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Crystal structures of VAP1 reveal ADAMs' MDC domain architecture and its unique C‐shaped scaffold
Open accessAbstract
ADAMs (a disintegrin and metalloproteinase) are sheddases possessing extracellular metalloproteinase/disintegrin/cysteine-rich (MDC) domains. ADAMs uniquely display both proteolytic and adhesive activities on the cell surface, however, most of their physiological targets and adhesion mechanisms remain unclear. Here for the first time, we reveal the ADAMs' MDC architecture and a potential target-binding site by solving crystal structures of VAP1, a snake venom homolog of mammalian ADAMs. The D-domain protrudes from the M-domain opposing the catalytic site and constituting a C-shaped arm with cores of Ca2+ ions. The disintegrin-loop, supposed to interact with integrins, is packed by the C-domain and inaccessible for protein binding. Instead, the hyper-variable region (HVR) in the C-domain, which has a novel fold stabilized by the strictly conserved disulfide bridges, constitutes a potential protein-protein adhesive interface. The HVR is located at the distal end of the arm and faces toward the catalytic site. The C-shaped structure implies interplay between the ADAMs' proteolytic and adhesive domains and suggests a molecular mechanism for ADAMs' target recognition for shedding.
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“Based on the model, known mutations that cause disease (magenta spheres in Fig. 3A) could act by hindering catalysis (R26K, R32Q, and L50P, near active site) or produce steric clashes (G154R) (19) in the hydrophobic core.”
From Accurate prediction of protein structures and interactions using a 3-track network (2021) · cites this paper as [19]
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“Modified from [15].”
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“The crystal structure of bothropasin complexed with the inhibitor POL647 showed the major features already described for VAP-I (Igarashi et al., 2007; Takeda et al., 2006): The catalytic domain is consisted of two sub-domains including the zinc and calcium-binding sites.”
BackgroundStatus update on iRhom and ADAM17: It's still complicated
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“4A and B, atragin maintains a C-shaped architecture as its structure adopts a similar D-shoulder (Ds) domain (a.a. 410–442) with three disulfide bonds (pairs of 3, 4, and 5) and a D-arm (Da) domain (a.a. 443–493) with another three disulfide bonds (pairs of 7, 8, and 9) constituting the C-shaped arm as in VAP1 and VAP…”
BackgroundInfluentialProcessing of Snake Venom Metalloproteinases: Generation of Toxin Diversity and Enzyme Inactivation
Moura-da-Silva, A. M., de Almeida, M. T., Portes-Junior, J. A., Nicolau, C. A., Gomes‐Neto, F., & Valente, R. H. (2016) · Toxins · doi:10.3390/toxins8060183 · Cited by 62
“Class P-III SVMPs VAP1 and VAP2 from Crotalus atrox have been crystallized in their dimeric form [74,75] exerting potent pro-apoptotic activity in endothelial cell cultures [76].”
BackgroundTanjoni, I., Evangelista, K. S., Della-Casa, M. S., Butera, D., Magalhães, G. S., Baldo, C., Clissa, P. B., Fernandes, I., Eble, J. A., & Moura-da-Silva, A. M. (2010) · Toxicon · doi:10.1016/j.toxicon.2009.12.010 · Cited by 57
The role of proteases in regulating Eph/ephrin signaling
Atapattu, L., Lackmann, M., & Janes, P. W. (2014) · Cell Adhesion & Migration · doi:10.4161/19336918.2014.970026 · Cited by 55
“For example the VAP1 structure shares a curved DCC domain structure with ADAM10, which confers an overall C-shape structure with the MP domain in proximity to the substrate binding region of the C domain, consistent with the idea binding to the C domain controls specificity by positioning the substrate for cleavage.(3…”
BackgroundJoo, C.-K., Kim, H. S., Park, J.-Y., Seomun, Y., Son, M.-J., & Kim, J.-T. (2007) · Oncogene · doi:10.1038/sj.onc.1210649 · Cited by 55
Ectodomain shedding and remnant peptide signalling of EGFRs and their ligands
Higashiyama, S., Nanba, D., Nakayama, H., Inoue, H., & Fukuda, S. (2011) · The Journal of Biochemistry · doi:10.1093/jb/mvr068 · Cited by 52
Chen, H.-S., Tsai, H.-Y., Wang, Y., & Tsai, I. (2008) · Biochimie · doi:10.1016/j.biochi.2008.05.012 · Cited by 51
Targeting ADAM17 Sheddase Activity in Cancer
Rossello, A., Nuti, E., Ferrini, S., & Fabbi, M. (2016) · Current Drug Targets · doi:10.2174/1389450117666160727143618 · Cited by 51
Kawasaki, K., Freimuth, J., Meyer, D. S., Lee, M. M., Tochimoto-Okamoto, A., Benzinou, M., Clermont, F. F., Wu, G., Roy, R., Letteboer, T. G. W., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1318761111 · Cited by 47
“Ileu613Val variant is located within the cysteine-rich substrate recognition domain (43); thus, variation in Adam17 p.”
