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

Li-Ying Chen,Phimonphan Chuankhayan,Shih-Tsung Huang,Yin-Cheng Hsieh,Masato Yoshimura,Ming-Hong Tai,Yen-Chieh Huang,Chun-Jung Chen,Hong-Hsiang Guan,Nai-Chi Chen

doi:10.1038/s41598-017-18510-8

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.

Highlights

Human hepatoma-derived growth factor (HDGF) is highly expressed in the developing heart, tumour cell lines and normal tissue ubiquitously with mitogenic and angiogenic activities[1,2,3]
The protein concentration can affect the formation of multiple forms of the apo PWWP domain, and the dimeric apo PWWP domain can be readily obtained by increasing the protein concentration during purification (Fig. S1C, S1D)
The apo PWWP domain has been demonstrated to potentially form a dimer to bind to heparin on the cell surface with a binding affinity greater than that of the monomer; its transformation between dimers and monomers depends on the freshness of the sample preparation[27]

Summary

Introduction

Human hepatoma-derived growth factor (HDGF) is highly expressed in the developing heart, tumour cell lines and normal tissue ubiquitously with mitogenic and angiogenic activities[1,2,3]. HDGF generally comprises two portions, an N-terminal domain with a highly conserved PWWP motif (residues 1–100 for human HDGF) and a variable C-terminal domain (residues 101–240)[13]. These two domains play distinct roles in physiology. The mammalian DNA methyltransferase, DNMT3B, which contains the PWWP domain, is linked to human immunodeficiency, centromere instability and facial anomalies syndrome and to distinct cancers[19,20,21] Another PWWP-containing protein, Lens epithelium-derived growth factor (LEDGF/p75), plays an essential role in the integration of HIV-1 cDNA into human chromosomes[22,23,24,25]. With physiological assays, provide new insights into the PWWP-DNA interaction pattern, which might facilitate research into the role of the PWWP domain in nucleosomal functions

Methods

Results

Conclusion