8u0v

S. cerevisiae Pex1/Pex6 with 1 mM ATPS. cerevisiae Pex1/Pex6 with 1 mM ATP

Structural highlights

8u0v is a 6 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.89Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PEX1_YEAST Component of the PEX1-PEX6 AAA ATPase complex, a protein dislocase complex that mediates the ATP-dependent extraction of the PEX5 receptor from peroxisomal membranes, an essential step for PEX5 recycling (PubMed:15634331, PubMed:16007078, PubMed:16911527, PubMed:26170309, PubMed:26066397, PubMed:29321502). Specifically recognizes PEX5 monoubiquitinated at 'Cys-6', and pulls it out of the peroxisome lumen through the PEX2-PEX10-PEX12 retrotranslocation channel (PubMed:26170309, PubMed:26066397, PubMed:29321502). Extraction by the PEX1-PEX6 AAA ATPase complex is accompanied by unfolding of the TPR repeats and release of bound cargo from PEX5 (PubMed:29321502).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

The heterohexameric AAA-ATPase Pex1/Pex6 is essential for the formation and maintenance of peroxisomes. Pex1/Pex6, similar to other AAA-ATPases, uses the energy from ATP hydrolysis to mechanically thread substrate proteins through its central pore, thereby unfolding them. In related AAA-ATPase motors, substrates are recruited through binding to the motor's N-terminal domains or N-terminally bound co-factors. Here we use structural and biochemical techniques to characterize the function of the N1 domain in Pex6 from budding yeast, S. cerevisiae. We found that although Pex1/DeltaN1-Pex6 is an active ATPase in vitro, it does not support Pex1/Pex6 function at the peroxisome in vivo. An X-ray crystal structure of the isolated Pex6 N1 domain shows that the Pex6 N1 domain shares the same fold as the N terminal domains of PEX1, CDC48, and NSF, despite poor sequence conservation. Integrating this structure with a cryo-EM reconstruction of Pex1/Pex6, AlphaFold2 predictions, and biochemical assays shows that Pex6 N1 mediates binding to both the peroxisomal membrane tether Pex15 and an extended loop from the D2 ATPase domain of Pex1 that influences Pex1/Pex6 heterohexamer stability. Given the direct interactions with both Pex15 and the D2 ATPase domains, the Pex6 N1 domain is poised to coordinate binding of co-factors and substrates with Pex1/Pex6 ATPase activity.

The N1 domain of the peroxisomal AAA-ATPase Pex6 is required for Pex15 binding and proper assembly with Pex1.,Ali BA, Judy RM, Chowdhury S, Jacobsen NK, Castanzo DT, Carr KL, Richardson CD, Lander GC, Martin A, Gardner BM J Biol Chem. 2023 Nov 28:105504. doi: 10.1016/j.jbc.2023.105504. PMID:38036174^[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Birschmann I, Rosenkranz K, Erdmann R, Kunau WH. Structural and functional analysis of the interaction of the AAA-peroxins Pex1p and Pex6p. FEBS J. 2005 Jan;272(1):47-58. PMID:15634331 doi:10.1111/j.1432-1033.2004.04393.x
↑ Platta HW, Grunau S, Rosenkranz K, Girzalsky W, Erdmann R. Functional role of the AAA peroxins in dislocation of the cycling PTS1 receptor back to the cytosol. Nat Cell Biol. 2005 Aug;7(8):817-22. PMID:16007078 doi:10.1038/ncb1281
↑ Rosenkranz K, Birschmann I, Grunau S, Girzalsky W, Kunau WH, Erdmann R. Functional association of the AAA complex and the peroxisomal importomer. FEBS J. 2006 Aug;273(16):3804-15. PMID:16911527 doi:10.1111/j.1742-4658.2006.05388.x
↑ Ciniawsky S, Grimm I, Saffian D, Girzalsky W, Erdmann R, Wendler P. Molecular snapshots of the Pex1/6 AAA+ complex in action. Nat Commun. 2015 Jun 12;6:7331. PMID:26066397 doi:10.1038/ncomms8331
↑ Blok NB, Tan D, Wang RY, Penczek PA, Baker D, DiMaio F, Rapoport TA, Walz T. Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy. Proc Natl Acad Sci U S A. 2015 Jul 28;112(30):E4017-25. PMID:26170309 doi:10.1073/pnas.1500257112
↑ Gardner BM, Castanzo DT, Chowdhury S, Stjepanovic G, Stefely MS, Hurley JH, Lander GC, Martin A. The peroxisomal AAA-ATPase Pex1/Pex6 unfolds substrates by processive threading. Nat Commun. 2018 Jan 10;9(1):135. doi: 10.1038/s41467-017-02474-4. PMID:29321502 doi:http://dx.doi.org/10.1038/s41467-017-02474-4
↑ Ali BA, Judy RM, Chowdhury S, Jacobsen NK, Castanzo DT, Carr KL, Richardson CD, Lander GC, Martin A, Gardner BM. The N1 domain of the peroxisomal AAA-ATPase Pex6 is required for Pex15 binding and proper assembly with Pex1. J Biol Chem. 2023 Nov 28:105504. PMID:38036174 doi:10.1016/j.jbc.2023.105504

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OCA

[1] Birschmann I, Rosenkranz K, Erdmann R, Kunau WH. Structural and functional analysis of the interaction of the AAA-peroxins Pex1p and Pex6p. FEBS J. 2005 Jan;272(1):47-58. PMID:15634331 doi:10.1111/j.1432-1033.2004.04393.x

[2] Platta HW, Grunau S, Rosenkranz K, Girzalsky W, Erdmann R. Functional role of the AAA peroxins in dislocation of the cycling PTS1 receptor back to the cytosol. Nat Cell Biol. 2005 Aug;7(8):817-22. PMID:16007078 doi:10.1038/ncb1281

[3] Rosenkranz K, Birschmann I, Grunau S, Girzalsky W, Kunau WH, Erdmann R. Functional association of the AAA complex and the peroxisomal importomer. FEBS J. 2006 Aug;273(16):3804-15. PMID:16911527 doi:10.1111/j.1742-4658.2006.05388.x

[4] Ciniawsky S, Grimm I, Saffian D, Girzalsky W, Erdmann R, Wendler P. Molecular snapshots of the Pex1/6 AAA+ complex in action. Nat Commun. 2015 Jun 12;6:7331. PMID:26066397 doi:10.1038/ncomms8331

[5] Blok NB, Tan D, Wang RY, Penczek PA, Baker D, DiMaio F, Rapoport TA, Walz T. Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy. Proc Natl Acad Sci U S A. 2015 Jul 28;112(30):E4017-25. PMID:26170309 doi:10.1073/pnas.1500257112

[6] Gardner BM, Castanzo DT, Chowdhury S, Stjepanovic G, Stefely MS, Hurley JH, Lander GC, Martin A. The peroxisomal AAA-ATPase Pex1/Pex6 unfolds substrates by processive threading. Nat Commun. 2018 Jan 10;9(1):135. doi: 10.1038/s41467-017-02474-4. PMID:29321502 doi:http://dx.doi.org/10.1038/s41467-017-02474-4

[7] Ali BA, Judy RM, Chowdhury S, Jacobsen NK, Castanzo DT, Carr KL, Richardson CD, Lander GC, Martin A, Gardner BM. The N1 domain of the peroxisomal AAA-ATPase Pex6 is required for Pex15 binding and proper assembly with Pex1. J Biol Chem. 2023 Nov 28:105504. PMID:38036174 doi:10.1016/j.jbc.2023.105504

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