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1. InterPro in 2017-beyond protein family and domain annotations.

Author

Finn, Robert D, Finn, Robert D, Attwood, Teresa K, Babbitt, Patricia C, Bateman, Alex, Bork, Peer, Bridge, Alan J, Chang, Hsin-Yu, Dosztányi, Zsuzsanna, El-Gebali, Sara, Fraser, Matthew, Gough, Julian, Haft, David, Holliday, Gemma L, Huang, Hongzhan, Huang, Xiaosong, Letunic, Ivica, Lopez, Rodrigo, Lu, Shennan, Marchler-Bauer, Aron, Mi, Huaiyu, Mistry, Jaina, Natale, Darren A, Necci, Marco, Nuka, Gift, Orengo, Christine A, Park, Youngmi, Pesseat, Sebastien, Piovesan, Damiano, Potter, Simon C, Rawlings, Neil D, Redaschi, Nicole, Richardson, Lorna, Rivoire, Catherine, Sangrador-Vegas, Amaia, Sigrist, Christian, Sillitoe, Ian, Smithers, Ben, Squizzato, Silvano, Sutton, Granger, Thanki, Narmada, Thomas, Paul D, Tosatto, Silvio CE, Wu, Cathy H, Xenarios, Ioannis, Yeh, Lai-Su, Young, Siew-Yit, Mitchell, Alex L, Finn, Robert D, Finn, Robert D, Attwood, Teresa K, Babbitt, Patricia C, Bateman, Alex, Bork, Peer, Bridge, Alan J, Chang, Hsin-Yu, Dosztányi, Zsuzsanna, El-Gebali, Sara, Fraser, Matthew, Gough, Julian, Haft, David, Holliday, Gemma L, Huang, Hongzhan, Huang, Xiaosong, Letunic, Ivica, Lopez, Rodrigo, Lu, Shennan, Marchler-Bauer, Aron, Mi, Huaiyu, Mistry, Jaina, Natale, Darren A, Necci, Marco, Nuka, Gift, Orengo, Christine A, Park, Youngmi, Pesseat, Sebastien, Piovesan, Damiano, Potter, Simon C, Rawlings, Neil D, Redaschi, Nicole, Richardson, Lorna, Rivoire, Catherine, Sangrador-Vegas, Amaia, Sigrist, Christian, Sillitoe, Ian, Smithers, Ben, Squizzato, Silvano, Sutton, Granger, Thanki, Narmada, Thomas, Paul D, Tosatto, Silvio CE, Wu, Cathy H, Xenarios, Ioannis, Yeh, Lai-Su, Young, Siew-Yit, and Mitchell, Alex L

Abstract

InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by InterPro, increase the overall number of residues annotated and allow more specific functional inferences.

Published
2017

2. InterPro in 2017-beyond protein family and domain annotations.

Author

Finn, Robert D, Finn, Robert D, Attwood, Teresa K, Babbitt, Patricia C, Bateman, Alex, Bork, Peer, Bridge, Alan J, Chang, Hsin-Yu, Dosztányi, Zsuzsanna, El-Gebali, Sara, Fraser, Matthew, Gough, Julian, Haft, David, Holliday, Gemma L, Huang, Hongzhan, Huang, Xiaosong, Letunic, Ivica, Lopez, Rodrigo, Lu, Shennan, Marchler-Bauer, Aron, Mi, Huaiyu, Mistry, Jaina, Natale, Darren A, Necci, Marco, Nuka, Gift, Orengo, Christine A, Park, Youngmi, Pesseat, Sebastien, Piovesan, Damiano, Potter, Simon C, Rawlings, Neil D, Redaschi, Nicole, Richardson, Lorna, Rivoire, Catherine, Sangrador-Vegas, Amaia, Sigrist, Christian, Sillitoe, Ian, Smithers, Ben, Squizzato, Silvano, Sutton, Granger, Thanki, Narmada, Thomas, Paul D, Tosatto, Silvio CE, Wu, Cathy H, Xenarios, Ioannis, Yeh, Lai-Su, Young, Siew-Yit, Mitchell, Alex L, Finn, Robert D, Finn, Robert D, Attwood, Teresa K, Babbitt, Patricia C, Bateman, Alex, Bork, Peer, Bridge, Alan J, Chang, Hsin-Yu, Dosztányi, Zsuzsanna, El-Gebali, Sara, Fraser, Matthew, Gough, Julian, Haft, David, Holliday, Gemma L, Huang, Hongzhan, Huang, Xiaosong, Letunic, Ivica, Lopez, Rodrigo, Lu, Shennan, Marchler-Bauer, Aron, Mi, Huaiyu, Mistry, Jaina, Natale, Darren A, Necci, Marco, Nuka, Gift, Orengo, Christine A, Park, Youngmi, Pesseat, Sebastien, Piovesan, Damiano, Potter, Simon C, Rawlings, Neil D, Redaschi, Nicole, Richardson, Lorna, Rivoire, Catherine, Sangrador-Vegas, Amaia, Sigrist, Christian, Sillitoe, Ian, Smithers, Ben, Squizzato, Silvano, Sutton, Granger, Thanki, Narmada, Thomas, Paul D, Tosatto, Silvio CE, Wu, Cathy H, Xenarios, Ioannis, Yeh, Lai-Su, Young, Siew-Yit, and Mitchell, Alex L

