Volume 26, Issue 1, Pages 85-95.e3 (January 2018) DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants  Chao Xu, Ke Liu, Ming Lei, Ally Yang, Yanjun Li, Timothy R. Hughes, Jinrong Min  Structure  Volume 26, Issue 1, Pages 85-95.e3 (January 2018) DOI: 10.1016/j.str.2017.11.022 Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 1 Domain Organization of 12 Human CXXC Proteins, Including CFP1, MLL1, MLL2, KDM2A, KDM2B, FBXL19, MBD1, DNMT1, CXXC4, CXXC5, TET1, and TET3 CXXC, CXXC-type zinc finger domain; MBD, methyl-CpG-binding domain; AT hook, DNA-binding domain with preference for AT-rich regions; PHD, plant homeodomain; BRD, bromodomain; Tudor, Tudor domain; FYR, FY-rich domain; SET, (Su(var)3–9, enhancer-of-zeste, trithorax) domain; Post-SET, cysteine-rich motif following a subset of SET domains; F box, F box domain; TRD, transcriptional repression domain; LRR, leucine-rich repeat; DMAP binding, DNA methyltransferase-associated protein-binding domain; BAH, bromo-adjacent homology; MTase, SAM-dependent methyltransferase C5-type domain; JmjC, Jumonji C domain; Dioxygenase, methylcytosine dioxygenase. Detailed construct information of CXXC or CXXC-PHD domain is also labeled. See also Figure 2 and Table S3. Structure 2018 26, 85-95.e3DOI: (10.1016/j.str.2017.11.022) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 2 Four Classes of Human CXXC Domains: CpGpG, CpG, CpN, and Weak or No Binding (A) The sequence alignment of 14 human CXXC domains, with the logo representing each class. Conserved residues are highlighted with red columns, while similar residues are colored in red. (B) PBM of the GST-tagged fusion CXXC domains of CFP1, MLL1, KDM2A, KDM2B, FBXL19, TET1, TET3, and CXXC4. The binding motifs are highlighted in red. See also Figure 1, Data S1, and Tables 1 and S1. Structure 2018 26, 85-95.e3DOI: (10.1016/j.str.2017.11.022) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 3 The MLL2 CXXC Domain Specifically Recognizes CpG dsDNA (A) Left: Overall structure of the MLL2-CCGG complex. Protein and DNA are shown in blue and green cartoon, respectively, with the CpG base pairs (C6-G6′ and G7-C7′) in red cartoon. Middle: The electrostatic surface of MLL2 in complex with dsDNA (green). Right: The detailed interactions between MLL2 and dsDNA, with backbone and side-chain hydrogen bonds indicated by gray and red arrows, respectively. (B) The detailed interactions between the MLL2 CXXC domain with C6-G6′ (left) and G7-C7′ (right) base pairs, respectively. The protein and DNA are shown as blue and green cartoon, respectively. The interaction residues and bases are shown in stick model. See also Figures 2, 4, S1, and S3. Structure 2018 26, 85-95.e3DOI: (10.1016/j.str.2017.11.022) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 4 The CFP1 CXXC Domain Is the Only Member of the Class I CXXC Domain that Prefers CpGpG (A) Left: the overall structure of the CFP1-CCGG complex, in which the protein and DNA are shown in the same way as in Figure 3A. The CGG are shown in red. Right: The CFP1 CXXC domain specifically recognizes CpGpG, that is, C6-G6′, G7-C7′, and G8-C8′ base pairs. (B–D) Structure comparisons of the class II CXXC domains with the that of CFP1, including (B) MLL2, (C) MBD1_C3, and (D) FBXL19. In all three figures, the CFP1 and the class II CXXC domains are shown in blue and orange ribbon, respectively. The DNAs are shown in gray cartoon, with G8-C8′ shown in red. The protein residues, such as Arg213 and Tyr216 of CFP1, as well as Met382 and Leu385 of MBD1_C3, are shown in stick model. See also Figures 2 and 3, and Table S1. Structure 2018 26, 85-95.e3DOI: (10.1016/j.str.2017.11.022) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 5 Base-Specific Interactions between Class III CXXC Domains and Their Respective dsDNA Ligands (A) TET3-ACGT; (B) TET1-CCGG; (C) CXXC4-ACGT; (D) CXXC5-ACGT. The figures are shown in the same way as Figure 3. See also Figures 2 and S1–S4, and Tables 1 and S1. Structure 2018 26, 85-95.e3DOI: (10.1016/j.str.2017.11.022) Copyright © 2017 Elsevier Ltd Terms and Conditions