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1.
Figure 4

Figure 4. From: Structure and Mechanisms of Lysine Methylation Recognition by the Chromodomain in Gene Transcription.

Depiction of H3K9me3 and S10 side chains in the Pc-H3K27me3 structure, with Pc depicted in surface representation. Polar contacts made between the side chain of Pc E58 and H3S10 (backbone nitrogen in blue, side chain oxygen in red and denoted Oγ) illustrate how phosphorylation at S10 could disrupt the interaction. Aromatic cage residue side chains are also shown in stick representation.

Kyoko L. Yap, et al. Biochemistry. ;50(12):1966-1980.
2.
Figure 2

Figure 2. From: Structure and Mechanisms of Lysine Methylation Recognition by the Chromodomain in Gene Transcription.

Domain layout of human chromodomain-containing proteins. Chromo barrel domains are denoted by asterisks. CD: chromodomain. RBB1NT: N-terminal to ARID/BRIGHT domain in Rb-binding protein 1 family. CHSH: chromoshadow domain. ANK: four ankyrin repeats. DEXDc: DEAD-like helicase domain. HELICc: helicase domain. HD-like: homeodomain-like. CHDN: N-terminal NUC034/HMG-box helicase domain. DUF1087, DUF1086: domains of unknown function. CHDCT2: C-terminal NUC038 helicase domain.

Kyoko L. Yap, et al. Biochemistry. ;50(12):1966-1980.
3.
Figure 3

Figure 3. From: Structure and Mechanisms of Lysine Methylation Recognition by the Chromodomain in Gene Transcription.

Structures of chromodomains and chromo barrel domains. Secondary structure elements are labeled as defined in Figure 1B and the text. Residues interacting with the methylated lysine are labeled in inset images. A, Chromodomain of uncomplexed HP1β (PDB code 3F2U, magenta) and Drosophila Pc (1PDQ, red) in complex with H3K27me3 peptide (yellow). B, CHD1 (2B2W) chromodomains 1 (light purple) and 2 (dark blue) in complex with H3K4me3 (yellow). C, Left, chromo barrel domain of Eaf3 (2K3Y, green) in complex with fused H3K36me2 peptide (purple). Right, MSL3 chromo barrel domain (3M9P, light green) in complex with H4K20me1 peptide (cyan) and DNA (orange). β-strand that mimics the H3 peptide of the Pc complex is indicated with an asterisk. Center, aromatic cage residues that coordinate the methylated lysine of Pc+H3K27me3 (red/yellow), Eaf3+H3K36me2 (green/purple) and MSL3+H4K20me1 (light green/cyan) complex structures.

Kyoko L. Yap, et al. Biochemistry. ;50(12):1966-1980.
4.
Figure 1

Figure 1. From: Structure and Mechanisms of Lysine Methylation Recognition by the Chromodomain in Gene Transcription.

Chromodomains and chromo barrel domains in the human genome. A, Unrooted phylogenetic tree of chromodomains and chromo barrel domains (in green). B, Alignment of sequences used to generate the tree in A. Residue numbers of first and last amino acids in the alignment are noted. Secondary structure elements (orange, denoted α for helices; cyan, denoted β for strands) defined for HP1β (from PDB code 3F2U), Pc (1PDQ) and CHD1 (2B2W) are shown at top, and those defined for MSL3 chromo barrel domain (3M9P) are shown at bottom. Subgroups within the chromodomain superfamily are colored separately. Residues highlighted in yellow form the aromatic cage; those in magenta are additional aromatic residues known from structural studies to supplement the coordination of the methylated lysine; those in bold are well-conserved residues structurally on the periphery of the aromatic cage, with non-conserved residues highlighted in black; those in green are conserved phosphorylatable residues at the position of a residue known to be phosphorylated by casein kinase II in HP1. Those marked with an asterisk are notable residues conserved in chromodomains but not among chromo barrel domains.

Kyoko L. Yap, et al. Biochemistry. ;50(12):1966-1980.

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