Abstract

InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by InterPro, increase the overall number of residues annotated and allow more specific functional inferences.

Published
2017

3. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.

Author

Babbitt, Patricia C, Babbitt, Patricia C, Bagos, Pantelis G, Bairoch, Amos, Bateman, Alex, Chatonnet, Arnaud, Chen, Mark Jinan, Craik, David J, Finn, Robert D, Gloriam, David, Haft, Daniel H, Henrissat, Bernard, Holliday, Gemma L, Isberg, Vignir, Kaas, Quentin, Landsman, David, Lenfant, Nicolas, Manning, Gerard, Nagano, Nozomi, Srinivasan, Narayanaswamy, O'Donovan, Claire, Pruitt, Kim D, Sowdhamini, Ramanathan, Rawlings, Neil D, Saier, Milton H, Sharman, Joanna L, Spedding, Michael, Tsirigos, Konstantinos D, Vastermark, Ake, Vriend, Gerrit, Babbitt, Patricia C, Babbitt, Patricia C, Bagos, Pantelis G, Bairoch, Amos, Bateman, Alex, Chatonnet, Arnaud, Chen, Mark Jinan, Craik, David J, Finn, Robert D, Gloriam, David, Haft, Daniel H, Henrissat, Bernard, Holliday, Gemma L, Isberg, Vignir, Kaas, Quentin, Landsman, David, Lenfant, Nicolas, Manning, Gerard, Nagano, Nozomi, Srinivasan, Narayanaswamy, O'Donovan, Claire, Pruitt, Kim D, Sowdhamini, Ramanathan, Rawlings, Neil D, Saier, Milton H, Sharman, Joanna L, Spedding, Michael, Tsirigos, Konstantinos D, Vastermark, Ake, and Vriend, Gerrit

Abstract

During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

Published
2015

4. Creating a specialist protein resource network : a meeting report for the protein bioinformatics and community resources retreat

Author

Babbitt, Patricia C., Bagos, Pantelis G., Bairoch, Amos, Bateman, Alex, Chatonnet, Arnaud, Chen, Mark Jinan, Craik, David J., Finn, Robert D., Gloriam, David, Haft, Daniel H., Henrissat, Bernard, Holliday, Gemma L., Isberg, Vignir, Kaas, Quentin, Landsman, David, Lenfant, Nicolas, Manning, Gerard, Nagano, Nozomi, Srinivasan, Narayanaswamy, O'Donovan, Claire, Pruitt, Kim D., Sowdhamini, Ramanathan, Rawlings, Neil D., Saier, Milton H., Sharman, Joanna L., Spedding, Michael, Tsirigos, Konstantinos D., Vastermark, Ake, Vriend, Gerrit, Babbitt, Patricia C., Bagos, Pantelis G., Bairoch, Amos, Bateman, Alex, Chatonnet, Arnaud, Chen, Mark Jinan, Craik, David J., Finn, Robert D., Gloriam, David, Haft, Daniel H., Henrissat, Bernard, Holliday, Gemma L., Isberg, Vignir, Kaas, Quentin, Landsman, David, Lenfant, Nicolas, Manning, Gerard, Nagano, Nozomi, Srinivasan, Narayanaswamy, O'Donovan, Claire, Pruitt, Kim D., Sowdhamini, Ramanathan, Rawlings, Neil D., Saier, Milton H., Sharman, Joanna L., Spedding, Michael, Tsirigos, Konstantinos D., Vastermark, Ake, and Vriend, Gerrit

