], S-adenosyl-L-methionine synthetases [161] or S-adenosyl-L-homocysteine hydrolases [157,162,163]. As a result, not only was the range of catalyzed reactions broadened, but additional mechanisms were also created to positively or negatively regulate enzymatic activity, e.g., through the effect of cation on substrate bonding [156].…”

S-adenosyl-l-homocysteine Hydrolase: A Structural Perspective on the Enzyme with Two Rossmann-Fold Domains

“…Those studies included enzymes of eukaryotic origin from mammals ( Homo sapiens [ 8 ], Rattus norvegicus [ 9 ], Mus musculus [ 19 ]), protozoans ( Plasmodium falciparum [ 20 ], Trypanosoma brucei [PDB code 3H9U, unpublished], Leishmania major [3G1U, unpublished], Cryptosporidium parvum [5HM8 unpublished], Acanthamoeba castellanii [6UK3, unpublished], Naegleria fowleri [5V96, unpublished], and plants ( Lupinus luteus [ 21 ]). Crystallographic studies were also conducted for some bacterial SAHases, including enzymes from Mycobacterium tuberculosis [ 22 ], Bradyrhizobium elkanii [ 23 , 24 ], Cytophaga hutchinsonii [ 25 ], Pseudomonas aeruginosa [ 26 ], Burkholderia pseudomalei (3D64, 3GLQ, unpublished), Brucella abortus (3N58, unpublished), and Elizabethkingia anopheles (6APH, unpublished). Additionally, crystal structures of an archaeal-type SAHase from hyperthermophilic bacterium Thermotoga maritima were determined for the enzyme in its active and inactive conformations [ 27 , 28 ].…”