S-adenosyl-L-methionine (AdoMet) dependent methyltransferases (MTases) are involved in biosynthesis, signal transduction, protein repair, chromatin regulation and gene silencing. Five different structural folds (I-V) have been described that bind AdoMet and catalyze methyltransfer to diverse substrates, although the great majority of known MTases have the Class I fold. Even within a particular MTase class the amino-acid sequence similarity can be as low as 10%. Thus, the structural and catalytic requirements for methyltransfer from AdoMet appear to be remarkably flexible.'There are many paths to the top of the mountain, but the view is always the same.'…Chinese proverb [(1996) The Columbia World of Quotations, New York Columbia University Press] Following ATP, S-adenosyl-L-methionine (AdoMet) is the second most widely used enzyme substrate [1]. The majority of AdoMet-dependent reactions involve methyltransfer, leaving the product S-adenosyl-L-homocysteine (AdoHcy). The huge preference for AdoMet over other methyl donors, such as folate, reflects favorable energetics resulting from the charged methylsulfonium center: the ΔG° for (AdoMet + Hcy → AdoHcy + Met) is −17 kcal mol −1 -over double that for (ATP → ADP + P i ) [1]. Methylation substrates range in size from arsenite to DNA and proteins, and the atomic targets can be carbon, oxygen, nitrogen, sulfur or even halides [2,3].The first structure of an AdoMet-dependent methyltransferase (MTase), determined in 1993, was for the DNA C5-cytosine MTase M.HhaI [4]. For several years thereafter, a variety of additional MTases, with a wide range of different substrates, were found to share the same basic structure. More recently however, AdoMet-dependent methylation has been found to be the target of functional convergence that is catalyzed by enzymes with remarkably distinct structures. The Protein Data Bank (PDB) currently includes >100 structures for 50 distinct AdoMet-dependent MTases from 31 different classes of enzymes as defined by the Enzyme Classification (EC) system (Table 1; for a more extensive list see Ref.[5]).The purpose of this review is to compare and contrast the five known structurally distinct families of AdoMet-dependent MTases (Classes I-V). The phenomenon of enzymes from distinct structural families catalyzing the same reaction, termed enzyme analogy, has been noted for several decades [6] pluripotency that can be shaped by mutation and selection [7,8]. This can lead to a given protein structure playing several distinct catalytic roles [9], but also results in distinct protein structures playing a common catalytic role. Perhaps such flexibility is particularly easy where highly exergonic reactions are involved. As ATP is the only enzyme substrate more widely used than AdoMet, it seems logical that the current champion for greatest number of analogous families is the ATP-dependent protein phosphoryltransferases (protein kinases), with seven known structurally distinct families [10]. Nonetheless, this degree of analogy appears to be quite ra...

Ubiquitin-binding domains (UBDs) are a collection of modular protein domains that non-covalently bind to ubiquitin. These recently discovered motifs interpret and transmit information conferred by protein ubiquitylation to control various cellular events. Detailed molecular structures are known for a number of UBDs, but to understand their mechanism of action, we also need to know how binding specificity is determined, how ubiquitin binding is regulated, and the function of UBDs in the context of full-length proteins. Such knowledge will be key to our understanding of how ubiquitin regulates cellular proteins and processes.

We report the crystal structure of the catalytic domain of human ADAR2, an RNA editing enzyme, at 1.7 angstrom resolution. The structure reveals a zinc ion in the active site and suggests how the substrate adenosine is recognized. Unexpectedly, inositol hexakisphosphate (IP 6 ) is buried within the enzyme core, contributing to the protein fold. Although there are no reports that adenosine deaminases that act on RNA (ADARs) require a cofactor, we show that IP 6 is required for activity. Amino acids that coordinate IP 6 in the crystal structure are conserved in some adenosine deaminases that act on transfer RNA (tRNA) (ADATs), related enzymes that edit tRNA. Indeed, IP 6 is also essential for in vivo and in vitro deamination of adenosine 37 of tRNA ala by ADAT1.One form of RNA editing is catalyzed by adenosine deaminases that act on RNA (ADARs), a family of enzymes that deaminate adenosine to form inosine in double-stranded RNA (dsRNA) (Fig. 1A) (1). ADARs are important for proper neuronal function (2-4) and also are implicated in the regulation of RNA interference (RNAi) (5-7). Inosine is recognized as guanosine by most cellular proteins and the translation machinery, and it pairs most stably with cytidine. Therefore, editing of RNA can alter a codon, create splice sites, and change its structure. The latter occurs when an AU base pair is changed to an IU mismatch and may be important for the effects of ADARs on the RNAi pathway.ADARs from all organisms have a common domain structure consisting of one to three dsRNA binding motifs (dsRBMs) near the N terminus, followed by a conserved C-terminal catalytic domain (1,8). Human ADAR2 (hADAR2) contains two dsRBMs, and its best characterized substrates are the pre-mRNAs of glutamate and serotonin receptors (9,10). Editing of codons within these RNAs leads to altered amino acids and generates receptors with altered function. hADAR2 also edits its own message to create a new splice site (11). Purified hADAR2 deaminates substrates in vitro (12) in the absence of any added cofactors, and deletions of Nterminal sequences, including dsRBM1, result in an active protein that accurately edits an RNA substrate (13). In addition, we found that a protein consisting of only the catalytic deaminase domain of hADAR2 (hADAR2-D, residues 299 to 701) ( fig. S1A) was active in vitro, although it deaminates RNA less efficiently than full-length hADAR2 ( fig. S1B).

Protein tyrosine phosphatases (PTPases) and kinases coregulate the critical levels of phosphorylation necessary for intracellular signalling, cell growth and differentiation. Yersinia, the causative bacteria of the bubonic plague and other enteric diseases, secrete an active PTPase, Yop51, that enters and suppresses host immune cells. Though the catalytic domain is only approximately 20% identical to human PTP1B, the Yersinia PTPase contains all of the invariant residues present in eukaryotic PTPases, including the nucleophilic Cys 403 which forms a phosphocysteine intermediate during catalysis. We present here structures of the unliganded (2.5 A resolution) and tungstate-bound (2.6 A) crystal forms which reveal that Cys 403 is positioned at the centre of a distinctive phosphate-binding loop. This loop is at the hub of several hydrogen-bond arrays that not only stabilize a bound oxyanion, but may activate Cys 403 as a reactive thiolate. Binding of tungstate triggers a conformational change that traps the oxyanion and swings Asp 356, an important catalytic residue, by approximately 6 A into the active site. The same anion-binding loop in PTPases is also found in the enzyme rhodanese.