Domain swapping and SMYD1 interactions with the PWWP domain of human hepatoma-derived growth factor

Abstract

The human hepatoma-derived growth factor (HDGF), containing the chromatin-associated N-terminal PWWP domain capable of binding the SMYD1 promoter, participates in various cellular processes and is involved in human cancers. We report the first crystal structures of the human HDGF PWWP domain (residues 1–100) in a complex with SMYD1 of 10 bp at 2.84 Å resolution and its apo form at 3.3 Å, respectively. The structure of the apo PWWP domain comprises mainly four β-strands and two α-helices. The PWWP domain undergoes domain swapping to dramatically transform its secondary structures, altering the overall conformation from monomeric globular folding into an extended dimeric structure upon DNA binding. The flexible loop2, as a hinge loop with the partially built structure in the apo PWWP domain, notably refolds into a visible and stable α-helix in the DNA complex. The swapped PWWP domain interacts with the minor grooves of the DNA through residues Lys19, Gly22, Arg79 and Lys80 in varied ways on loops 1 and 4 of the two chains, and the structure becomes more rigid than the apo form. These novel structural findings, together with physiological and activity assays of HDGF and the PWWP domain, provide new insights into the DNA-binding mechanism of HDGF during nucleosomal functions.

Role of hepatoma‐derived growth factor in promoting de novo lipogenesis and tumorigenesis in hepatocellular carcinoma

“…HDGF is a unique growth factor and may act through either a receptor‐mediated pathway or a more direct way, that is, DNA, RNA, or protein binding(Chen et al ., 2018; Hung et al ., 2015; Rona et al ., 2016). We found that HDGF mainly colocalized with SREBP‐1a within the nucleus, implying that nHDGF rather than receptor‐bound HDGF involved in SREBP‐mediated transcription (Fig.…”

“…The PWWP domain was first characterized from the WHSC1 (Wolf-Hirschhorn syndrome candidate 1) gene and was previously known as the HATH domain (Bao et al, 2014b). Proteins that contain the PWWP domain are involved in transcriptional regulation, DNA methylation, histone modification, and DNA repair by interacting with histone, double-stranded DNA, and negatively charged molecules such as heparin (Chen et al, 2018;Hung et al, 2015;Rona et al, 2016). The type of PWWP domain modulates its binding and protein-protein interaction (Hung et al, 2015).…”

“…4A). HDGF contains a conserved PWWP domain previously known as the HATH domain, which is required for binding with heparin, DNA, and protein (Chen et al, 2018;Hung et al, 2015;Rona et al, 2016). According to the first amino acid, the PWWP domain is classified into P-type (Pro-His-Trp-Pro) and A-type (Ala-His-Trp-Pro).…”

Unresolved Complexity in the Gene Regulatory Network Underlying EMT

“…Whether mutant DNMT3A has enhanced or diminished recruitment by the aforementioned pioneer factor HSF1 also remains to be seen. Studies that examine human cancers for the presence of these and other PWWP mutations would be worthwhile, as the PWWP binding motif is highly conserved in human hepatoma-derived growth factor (HDGF) which is overexpressed in a number of human cancers and is involved in PI3K signaling (159). We cannot rule out a causative-or at the very least a contributing-role for PWWP domain mutations in EMT development in cancer, thus deciphering the unknowns that still surround the PWWP domain is of great importance.…”

Reading More than Histones: The Prevalence of Nucleic Acid Binding among Reader Domains

“…Recently, a crystal structure of the Rattus norvegicus HDGF PWWP was solved in complex with 10bp of the SMYD1 promoter DNA sequence. Within this complex, the PWWP crystallized as a domain-swapped dimer, where residues 19–22 from one monomer and 77–80 of the second monomer interact with DNA [ 83 ]. The binding interface predicted from NMR-based studies includes these two regions, but extends to cover a wider portion of the surface basic patch.…”