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A three-level regulatory mechanism of the aldo-keto reductase subfamily AKR12D

Author

Listed:
  • Zhihong Xiao

    (Shanghai Jiao Tong University)

  • Jinyin Zha

    (Shanghai Jiao Tong University School of Medicine)

  • Xu Yang

    (Shanghai Jiao Tong University)

  • Tingting Huang

    (Shanghai Jiao Tong University)

  • Shuxin Huang

    (Shanghai Jiao Tong University)

  • Qi Liu

    (Shanghai Jiao Tong University)

  • Xiaozheng Wang

    (Shanghai Jiao Tong University)

  • Jie Zhong

    (Shanghai Jiao Tong University School of Medicine)

  • Jianting Zheng

    (Shanghai Jiao Tong University)

  • Rubing Liang

    (Shanghai Jiao Tong University)

  • Zixin Deng

    (Shanghai Jiao Tong University)

  • Jian Zhang

    (Shanghai Jiao Tong University School of Medicine)

  • Shuangjun Lin

    (Shanghai Jiao Tong University
    Haihe Laboratory of Synthetic Biology
    Shanghai Jiao Tong University)

  • Shaobo Dai

    (Shanghai Jiao Tong University)

Abstract

Modulation of protein function through allosteric regulation is central in biology, but biomacromolecular systems involving multiple subunits and ligands may exhibit complex regulatory mechanisms at different levels, which remain poorly understood. Here, we discover an aldo-keto reductase termed AKRtyl and present its three-level regulatory mechanism. Specifically, by combining steady-state and transient kinetics, X-ray crystallography and molecular dynamics simulation, we demonstrate that AKRtyl exhibits a positive synergy mediated by an unusual Monod-Wyman-Changeux (MWC) paradigm of allosteric regulation at low concentrations of the cofactor NADPH, but an inhibitory effect at high concentrations is observed. While the substrate tylosin binds at a remote allosteric site with positive cooperativity. We further reveal that these regulatory mechanisms are conserved in AKR12D subfamily, and that substrate cooperativity is common in AKRs across three kingdoms of life. This work provides an intriguing example for understanding complex allosteric regulatory networks.

Suggested Citation

  • Zhihong Xiao & Jinyin Zha & Xu Yang & Tingting Huang & Shuxin Huang & Qi Liu & Xiaozheng Wang & Jie Zhong & Jianting Zheng & Rubing Liang & Zixin Deng & Jian Zhang & Shuangjun Lin & Shaobo Dai, 2024. "A three-level regulatory mechanism of the aldo-keto reductase subfamily AKR12D," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46363-z
    DOI: 10.1038/s41467-024-46363-z
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    1. Christopher J. Draper-Joyce & Rebecca Bhola & Jinan Wang & Apurba Bhattarai & Anh T. N. Nguyen & India Cowie-Kent & Kelly O’Sullivan & Ling Yeong Chia & Hariprasad Venugopal & Celine Valant & David M., 2021. "Positive allosteric mechanisms of adenosine A1 receptor-mediated analgesia," Nature, Nature, vol. 597(7877), pages 571-576, September.
    2. Allan Chris M. Ferreon & Josephine C. Ferreon & Peter E. Wright & Ashok A. Deniz, 2013. "Modulation of allostery by protein intrinsic disorder," Nature, Nature, vol. 498(7454), pages 390-394, June.
    3. Robert A. Langan & Scott E. Boyken & Andrew H. Ng & Jennifer A. Samson & Galen Dods & Alexandra M. Westbrook & Taylor H. Nguyen & Marc J. Lajoie & Zibo Chen & Stephanie Berger & Vikram Khipple Mulliga, 2019. "De novo design of bioactive protein switches," Nature, Nature, vol. 572(7768), pages 205-210, August.
    4. Hesam N. Motlagh & James O. Wrabl & Jing Li & Vincent J. Hilser, 2014. "The ensemble nature of allostery," Nature, Nature, vol. 508(7496), pages 331-339, April.
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