Crystal structures methyl binding domains

Although traditionally found in tRNA, m U is also seen in ribosomal RNA (rRNA). The enzyme RumA catalyzes the site-specific methylation of U1939 in rRNA, and is distinguished from enzymes in the RUMT family in that it contains sequence homology with the putative RNA-binding TRAM domain in the N-terminus. With a crystal structure determined to 1.95 A, four conserved cysteine residues were found in... 

The X-ray crystal structure of mammalian 15-LOXl has revealed two domains, a catalytic domain and a j3-barrel domain [32], The P-barrel domain is similar to C2 domains found on other proteins and directs the binding of this enzyme to phospholipid membranes, the source of either AA or phospholipids for the oxidation process. The catalytic domain, which contains the histidine-coordinated Fe(III), holds the AA assisted by an ionic bond between R403 and the ionized carboxyl group of AA. The methyl terminus of AA is thus placed deep within a hydrophobic binding cleft in an arrangement that is likely similar to that of other lipoxygenases. 

Three crystal structures of ACS have been reported, two of CODH/ACS from M. thermoacetica [90,91] and one of the monomeric ACS from C. hydrogeno-formans [104]. ACS consists of three globular domains with the catalytic A-cluster bound to domain 3 at its interface with domain 1. As mentioned above, CODH/ACS has a hydrophobic tunnel network that allows CO, the product of Eq. 2 catalyzed by the C-cluster, to diffuse to the A-cluster where it combines with the methyl group donated by CFeSP to form an acetyl group that, in turn, binds to coenzyme A (Eq. 4). The presence of a tunnel connecting the two active sites was predicted before the structure was determined because, under normal turnover conditions, no CO was detected in the reaction medium [9,10]. 

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