Abstract

During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

Published
2015
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5. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

Author

Woo, Yong H, Ansari, Hifzur, Otto, Thomas D, Klinger, Christen M, Kolisko, Martin, Michalek, Jan, Saxena, Alka, Shanmugam, Dhanasekaran, Tayyrov, Annageldi, Veluchamy, Alaguraj, Ali, Shahjahan, Bernal, Axel, del, Campo Javier, Cihlář, Jaromír, Flegontov, Pavel, Gornik, Sebastian G, Hajdušková, Eva, Horák, Aleš, Janouškovec, Jan, Katris, Nicholas J, Mast, Fred D, Miranda-Saavedra, Diego, Mourier, Tobias, Naeem, Raeece, Nair, Mridul, Panigrahi, Aswini K, Rawlings, Neil D, Padron-Regalado, Eriko, Ramaprasad, Abhinay, Samad, Nadira, Tomčala, Aleš, Wilkes, Jon, Neafsey, Daniel E, Doerig, Christian, Bowler, Chris, Keeling, Patrick J, Roos, David S, Dacks, Joel B, Templeton, Thomas J, Waller, Ross F, Lukeš, Julius, Obornik, Miroslav, Pain, Arnab, Woo, Yong H, Ansari, Hifzur, Otto, Thomas D, Klinger, Christen M, Kolisko, Martin, Michalek, Jan, Saxena, Alka, Shanmugam, Dhanasekaran, Tayyrov, Annageldi, Veluchamy, Alaguraj, Ali, Shahjahan, Bernal, Axel, del, Campo Javier, Cihlář, Jaromír, Flegontov, Pavel, Gornik, Sebastian G, Hajdušková, Eva, Horák, Aleš, Janouškovec, Jan, Katris, Nicholas J, Mast, Fred D, Miranda-Saavedra, Diego, Mourier, Tobias, Naeem, Raeece, Nair, Mridul, Panigrahi, Aswini K, Rawlings, Neil D, Padron-Regalado, Eriko, Ramaprasad, Abhinay, Samad, Nadira, Tomčala, Aleš, Wilkes, Jon, Neafsey, Daniel E, Doerig, Christian, Bowler, Chris, Keeling, Patrick J, Roos, David S, Dacks, Joel B, Templeton, Thomas J, Waller, Ross F, Lukeš, Julius, Obornik, Miroslav, and Pain, Arnab

Abstract

The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites of humans and animals with immense socio-economic and health impacts. We sequenced nuclear genomes of Chromera velia and Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pathways and from the endomembrane trafficking systems associated with a free-living lifestyle have been progressively and non-randomly lost during adaptation to parasitism. The free-living ancestor contained a broad repertoire of genes many of which were repurposed for parasitic processes, such as extracellular proteins, components of a motility apparatus, and DNA- and RNA-binding protein families. Based on transcriptome analyses across 36 environmental conditions, Chromera orthologs of apicomplexan invasion-related motility genes were co-regulated with genes encoding the flagellar apparatus, supporting the functional contribution of flagella to the evolution of invasion machinery. This study provides insights into how obligate parasites with diverse life strategies arose from a once free-living phototrophic marine alga., eLife, 4, E06974; 2015

Published
2015

6. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.

