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Crystallizing Membrane Proteins for Structure Determination using Lipidic Mesophases
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Unique RING finger structure from the human HRD1 protein.

Kazuhide Miyamoto1, Yukari Taguchi1, Kazuki Saito1

  • 1Department of Pharmaceutical Health Care, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Hyogo, Japan.

Protein Science : a Publication of the Protein Society
|October 23, 2018
PubMed
Summary

We elucidated the atypical structure of the HRD1-RING domain, revealing its unique zinc binding and E2 enzyme interaction. This finding advances understanding of endoplasmic reticulum protein degradation pathways.

Keywords:
E3 enzymeHRD1NMR structureRING fingerartificial RING fingerubiquitination

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Background:

  • Human hydroxymethylglutaryl-coenzyme A reductase degradation protein 1 (HRD1) targets endoplasmic reticulum (ER) proteins for degradation.
  • The HRD1 RING finger domain (HRD1_RING) acts as a crucial ubiquitin ligase (E3) enzyme in this process.

Purpose of the Study:

  • To determine the solution structure of the HRD1_RING domain.
  • To investigate the zinc ion stoichiometry and binding characteristics of HRD1_RING.
  • To clarify the structural basis for HRD1's interaction with ubiquitin-conjugating enzyme (E2).

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy for solution structure determination.
  • Spectrophotometry using a metallochromic indicator to determine zinc ion stoichiometry.
  • Bioinformatic analysis using the Simple Modular Architecture Research Tool (SMART) database.

Main Results:

  • The solution structure of HRD1_RING was determined.
  • HRD1_RING was found to bind two zinc atoms.
  • Contrary to predictions, HRD1_RING adopts an atypical RING-H2 fold, not a typical RING finger structure.
  • The study precisely mapped the active site of HRD1_RING.

Conclusions:

  • The atypical RING-H2 structure of HRD1_RING is critical for its function.
  • Structural insights explain HRD1's specific E2-binding capability.
  • This work provides a foundation for understanding ER protein degradation mechanisms.