PDBsum entry 2fui

Protein binding

PDB id

2fui

Contents

			Protein chain

					62 a.a.

References listed in PDB file

Key reference

Title

Molecular basis for site-Specific read-Out of histone h3k4me3 by the bptf phd finger of nurf.

Authors

H.Li, S.Ilin, W.Wang, E.M.Duncan, J.Wysocka, C.D.Allis, D.J.Patel.

Ref.

Nature, 2006, 442, 91-95. [DOI no: 10.1038/nature04802]

PubMed id

16728978

Abstract

Mono-, di- and trimethylated states of particular histone lysine residues are selectively found in different regions of chromatin, thereby implying specialized biological functions for these marks ranging from heterochromatin formation to X-chromosome inactivation and transcriptional regulation. A major challenge in chromatin biology has centred on efforts to define the connection between specific methylation states and distinct biological read-outs impacting on function. For example, histone H3 trimethylated at lysine 4 (H3K4me3) is associated with transcription start sites of active genes, but the molecular 'effectors' involved in specific recognition of H3K4me3 tails remain poorly understood. Here we demonstrate the molecular basis for specific recognition of H3(1-15)K4me3 (residues 1-15 of histone H3 trimethylated at K4) by a plant homeodomain (PHD) finger of human BPTF (bromodomain and PHD domain transcription factor), the largest subunit of the ATP-dependent chromatin-remodelling complex, NURF (nucleosome remodelling factor). We report on crystallographic and NMR structures of the bromodomain-proximal PHD finger of BPTF in free and H3(1-15)K4me3-bound states. H3(1-15)K4me3 interacts through anti-parallel beta-sheet formation on the surface of the PHD finger, with the long side chains of arginine 2 (R2) and K4me3 fitting snugly in adjacent pre-formed surface pockets, and bracketing an invariant tryptophan. The observed stapling role by non-adjacent R2 and K4me3 provides a molecular explanation for H3K4me3 site specificity. Binding studies establish that the BPTF PHD finger exhibits a modest preference for K4me3- over K4me2-containing H3 peptides, and discriminates against monomethylated and unmodified counterparts. Furthermore, we identified key specificity-determining residues from binding studies of H3(1-15)K4me3 with PHD finger point mutants. Our findings call attention to the PHD finger as a previously uncharacterized chromatin-binding module found in a large number of chromatin-associated proteins.



	Figure 2. Figure 2: Crystal structures of human BPTF PHD finger-linker-bromodomain in the free state and bound to H3(1–15)K4me3. a, Domain architecture of BPTF bromodomain and proximal PHD finger. b, Ribbon representation of the crystal structure of the BPTF PHD finger-linker-bromodomain in the free state. Two bound Zn ions within the PHD fold are shown as balls. c, Crystal structure of the H3(1–15)K4me3-bound complex, with bound peptide shown in a space-filling representation. d, Structure of the PHD finger complex with the 2F[o] - F[c] omit electron density (0.8 level) highlighted for the bound H3(1–15)K4me3 peptide. e, Positioning of the H3(1–15)K4me3 peptide (space-filling representation) on the surface of the PHD finger portion (electrostatic surface representation with red as negatively charged and blue as positively charged surface) of the complex. f, Different view emphasizing the positioning of R2 and K4me3 in adjacent channels.		Figure 3. Figure 3: Details of the intermolecular contacts in the H3(1–15)K4me3 peptide–BPTF PHD finger complex and comparison with its H3(1–15)K4me2-bound counterpart. a, Intermolecular backbone interactions between the A1–T6 segment of bound H3(1–15)K4me3 peptide and the PHD finger in the complex. b, Intermolecular hydrogen-bonding interactions involving the guanidinium group of R2 in the complex. c, Superposition of free (coloured green) and H3(1–15)K4me3-bound complex (coloured yellow) of the BPTF PHD finger. d, e, Positioning of the trimethylated lysine of the H3(1–15)K4me3 peptide (d) and the dimethylated lysine of the H3(1–15)K4me2 peptide (e) within a four-aromatic-amino-acid cage of the BPTF PHD finger. Two bridging water molecules link the NH of K4me2 to the carboxylate of D6, as indicated by dashed lines.

PROCHECK

	Headers