8D8O

Cryo-EM structure of substrate unbound PAPP-A

Summary for 8D8O

• Entry DOI: 10.2210/pdb8d8o/pdb
• EMDB information: 26475 27253
• Descriptor: Pappalysin-1, ZINC ION (2 entities in total)
• Functional Keywords: metalloprotease, metal-binding, hydrolase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 352748.82

Authors

Judge, R.A.,Jain, R.,Hao, Q.,Ouch, C.,Sridar, J.,Smith, C.L.,Wang, J.C.K.,Eaton, D. (deposition date: 2022-06-08, release date: 2022-09-28)

Primary citation

Judge, R.A.,Sridar, J.,Tunyasunvunakool, K.,Jain, R.,Wang, J.C.K.,Ouch, C.,Xu, J.,Mafi, A.,Nile, A.H.,Remarcik, C.,Smith, C.L.,Ghosh, C.,Xu, C.,Stoll, V.,Jumper, J.,Singh, A.H.,Eaton, D.,Hao, Q.
Structure of the PAPP-ABP5 complex reveals mechanism of substrate recognition
Nat Commun, 13:5500-, 2022

PubMed Abstract: Insulin-like growth factor (IGF) signaling is highly conserved and tightly regulated by proteases including Pregnancy-Associated Plasma Protein A (PAPP-A). PAPP-A and its paralog PAPP-A2 are metalloproteases that mediate IGF bioavailability through cleavage of IGF binding proteins (IGFBPs). Here, we present single-particle cryo-EM structures of the catalytically inactive mutant PAPP-A (E483A) in complex with a peptide from its substrate IGFBP5 (PAPP-A) and also in its substrate-free form, by leveraging the power of AlphaFold to generate a high quality predicted model as a starting template. We show that PAPP-A is a flexible trans-dimer that binds IGFBP5 via a 25-amino acid anchor peptide which extends into the metalloprotease active site. This unique IGFBP5 anchor peptide that mediates the specific PAPP-A-IGFBP5 interaction is not found in other PAPP-A substrates. Additionally, we illustrate the critical role of the PAPP-A central domain as it mediates both IGFBP5 recognition and trans-dimerization. We further demonstrate that PAPP-A trans-dimer formation and distal inter-domain interactions are both required for efficient proteolysis of IGFBP4, but dispensable for IGFBP5 cleavage. Together the structural and biochemical studies reveal the mechanism of PAPP-A substrate binding and selectivity.

PubMed: 36127359
DOI: 10.1038/s41467-022-33175-2

Experimental method

ELECTRON MICROSCOPY (3.35 Å)