Structural Basis of Plant Homeodomain Finger 6 (PHF6) Recognition by the Retinoblastoma Binding Protein 4 (RBBP4) Component of the Nucleosome Remodeling and Deacetylase (NuRD) Complex

• Published in: The Journal of biological chemistry 2015-03, Vol.290 (10), p.6630-6638
• Main Authors: Liu, Zhonghua, Li, Fudong, Zhang, Beibei, Li, Sai, Wu, Jihui, Shi, Yunyu
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; BFLS; Carrier Proteins - chemistry; Carrier Proteins - genetics; Chromatin Assembly and Disassembly; Chromatin Regulation; Crystallography, X-Ray; Gene Regulation; HEK293 Cells; Humans; Mi-2 Nucleosome Remodeling and Deacetylase Complex - chemistry; Mi-2 Nucleosome Remodeling and Deacetylase Complex - metabolism; NuRD Complex; Peptides - chemistry; Peptides - metabolism; PHF6; Precursor T-Cell Lymphoblastic Leukemia-Lymphoma - genetics; Precursor T-Cell Lymphoblastic Leukemia-Lymphoma - pathology; Protein Binding; Protein Crystallization; Protein Interaction Maps; Protein Structure and Folding; Protein Structure, Tertiary; Protein-Protein Interaction; RBBP4/RbAp48; Repressor Proteins; Retinoblastoma-Binding Protein 4 - chemistry; Retinoblastoma-Binding Protein 4 - genetics; Retinoblastoma-Binding Protein 4 - metabolism; Structural Biology; T-ALL; Transcription, Genetic
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M114.610196

The NuRD complex is a conserved transcriptional coregulator that contains both chromatin-remodeling and histone deacetylase activities. Mutations of PHF6 are found in patients with Börjeson-Forssman-Lehmann syndrome, T-cell acute lymphoblastic leukemia, or acute myeloid leukemia. Recently, PHF6 was identified to interact with the NuRD complex, and this interaction is mediated by the RBBP4 component. However, little is known about the molecular basis for the interaction. Here, we present the crystal structure of the complex of the NuRD subunit RBBP4 bound to the PHF6 peptide (residues 162–170). The PHF6 peptide binds to the top surface of the RBBP4 β-propeller. A pair of positively charged residues of the PHF6 peptide insert into the negatively charged pocket of RBBP4, which is critical for the interaction between PHF6 and RBBP4. Corresponding PHF6 mutants impair this interaction in vitro and in vivo. Structural comparison shows that the PHF6-binding pocket overlaps with FOG1 and histone H3 on RBBP4/Nurf55, but it is distinct from the pocket recognizing histone H4, Su(z)12, and MTA1. We further show that the middle disordered region (residues 145–207, containing the RBBP4-binding motif) is sufficient for the transcriptional repression mediated by PHF6 on the GAL4 reporter, and knockdown of RBBP4 diminished the PHF6-mediated repression. Our RBBP4-PHF6 complex structure provides insights into the molecular basis of PHF6-NuRD complex interaction and implicates a role for PHF6 in chromatin structure modulation and gene regulation. Background: The PHF6 gene is mutated in patients with Börjeson-Forssman-Lehmann syndrome, T-cell acute lymphoblastic leukemia, and acute myeloid leukemia. The PHF6 protein is a newly identified interactor with the NuRD complex. Results: The complex structure of the NoLS region of PHF6 bound to RBBP4 was solved. Conclusion: By interacting with the RBBP4 component, PHF6 associates with the NuRD complex. Significance: Association with the NuRD complex implicates a role for PHF6 in chromatin structure modulation and gene regulation.