Author

Babbitt, Patricia C, Babbitt, Patricia C, Bagos, Pantelis G, Bairoch, Amos, Bateman, Alex, Chatonnet, Arnaud, Chen, Mark Jinan, Craik, David J, Finn, Robert D, Gloriam, David, Haft, Daniel H, Henrissat, Bernard, Holliday, Gemma L, Isberg, Vignir, Kaas, Quentin, Landsman, David, Lenfant, Nicolas, Manning, Gerard, Nagano, Nozomi, Srinivasan, Narayanaswamy, O'Donovan, Claire, Pruitt, Kim D, Sowdhamini, Ramanathan, Rawlings, Neil D, Saier, Milton H, Sharman, Joanna L, Spedding, Michael, Tsirigos, Konstantinos D, Vastermark, Ake, Vriend, Gerrit, Babbitt, Patricia C, Babbitt, Patricia C, Bagos, Pantelis G, Bairoch, Amos, Bateman, Alex, Chatonnet, Arnaud, Chen, Mark Jinan, Craik, David J, Finn, Robert D, Gloriam, David, Haft, Daniel H, Henrissat, Bernard, Holliday, Gemma L, Isberg, Vignir, Kaas, Quentin, Landsman, David, Lenfant, Nicolas, Manning, Gerard, Nagano, Nozomi, Srinivasan, Narayanaswamy, O'Donovan, Claire, Pruitt, Kim D, Sowdhamini, Ramanathan, Rawlings, Neil D, Saier, Milton H, Sharman, Joanna L, Spedding, Michael, Tsirigos, Konstantinos D, Vastermark, Ake, and Vriend, Gerrit

Abstract

During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

Published
2015

7. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

Author

Woo, Yong H., Ansari, Hifzur, Otto, Thomas D., Klinger, Christen M., Kolisko, Martin, Michálek, Jan, Saxena, Alka, Shanmugam, Dhanasekaran, Tayyrov, Annageldi, Veluchamy, Alaguraj, Ali, Shahjahan, Bernal, Axel, del Campo, Javier, Cihlář, Jaromír, Flegontov, Pavel, Gornik, Sebastian G., Hajduškova, Eva, Horák, Aleš, Janouškovec, Jan, Katris, Nicholas J., Mast, Fred D., Miranda-Saavedra, Diego, Mourier, Tobias, Naeem, Raeece, Nair, Mridul, Panigrahi, Aswini K., Rawlings, Neil D., Padron-Regalado, Eriko, Ramaprasad, Abhinay, Samad, Nadira, Tomčala, Aleš, Wilkes, Jon, Neafsey, Daniel E., Doerig, Christian, Bowler, Chris, Keeling, Patrick J., Roos, David S., Dacks, Joel B., Templeton, Thomas J., Waller, Ross F., Lukeš, Julius, Oborník, Miroslav, Pain, Arnab, Woo, Yong H., Ansari, Hifzur, Otto, Thomas D., Klinger, Christen M., Kolisko, Martin, Michálek, Jan, Saxena, Alka, Shanmugam, Dhanasekaran, Tayyrov, Annageldi, Veluchamy, Alaguraj, Ali, Shahjahan, Bernal, Axel, del Campo, Javier, Cihlář, Jaromír, Flegontov, Pavel, Gornik, Sebastian G., Hajduškova, Eva, Horák, Aleš, Janouškovec, Jan, Katris, Nicholas J., Mast, Fred D., Miranda-Saavedra, Diego, Mourier, Tobias, Naeem, Raeece, Nair, Mridul, Panigrahi, Aswini K., Rawlings, Neil D., Padron-Regalado, Eriko, Ramaprasad, Abhinay, Samad, Nadira, Tomčala, Aleš, Wilkes, Jon, Neafsey, Daniel E., Doerig, Christian, Bowler, Chris, Keeling, Patrick J., Roos, David S., Dacks, Joel B., Templeton, Thomas J., Waller, Ross F., Lukeš, Julius, Oborník, Miroslav, and Pain, Arnab

Published
2015

8. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

Author

Babbitt, Patricia C., Bagos, Pantelis G., Bairoch, Amos, Bateman, Alex, Chatonnet, Arnaud, Chen, Mark Jinan, Craik, David J., Finn, Robert D., Gloriam, David, Haft, Daniel H., Henrissat, Bernard, Holliday, Gemma L., Isberg, Vignir, Kaas, Quentin, Landsman, David, Lenfant, Nicolas, Manning, Gerard, Nagano, Nozomi, Srinivasan, Narayanaswamy, O’Donovan, Claire, Pruitt, Kim D., Sowdhamini, Ramanathan, Rawlings, Neil D., Saier, Milton H., Sharman, Joanna L., Spedding, Michael, Tsirigos, Konstantinos D., Vastermark, Ake, Vriend, Gerrit, Babbitt, Patricia C., Bagos, Pantelis G., Bairoch, Amos, Bateman, Alex, Chatonnet, Arnaud, Chen, Mark Jinan, Craik, David J., Finn, Robert D., Gloriam, David, Haft, Daniel H., Henrissat, Bernard, Holliday, Gemma L., Isberg, Vignir, Kaas, Quentin, Landsman, David, Lenfant, Nicolas, Manning, Gerard, Nagano, Nozomi, Srinivasan, Narayanaswamy, O’Donovan, Claire, Pruitt, Kim D., Sowdhamini, Ramanathan, Rawlings, Neil D., Saier, Milton H., Sharman, Joanna L., Spedding, Michael, Tsirigos, Konstantinos D., Vastermark, Ake, and Vriend, Gerrit

