Structures and mechanism of the human mitochondrial pyruvate carrier

Jiaming Liang, Junhui Shi, Ailong Song, Meihua Lu, Kairan Zhang, Meng Xu, Gaoxingyu Huang, Peilong Lu, Xudong Wu () and Dan Ma ()
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Jiaming Liang: Fudan University
Junhui Shi: Fudan University
Ailong Song: Fudan University
Meihua Lu: Westlake University
Kairan Zhang: Westlake University
Meng Xu: Fudan University
Gaoxingyu Huang: Westlake University
Peilong Lu: Westlake University
Xudong Wu: Westlake University
Dan Ma: Westlake University

Nature, 2025, vol. 641, issue 8061, 258-265

Abstract: Abstract The mitochondrial pyruvate carrier (MPC) is a mitochondrial inner membrane protein complex that is essential for the uptake of pyruvate into the mitochondrial matrix as the primary carbon source for the tricarboxylic acid cycle1,2. Here we present six cryo-electron microscopy structures of human MPC in three states: three structures in the intermembrane space (IMS)-open state, obtained in different conditions; a structure of pyruvate-treated MPC in the occluded state; and two structures in the matrix-facing state, bound with the inhibitor UK5099 or with an inhibitory nanobody on the matrix side. MPC is a heterodimer consisting of MPC1 and MPC2, with the transmembrane domain adopting pseudo-C2 symmetry. Approximate rigid-body movements occur between the IMS-open state and the occluded state, whereas structural changes, mainly on the matrix side, facilitate the transition between the occluded state and the matrix-facing state, revealing an alternating access mechanism during pyruvate transport. In the UK5099-bound structure, the inhibitor fits well and interacts extensively with a pocket that opens to the matrix side. Our findings provide key insights into the mechanisms that underlie MPC-mediated substrate transport, and shed light on the recognition and inhibition of MPC by UK5099, which will facilitate the future development of drugs that target MPC.

Date: 2025
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DOI: 10.1038/s41586-025-08873-8

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