Solution structure of an atypical PHD finger in BRPF2 and its interaction with DNA Lei Liu, Su Qin, Jiahai Zhang, Peng Ji, Yunyu Shi ⇑ , Jihui Wu ⇑ Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, PR China article info Article history: Received 6 March 2012 Received in revised form 19 June 2012 Accepted 26 June 2012 Available online 20 July 2012 Keywords: PHD finger PZPM BRPF2 NMR structure DNA abstract Plant homeodomain (PHD) finger is found to be a versatile reader that functions in recruiting transcrip- tion factors and chromatin modification complexes. Bromodomain- and PHD finger-containing (BRPF) proteins are identified as scaffold component in a couple of histone acetyltransferase (HATs) complexes but the biological function of PHD fingers, composing the motif called PZPM (PHD/Zn-knuckle/PHD Motif), in BRPF proteins is far from being well understood. Here we report the three-dimensional solution structure of the second PHD finger of PZPM in human BRPF2. According to the structure, BRPF2 PHD2 pos- sesses a two-strand b sheet which is different from any other PHD fingers. Functionally, this PHD finger can potentially bind DNA non-specifically with an evolutionarily conserved and positively charged sur- face. We provide the structural and interaction information of this atypical PHD finger and categorize this BRPF2 PHD2 into a new subset of PHD finger. Moreover our work also shed light on the functional aspect of the PZPM. Ó 2012 Elsevier Inc. All rights reserved. 1. Introduction PHD (plant homeodomain) finger was first identified in HAT3.1 of Arabidopsis in 1993 (Schindler et al., 1993). It is characterized by chelating two zinc ions with a conserved Cys4-His-Cys3 motif. This 60-residue module exhibits a two-strand b-sheet flanked by two short alpha helices (Yap and Zhou, 2010). PHD fingers are categorized according to their different binding properties to histone H3 with different modifications. The first type PHD finger specifically recognizes tri-methylated K4 on histone H3 tails (H3K4me3) (Wysocka et al., 2006) by embracing the trimethylam- monium group with a hydrophobic pocket formed by side chains of several aromatic residues (Li et al., 2006; Palacios et al., 2006; Pena et al., 2006). The second type PHD finger, which does not possess the hydrophobic pocket, recognizes non-modified histone tails (Lan et al., 2007). The histone H3 tail forms an anti-parallel b-sheet with the PHD finger upon binding and the substrate specificity is determined cooperatively by amino terminus, Lys4 and Arg8 on histone H3 tail (Lan et al., 2007). In addition, two more PHD subsets were identified recently. One binds H3K9me3 (Mansfield et al., 2011; Musselman et al., 2009) the other recognizes acetylated ly- sine on histone H3 or H4 (Lange et al., 2008; Matsuyama et al., 2010; Zeng et al., 2010). These properties make PHD finger a versa- tile reader that functions in recruiting transcription factors and chromatin modification complexes (Slama and Geman, 2011). BRPF (Bromodomain-and PHD finger-containing proteins) is identified as a component of MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) histone acetyltransferase (HATs) complex (Brown et al., 2000; Li et al., 2007). It has three par- alogs, BRPF1, 2, and 3. BRPF1 and 2 are also referred to as BRD140 (bromodomain protein of 140 kDa) and BRD1 (bromodomain pro- tein 1), respectively. In the HAT complex, MOZ/MORF, the catalytic subunit (Doyon et al., 2006), is bridged with another two compo- nents, EAF6 (homolog of yeast Esa1-associated factor6) and ING5 (inhibitor of growth protein 5), by the scaffold protein BRPF (Pelle- tier et al., 2002; Ullah et al., 2008). Members of BRPF family contain a C-terminal PWWP domain which is a H3K36me3 binding module (Vezzoli et al., 2010), a bromodomain which associates with acetyl- lysine residues on proteins (Sanchez and Zhou, 2009), and a unique N-terminal PZPM (PHD/Zn-knuckle/PHD Motif) which consists of two PHD fingers linked by a mononuclear zinc knuckle. The PZPM defines the subfamilies III and IV of Epc-N (Enhancer of the Poly- comb-N-terminus) domain, a protein–protein interaction module found in chromatin associated proteins, and all proteins studied to date that contain PZPM have been implicated in histone methyl- ation and/or gene silencing (Perry, 2006). The first PHD finger of PZPM in BRPF proteins is highly conserved in yeast-NuA3-like HAT complexes and the one in BRPF2, which belongs to the second 1047-8477/$ - see front matter Ó 2012 Elsevier Inc. All rights reserved. http://dx.doi.org/10.1016/j.jsb.2012.06.014 Abbreviations: PHD, plant homeodomain; BRPF, bromodomain- and PHD finger- containing protein; HAT, histone acetyltransferase; PZPM, PHD/Zn-knuckle/PHD Motif; MOZ, monocytic leukemia zinc finger protein; MORF, MOZ-related factor; HBO1, human acetylase binding to ORC1; ING, inhibitor of growth protein; IR- EMSA, infrared electrophoretic mobility shift assays; FPA, fluorescence polarization assays; CD, circular dichroism. ⇑ Corresponding authors. Present address: School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, PR China. Fax: +86 551 3600374 (Y. Yu), (J. Wu). E-mail addresses: yyshi@ustc.edu.cn (Y. Shi), wujihui@ustc.edu.cn (J. Wu). Journal of Structural Biology 180 (2012) 165–173 Contents lists available at SciVerse ScienceDirect Journal of Structural Biology journal homepage: www.elsevier.com/locate/yjsbi