BackgroundADAM Proteins- Therapeutic Potential in Cancer
Lu, X., Lu, D., Scully, M. F., & Kakkar, V. V. (2008) · Current Cancer Drug Targets · doi:10.2174/156800908786733478 · Cited by 46
Programmed autologous cleavage of platelet receptors
Berndt, M. C., Karunakaran, D., Gardiner, E. E., & Andrews, R. K. (2007) · Journal of Thrombosis and Haemostasis · doi:10.1111/j.1538-7836.2007.02484.x · Cited by 46
Menezes, M. C., Leme, A. F. P., Melo, R. L. D., Alberto-Silva, C., Della-Casa, M. S., Bruni, F. M., Lima, C., Lopes‐Ferreira, M., de Camargo, A. C. M., Fox, J. W., et al. (2008) · FEBS Letters · doi:10.1016/j.febslet.2008.10.034 · Cited by 45
“In VAP1 and catrocollastatin/VAP2B, the HVR is located at the distal end of the arm constituted by disintegrin-like domain and faces toward the catalytic site [14,15].”
BackgroundInfluentialHiguchi, D. A., Almeida, M. C., Barros, C. C., Sánchez, E. F., Pesquero, P. R., Lang, E. A. S., Samaan, M., Araújo, R. C., Pesquero, J. B., & Pesquero, J. L. (2011) · Toxicon · doi:10.1016/j.toxicon.2011.05.013 · Cited by 43
Connective tissue growth factor is a substrate of ADAM28
Mochizuki, S., Tanaka, R., Shimoda, M., Onuma, J., Fujii, Y., Jinno, H., & Okada, Y. (2010) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2010.10.077 · Cited by 43
“5 and 1 mg/ml) of (465)CRPAKDECDLPEMC(478) corresponding to the disintegrin loop of the Dis domain [20], (567)QGGSDNLPWKGRIVT(581) and (582)FLTAKTFDPEDTSQEI(597) corresponding to the hyper-variable region of the CR domain [21] or an RGDS peptide (a negative control) prior to the binding assay.”
BackgroundMethodPinto, A. F. M., Terra, R. M. S., Guimarães, J. A., & Fox, J. W. (2006) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2006.10.010 · Cited by 41
Limam, I., Bazaa, A., Srairi‐Abid, N., Taboubi, S., Jebali, J., Zouari-Kessentini, R., Kallech-Ziri, O., Mejdoub, H., Hammami, A., Ayeb, M. E., et al. (2009) · Matrix Biology · doi:10.1016/j.matbio.2009.09.009 · Cited by 41
Wakatsuki, S., Yumoto, N., Komatsu, K., Araki, T., & Sehara‐Fujisawa, A. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m803191200 · Cited by 41
Shimoda, M., Hashimoto, G., Mochizuki, S., Ikeda, E., Nagai, N., Ishida, S., & Okada, Y. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m702414200 · Cited by 42
The EGFR-ADAM17 Axis in Chronic Obstructive Pulmonary Disease and Cystic Fibrosis Lung Pathology
Stolarczyk, M., & Scholte, B. J. (2018) · Mediators of Inflammation · doi:10.1155/2018/1067134 · Cited by 39
Chen, H., Chen, J., Lin, C., Khoo, K., & Tsai, I. (2008) · FEBS Journal · doi:10.1111/j.1742-4658.2008.06540.x · Cited by 39
Snake Venom Metalloproteinases
Fox, J. W., & Gutiérrez, J. M. (2017) · MDPI eBooks · doi:10.3390/books978-3-03842-427-7 · Cited by 40
Gordon, K., Balyasnikova, I. V., Nesterovitch, A. B., Schwartz, D. E., Sturrock, E. D., & Danilov, S. M. (2009) · Tissue Antigens · doi:10.1111/j.1399-0039.2009.01416.x · Cited by 36
Domain integration of ADAM family proteins: Emerging themes from structural studies
Seegar, T. C. M., & Blacklow, S. C. (2019) · Experimental Biology and Medicine · doi:10.1177/1535370219865901 · Cited by 35
“The ADAM cysteine-rich domain also contains a segment dubbed the “hypervariable region” (HVR), named for the significant divergence in length and amino acid composition among the different ADAMs in this region.(47) Within the ADAM family, the HVR ranges in length from 37 residues in ADAM17 to 87 residues in ADAM19.”
BackgroundCell surface annexins regulate ADAM-mediated ectodomain shedding of proamphiregulin
Nakayama, H., Fukuda, S., Inoue, H., Nishida‐Fukuda, H., Shirakata, Y., Hashimoto, K., & Higashiyama, S. (2012) · Molecular Biology of the Cell · doi:10.1091/mbc.e11-08-0683 · Cited by 32
“Previous reports have shown that the hypervariable region (HVR) of ADAMs may have a significant effect on substrate recognition and may adjust the spatial alignment of the catalytic and adhesion sites (Takeda et al., 2006; Igarashi et al., 2007).”
