Chromatin Modification: How to Put a HAT on the Histones Andrew Travers

Dispatch R23

Chromatin modification: How to put a HAT on the histones Andrew Travers

Specific patterns of acetylation of the core histones are specificity, acetylating not only histones in vitro but also associated with specific structures and functions of other transcription factors, including p53, TFIIEb, TFIIF chromatin. A basis for the specificity of acetylation is and the HMG-domain protein LEF-1 [5–7]. One basis for now apparent in the recent crystal structures of two these differences in substrate selection has recently been acetyltransferases. clarified by solution of the crystal structures of two acetyltransferase complexes, one of yeast Hat1 with bound Address: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK. acetyl-coenzyme A (acetyl-CoA) [8] and the second of an aminoglycoside 3-N-acetyltransferase from Serratia marce- Current Biology 1999, 9:R23–R25 sens with bound CoA [9]. Both these enzymes belong to http://biomednet.com/elecref/09609822009R0023 the superfamily of acetyltransferases typified by the © Elsevier Science Ltd ISSN 0960-9822 acetyltransferase domain of the co-activator Gcn5.

The histone acetyltransferases are a large superfamily of The yeast histone acetyltransferase Hat1 was the first of enzymes, included among which are the specific histone its type to be identified genetically [10], and is believed to acetyltransferases. The acetylation of histones can modify play an important role in replication-dependent nucleo- the structure and function of chromatin in highly specific some assembly. In higher eukaryotes, the specific modifi- ways, each of which is correlated with a particular pattern cation of the amino-terminal tails of newly synthesized of modification. Transcriptional competence has long histone H3 and H4 is required for their assembly as been associated with the hyperacetylation of the core (H3–H4)2 tetramers on newly replicated DNA by the histones, particularly H3 and H4, in nucleosomes. By assembly protein CAF-1 [11]. Hat1, despite its initial contrast, in the transcriptionally silent heterochromatin of assignment to the cytoplasmic compartment, is predomi- yeast nucleosomes, there is a single acetylated histone nantly present in the nucleus, where it specifically residue, lysine 12 of histone H4, suggesting that specific acetylates lysine 12 of free histone H4, but cannot modify patterns of acetylation may serve as tags for certain H4 that is assembled into nucleosomes [11]. By contrast, chromatin structures with their associated functions [1]. the aminoglycoside acetyltransferase from Serratia marcesens, SmAAT, catalyses the addition of acetyl groups These distinct patterns of histone modification imply the to certain aminoglycoside antibiotics, including existence of distinct and specific acetylase activities. A gentamicin and tobramicin [12]. number of these have been identified recently, including the transcriptional co-activators Gcn5, p300/CBP, Src-1, The acetyltransferases related to Gcn5 were initially ACTR and TAFII250 (reviewed in [2–4]). One of these characterised by four sequence motifs, A, B, C and D, of activators, p300/CBP, has a relatively broad substrate which A is the most highly conserved [13] and C is

Figure 1

Structures of (a) yeast histone acetyltransferase Hat1 in a complex with acetyl-CoA; and (b) Serratia marcesens aminoglycoside acetyltransferase in a complex with CoA. Note the position of cofactor (shown in ball-and-stick representation) in a pocket in each case. (Reproduced with permission from [8,9].) R24 Current Biology, Vol 9 No 1