Abstract

During 11–12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

Published
2015

9. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat

Author

Babbitt, Patricia C., Bagos, Pantelis G., Bairoch, Amos, Bateman, Alex, Chatonnet, Arnaud, Chen, Mark Jinan, Craik, David J., Finn, Robert D., Gloriam, David, Haft, Daniel H., Henrissat, Bernard, Holliday, Gemma L., Isberg, Vignir, Kaas, Quentin, Landsman, David, Lenfant, Nicolas, Manning, Gerard, Nagano, Nozomi, Srinivasan, Narayanaswamy, O’Donovan, Claire, Pruitt, Kim D., Sowdhamini, Ramanathan, Rawlings, Neil D., Saier, Milton H., Sharman, Joanna L., Spedding, Michael, Tsirigos, Konstantinos D., Vastermark, Ake, Vriend, Gerrit, Babbitt, Patricia C., Bagos, Pantelis G., Bairoch, Amos, Bateman, Alex, Chatonnet, Arnaud, Chen, Mark Jinan, Craik, David J., Finn, Robert D., Gloriam, David, Haft, Daniel H., Henrissat, Bernard, Holliday, Gemma L., Isberg, Vignir, Kaas, Quentin, Landsman, David, Lenfant, Nicolas, Manning, Gerard, Nagano, Nozomi, Srinivasan, Narayanaswamy, O’Donovan, Claire, Pruitt, Kim D., Sowdhamini, Ramanathan, Rawlings, Neil D., Saier, Milton H., Sharman, Joanna L., Spedding, Michael, Tsirigos, Konstantinos D., Vastermark, Ake, and Vriend, Gerrit

Abstract

During 11–12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

Published
2015

10. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

Author

Woo, Yong H., Ansari, Hifzur, Otto, Thomas D., Klinger, Christen M., Kolisko, Martin, Michálek, Jan, Saxena, Alka, Shanmugam, Dhanasekaran, Tayyrov, Annageldi, Veluchamy, Alaguraj, Ali, Shahjahan, Bernal, Axel, del Campo, Javier, Cihlář, Jaromír, Flegontov, Pavel, Gornik, Sebastian G., Hajduškova, Eva, Horák, Aleš, Janouškovec, Jan, Katris, Nicholas J., Mast, Fred D., Miranda-Saavedra, Diego, Mourier, Tobias, Naeem, Raeece, Nair, Mridul, Panigrahi, Aswini K., Rawlings, Neil D., Padron-Regalado, Eriko, Ramaprasad, Abhinay, Samad, Nadira, Tomčala, Aleš, Wilkes, Jon, Neafsey, Daniel E., Doerig, Christian, Bowler, Chris, Keeling, Patrick J., Roos, David S., Dacks, Joel B., Templeton, Thomas J., Waller, Ross F., Lukeš, Julius, Oborník, Miroslav, Pain, Arnab, Woo, Yong H., Ansari, Hifzur, Otto, Thomas D., Klinger, Christen M., Kolisko, Martin, Michálek, Jan, Saxena, Alka, Shanmugam, Dhanasekaran, Tayyrov, Annageldi, Veluchamy, Alaguraj, Ali, Shahjahan, Bernal, Axel, del Campo, Javier, Cihlář, Jaromír, Flegontov, Pavel, Gornik, Sebastian G., Hajduškova, Eva, Horák, Aleš, Janouškovec, Jan, Katris, Nicholas J., Mast, Fred D., Miranda-Saavedra, Diego, Mourier, Tobias, Naeem, Raeece, Nair, Mridul, Panigrahi, Aswini K., Rawlings, Neil D., Padron-Regalado, Eriko, Ramaprasad, Abhinay, Samad, Nadira, Tomčala, Aleš, Wilkes, Jon, Neafsey, Daniel E., Doerig, Christian, Bowler, Chris, Keeling, Patrick J., Roos, David S., Dacks, Joel B., Templeton, Thomas J., Waller, Ross F., Lukeš, Julius, Oborník, Miroslav, and Pain, Arnab

