EMD-26475
Structure of a metalloprotease in complex with its substrate.
EMD-26475
Single-particle3.28 Å
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Map released: 28/09/2022
Last modified: 23/10/2024
Sample Organism:
Homo sapiens
Sample: Complex of PAPP-A with IGFBP5
Fitted models: 7ufg (Avg. Q-score: 0.443)
Deposition Authors: Judge RA
,
Jain R,
Hao Q
,
Ouch C
,
Sridar J,
Smith CL,
Wang JCK
,
Eaton D
Sample: Complex of PAPP-A with IGFBP5
Fitted models: 7ufg (Avg. Q-score: 0.443)
Deposition Authors: Judge RA
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Structure of the PAPP-ABP5 complex reveals mechanism of substrate recognition
Judge RA
,
Sridar J,
Tunyasunvunakool K
,
Jain R,
Wang JCK
,
Ouch C
,
Xu J,
Mafi A,
Nile AH,
Remarcik C,
Smith CL,
Ghosh C,
Xu C,
Stoll V,
Jumper J
,
Singh AH,
Eaton D
,
Hao Q
(2022) Nat Commun , 13 , 5500
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(2022) Nat Commun , 13 , 5500
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-ABP5) 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.
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-ABP5) 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.