Figure 2 charged aminoglycoside antibiotics in presumably an appropriate configuration for acetylation. Different members of the aminoglycoside acetyltransferase family acetylate different amino groups in the same antibiotic, and it would be expected that the spatial arrangement of negative charge and other specificity determinants would Acidic differ between these enzymes. patch K16 Acetyl group The histone acetyltransferases similarly differ in their G14 A15 selectivity for the acetylatable lysines in the histone tails. Hydrophobic K12 pocket G13 In Hat1, the length of the putative substrate-binding cleft L10 by the active site is sufficient to accommodate a six-to- G11 Shallow Acidic seven residue peptide in an extended conformation. K8 groove patch G9 Docking the amino-terminal tail of H4, modeled as an extended chain, into the active site of Hat1 shows that lysine 12 can approach the carbonyl side chain of the bound acetyl-CoA only from one side of the gate over the acetyl-CoA-binding cleft (Figure 2). This selection may be facilitated by the positioning of leucine 10 of H4 in a Model of the binding of part of the amino-terminal tail of histone H4 to Hat1. (Reproduced with permission from [8].) hydrophobic pocket in the deepest part of the cleft, and of glycine 13 and glycine 14 in a shallow region of the cleft immediately adjacent to the proposed position of lysine 12. missing from Hat1. But although the structures of the A motifs in SmAAT [9] and Hat1 [8] are very similar overall, The modeling also provides an explanation for the lower the two proteins have somewhat different architectures. activity of Hat1 on the other acetylatable lysines — lysine The structure of a truncated derivative of Hat1, lacking 5, lysine 8 and lysine 16 in the amino-terminal tail of H4. the dispensable 54 amino acids at the carboxyl terminus, Both lysine 8 and lysine 16 could position lysine 12 by contains two domains connected by an extended loop interacting with acidic residues and thereby limit their which together form an extended curved structure [8] own acetylation, whereas the placement of lysine 5 in the (Figure 1a). The acetyl-CoA cofactor is bound in a cleft active site could be disfavored by the potential positioning located towards the center of the concave surface of the of arginine 3 in the hydrophobic pocket. According to this protein. By contrast the smaller SmAAT, also crystallized model, the substrate specificity is a consequence of as a truncated derivative lacking nine amino acids at the structural complementarity between the extended chain of carboxyl terminus, has a single domain fold, reminiscent the histone tail and the topography of the substrate cleft. of a ’right hand’ wrapped around a cylinder with an extended ‘thumb’ [9] (Figure 1b). Again, the CoA is Although the architecture of the binding site for the located in a substrate-binding cleft. histone tail may determine the specificity of the acetylation pattern, the accessibility of the ligand appears to be Substrate selection by acetyltransferases an important determinant of activity both in vivo and in The most similar region of the two structures is the vitro. For example, the transcriptional co-activator Gcn5 β–loop–α configuration specified by motif A. This motif can acetylate free histones in vitro but is unable to modify makes multiple contacts with the CoA moiety of the the same histones contained in nucleosomes [14]. Both cofactor. As revealed by the crystal structures [8,9], the genetic and biochemical evidence indicates that this latter highly conserved Q/RxxGxG/A sequence within motif A activity requires the association of Gcn5 with other pro- binds the pyrophosphate link between the adenosyl and teins to form larger complexes (two of which are known as pantetheine moieties of CoA. In both enzyme–cofactor Ada and SAGA complexes) [14] Once formed, these com- complexes, the bound CoA is bent and wraps around the plexes can be recruited to specific sites by the DNA- surface of the protein, positioning the acetyl group binding transcriptional activator Gcn4 [15]. The natural adjacent to the respective putative substrate-binding site chromatin substrate for these complexes is likely to be in Hat1. In SmAAT, the configuration of the CoA is condensed chromatin. slightly different and lies in a slot delineated by a loop in the ‘thumb’ on one side and helices H1 and H2 in the A further possible complication is the inferred propensity ‘hand’ on the other. of the amino-terminal region of histone H4 to adopt an α- helical configuration [16], although this is not observed Together these loops in the SmAAT structure create in the crystal structure of the nucleosome core particle negatively charged surfaces that would bind the positively [17]. The larger complexes might thus have additional Dispatch R25

abilities to increase the availability of the histone tails for modification by altering their conformation, and/or dis- rupting the interactions between adjacent nucleosomes If you found this dispatch interesting, you might also want to read the December 1998 issue of that would impair accessibility for the acetyltransferase activity. In this context, it is probably relevant that com- ponents both of the SAGA histone acetylase complex and Current Opinion in of the chromatin remodeling complexes Swi/Snf, Brm Structural Biology and RSC, which do not themselves have histone acetyltransferase activity, contain protein motifs that, by inter- which included the following reviews, edited acting directly with the histone tails, could act as by JoAnne Stubbe and Louise N Johnson, ‘grappling hooks’ for accessing condensed chromatin. on Catalysis and regulation:

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