Published
2015

11. Genomic analysis of the causative agents of coccidiosis in domestic chickens

Author

Reid, Adam J., Blake, Damer P., Ansari, Hifzur R., Billington, Karen, Browne, Hilary P., Bryant, Josephine, Dunn, Matt, Hung, Stacy S., Kawahara, Fumiya, Miranda-Saavedra, Diego, Malas, Tareq B., Mourier, Tobias, Naghra, Hardeep, Nair, Mridul, Otto, Thomas D., Rawlings, Neil D., Rivailler, Pierre, Sanchez-Flores, Alejandro, Sanders, Mandy, Subramaniam, Chandra, Tay, Yea-Ling, Woo, Yong, Wu, Xikun, Barrell, Bart, Dear, Paul H., Doerig, Christian, Gruber, Arthur, Ivens, Alasdair C., Parkinson, John, Rajandream, Marie-Adèle, Shirley, Martin W., Wan, Kiew-Lian, Berriman, Matthew, Tomley, Fiona M., Pain, Arnab, Reid, Adam J., Blake, Damer P., Ansari, Hifzur R., Billington, Karen, Browne, Hilary P., Bryant, Josephine, Dunn, Matt, Hung, Stacy S., Kawahara, Fumiya, Miranda-Saavedra, Diego, Malas, Tareq B., Mourier, Tobias, Naghra, Hardeep, Nair, Mridul, Otto, Thomas D., Rawlings, Neil D., Rivailler, Pierre, Sanchez-Flores, Alejandro, Sanders, Mandy, Subramaniam, Chandra, Tay, Yea-Ling, Woo, Yong, Wu, Xikun, Barrell, Bart, Dear, Paul H., Doerig, Christian, Gruber, Arthur, Ivens, Alasdair C., Parkinson, John, Rajandream, Marie-Adèle, Shirley, Martin W., Wan, Kiew-Lian, Berriman, Matthew, Tomley, Fiona M., and Pain, Arnab

Abstract

Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have produced annotated genome sequences of all seven species of Eimeria that infect domestic chickens, which reveal the full extent of previously described repeat-rich and repeat-poor regions and show that these parasites possess the most repeat-rich proteomes ever described. Furthermore, while no other apicomplexan has been found to possess retrotransposons, Eimeria is home to a family of chromoviruses. Analysis of Eimeria genes involved in basic biology and host-parasite interaction highlights adaptations to a relatively simple developmental life cycle and a complex array of co-expressed surface proteins involved in host cell binding.

Published
2014

12. Genomic analysis of the causative agents of coccidiosis in domestic chickens

Author

Reid, Adam J., Blake, Damer P., Ansari, Hifzur R., Billington, Karen, Browne, Hilary P., Bryant, Josephine, Dunn, Matt, Hung, Stacy S., Kawahara, Fumiya, Miranda-Saavedra, Diego, Malas, Tareq B., Mourier, Tobias, Naghra, Hardeep, Nair, Mridul, Otto, Thomas D., Rawlings, Neil D., Rivailler, Pierre, Sanchez-Flores, Alejandro, Sanders, Mandy, Subramaniam, Chandra, Tay, Yea-Ling, Woo, Yong, Wu, Xikun, Barrell, Bart, Dear, Paul H., Doerig, Christian, Gruber, Arthur, Ivens, Alasdair C., Parkinson, John, Rajandream, Marie-Adèle, Shirley, Martin W., Wan, Kiew-Lian, Berriman, Matthew, Tomley, Fiona M., Pain, Arnab, Reid, Adam J., Blake, Damer P., Ansari, Hifzur R., Billington, Karen, Browne, Hilary P., Bryant, Josephine, Dunn, Matt, Hung, Stacy S., Kawahara, Fumiya, Miranda-Saavedra, Diego, Malas, Tareq B., Mourier, Tobias, Naghra, Hardeep, Nair, Mridul, Otto, Thomas D., Rawlings, Neil D., Rivailler, Pierre, Sanchez-Flores, Alejandro, Sanders, Mandy, Subramaniam, Chandra, Tay, Yea-Ling, Woo, Yong, Wu, Xikun, Barrell, Bart, Dear, Paul H., Doerig, Christian, Gruber, Arthur, Ivens, Alasdair C., Parkinson, John, Rajandream, Marie-Adèle, Shirley, Martin W., Wan, Kiew-Lian, Berriman, Matthew, Tomley, Fiona M., and Pain, Arnab