BackgroundMarques-Porto, R., Lebrun, I., & Pimenta, D. C. (2008) · Comparative Biochemistry and Physiology Part C Toxicology & Pharmacology · doi:10.1016/j.cbpc.2008.01.011 · Cited by 30
Menezes, M. C., Oliveira, A. K., Melo, R. L. D., Lopes‐Ferreira, M., Rioli, V., Balan, A., Leme, A. F. P., & Serrano, S. M. T. (2010) · Biochimie · doi:10.1016/j.biochi.2010.10.007 · Cited by 29
Modulation of integrin α4β1 by ADAM28 promotes lymphocyte adhesion and transendothelial migration
McGinn, O. J., English, W., Roberts, S., Ager, A., Newham, P., & Murphy, G. (2011) · Cell Biology International · doi:10.1042/cbi20100885 · Cited by 28
“for binding to integrins since the disintegrin loop is buried within a MDC (metalloproteinase, disintegrin and cysteine-rich) fold (Takeda et al., 2006).”
BackgroundSajevic, T., Leonardi, A., Kovačič, L., Balija, M. L., Kurtović, T., Pungerčar, J., Halassy, B., Trampuš-Bakija, A., & Križaj, I. (2013) · Biochimie · doi:10.1016/j.biochi.2013.01.003 · Cited by 28
“Non-catalytic Dis and CR domains contain several substrate-binding sites located in the so-called disintegrin loop and in the hyper-variable region [5,6].”
BackgroundInfluentialThe proteinase-rich proteome of Bothrops jararaca venom
Serrano, S. M. T., Oliveira, A. K., Menezes, M. C., & Zelanis, A. (2014) · Toxin Reviews · doi:10.3109/15569543.2014.922581 · Cited by 27
“Interestingly, the determination of crystal structures of P-III class SVMPs also showed that the folding of the metalloproteinase domain is similar between these enzymes and those of the P-I class (Igarashi et al., 2007; Muniz et al., 2008; Takeda et al., 2006, 2007).”
BackgroundInfluentialCamacho, E. T., Villalobos, E., Sanz, L., Pérez, A., Escalante, T., Lomonte, B., Calvete, J. J., Gutiérrez, J. M., & Rucavado, A. (2014) · Biochimie · doi:10.1016/j.biochi.2014.01.008 · Cited by 26
Teklemariam, T., Seoane, A. I., Ramos, C. J., Sanchez, E. E., Lucena, S. E., Pérez, J. C., Mandal, S. A., & Soto, J. G. (2011) · Toxicon · doi:10.1016/j.toxicon.2011.01.007 · Cited by 26
“Crystallography studies of two PIII-SVMPs (VAP1 and catrocollastatin/VAP2B) indicate that their disintegrin-like loop is not accessible for integrin binding (Takeda et al., 2006; Igarashi et al., 2007).”
Brief History and Molecular Determinants of Snake Venom Disintegrin Evolution
Calvete, J. J. (2010) · Springer eBooks · doi:10.1007/978-90-481-9295-3_18 · Cited by 25
Interaction of Bothrops jararaca venom metalloproteinases with protein inhibitors
Asega, A. F., Oliveira, A. K., Menezes, M. C., Neves‐Ferreira, A. G. C., & Serrano, S. M. T. (2014) · Toxicon · doi:10.1016/j.toxicon.2014.01.001 · Cited by 25
Sant′Ana, E. M. C., Gouvêa, C. M. C. P., Nakaie, C. R., & Selistre-de-Araújo, H. S. (2008) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2008.07.030 · Cited by 24
Metadata
- Authors
- Takeda, S., Igarashi, T., Mori, H., & Araki, S.
- Affiliations
- SPring-8 (JP)
- National Cerebral and Cardiovascular Center (JP)
- Nagoya University (JP)
- Corresponding author
- Takeda, Soichi
- ORCID
- Takeda, Soichi
- Venue
- The EMBO Journal
- Published
- 2006-05-11
- Volume
- 25
- Issue
- 11
- Pages
- 2388-2396
- ISSN
- 0261-4189 (ISSN-L)
- 1460-2075
- PMC
- PMC1478178
- OpenAlex
- W2000001290
- Cited by
- 202
- References
- 45
- Citations by year
- 2025: 10 · 2024: 4 · 2023: 4 · 2022: 4 · 2021: 9 · 2020: 4 · 2019: 5 · 2018: 2 · 2017: 11 · 2016: 12 · 2015: 7 · 2014: 14 · 2013: 9 · 2012: 17
- FWCI
- 8.36
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The EMBO Journal (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Takeda Science Foundation
- Senri Life Science Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Protease and Inhibitor Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Health Sciences › Medicine › Hematology › Blood Coagulation and Thrombosis Mechanisms
- Keywords
- ADAMS, snake venom proteins, disintegrins, metalloproteinases, hypervariable region, disulfide bonds, calcium ions, extracellular matrix, crystal structure
- MeSH terms
- Amino Acid Sequence, Animals, Crotalid Venoms, Humans, Metalloendopeptidases, Models, Molecular, Molecular Sequence Data, Sequence Alignment, Protein Structure, Tertiary, Crystallography, X-Ray, Apoptosis Regulatory Proteins, ADAM Proteins
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