Crystal structure and mutational analysis of the human TRIM7 B30.2 domain provide insights into the molecular basis of its binding to glycogenin-1

María E. Carrizo,Christian J. Muñoz Sosa,Federico M. Issoglio

doi:10.1016/j.jbc.2021.100772

Abstract

Tripartite motif (TRIM)7 is an E3 ubiquitin ligase that was first identified through its interaction with glycogenin-1 (GN1), the autoglucosyltransferase that initiates glycogen biosynthesis. A growing body of evidence indicates that TRIM7 plays an important role in cancer development, viral pathogenesis, and atherosclerosis and, thus, represents a potential therapeutic target. TRIM family proteins share a multidomain architecture with a conserved N-terminal TRIM and a variable C-terminal domain. Human TRIM7 contains the canonical TRIM motif and a B30.2 domain at the C terminus. To contribute to the understanding of the mechanism of action of TRIM7, we solved the X-ray crystal structure of its B30.2 domain (TRIM7B30.2) in two crystal forms at resolutions of 1.6 Å and 1.8 Å. TRIM7B30.2 exhibits the typical B30.2 domain fold, consisting of two antiparallel β-sheets of seven and six strands, arranged as a distorted β-sandwich. Furthermore, two long loops partially cover the concave face of the β-sandwich defined by the β-sheet of six strands, thus forming a positively charged cavity. We used sequence conservation and mutational analyses to provide evidence of a putative binding interface for GN1. These studies showed that Leu423, Ser499, and Cys501 of TRIM7B30.2 and the C-terminal 33 amino acids of GN1 are critical for this binding interaction. Molecular dynamics simulations also revealed that hydrogen bond and hydrophobic interactions play a major role in the stability of a modeled TRIM7B30.2-GN1 C-terminal peptide complex. These data provide useful information that could be used to target this interaction for the development of potential therapeutic agents.

Highlights

Tripartite motif (TRIM) proteins constitute a family of over 80 members encoded in the human genome [1] that participate in diverse cellular processes including proliferation, differentiation, apoptosis, autophagy, oncogenesis, innate immunity, and viral replication
The structure of the human TRIM7 B30.2 domain has been solved in two different crystal forms (Table 1) using the molecular replacement method with the structure of the Butyrophilin 3A1 (BTN3A1) B30.2 domain (Protein Data Bank [PDB] ID 4N7I [24]) as a search model
TRIM7 was initially identified through its interaction with GN1, the protein that initiates glycogen biosynthesis, its name Glycogen Interacting Protein (GNIP)

Summary

Introduction

Tripartite motif (TRIM) proteins constitute a family of over 80 members encoded in the human genome [1] that participate in diverse cellular processes including proliferation, differentiation, apoptosis, autophagy, oncogenesis, innate immunity, and viral replication (reviewed in [1,2,3]). A structural similarity search using the Dali server [25] revealed that the closest homolog to TRIM7B30.2 was BTN3A1B30.2 (PDB ID 4N7I, Z-score = 28.9, RMSD = 1.1 Å over 187 residues [24]), which curiously does not belong to the TRIM protein family (Fig. 2A).

Results

Conclusion