Abstract

Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have produced annotated genome sequences of all seven species of Eimeria that infect domestic chickens, which reveal the full extent of previously described repeat-rich and repeat-poor regions and show that these parasites possess the most repeat-rich proteomes ever described. Furthermore, while no other apicomplexan has been found to possess retrotransposons, Eimeria is home to a family of chromoviruses. Analysis of Eimeria genes involved in basic biology and host-parasite interaction highlights adaptations to a relatively simple developmental life cycle and a complex array of co-expressed surface proteins involved in host cell binding.

Published
2014

13. Genomic analysis of the causative agents of coccidiosis in domestic chickens

Author

Reid, Adam J., Blake, Damer P., Ansari, Hifzur R., Billington, Karen, Browne, Hilary P., Bryant, Josephine, Dunn, Matt, Hung, Stacy S., Kawahara, Fumiya, Miranda-Saavedra, Diego, Malas, Tareq B., Mourier, Tobias, Naghra, Hardeep, Nair, Mridul, Otto, Thomas D., Rawlings, Neil D., Rivailler, Pierre, Sanchez-Flores, Alejandro, Sanders, Mandy, Subramaniam, Chandra, Tay, Yea-Ling, Woo, Yong, Wu, Xikun, Barrell, Bart, Dear, Paul H., Doerig, Christian, Gruber, Arthur, Ivens, Alasdair C., Parkinson, John, Rajandream, Marie-Adèle, Shirley, Martin W., Wan, Kiew-Lian, Berriman, Matthew, Tomley, Fiona M., Pain, Arnab, Reid, Adam J., Blake, Damer P., Ansari, Hifzur R., Billington, Karen, Browne, Hilary P., Bryant, Josephine, Dunn, Matt, Hung, Stacy S., Kawahara, Fumiya, Miranda-Saavedra, Diego, Malas, Tareq B., Mourier, Tobias, Naghra, Hardeep, Nair, Mridul, Otto, Thomas D., Rawlings, Neil D., Rivailler, Pierre, Sanchez-Flores, Alejandro, Sanders, Mandy, Subramaniam, Chandra, Tay, Yea-Ling, Woo, Yong, Wu, Xikun, Barrell, Bart, Dear, Paul H., Doerig, Christian, Gruber, Arthur, Ivens, Alasdair C., Parkinson, John, Rajandream, Marie-Adèle, Shirley, Martin W., Wan, Kiew-Lian, Berriman, Matthew, Tomley, Fiona M., and Pain, Arnab

Abstract

Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have produced annotated genome sequences of all seven species of Eimeria that infect domestic chickens, which reveal the full extent of previously described repeat-rich and repeat-poor regions and show that these parasites possess the most repeat-rich proteomes ever described. Furthermore, while no other apicomplexan has been found to possess retrotransposons, Eimeria is home to a family of chromoviruses. Analysis of Eimeria genes involved in basic biology and host-parasite interaction highlights adaptations to a relatively simple developmental life cycle and a complex array of co-expressed surface proteins involved in host cell binding.

Published
2014

14. Genomic analysis of the causative agents of coccidiosis in domestic chickens

Author

Reid, Adam J., Blake, Damer P., Ansari, Hifzur R., Billington, Karen, Browne, Hilary P., Bryant, Josephine, Dunn, Matt, Hung, Stacy S., Kawahara, Fumiya, Miranda-Saavedra, Diego, Malas, Tareq B., Mourier, Tobias, Naghra, Hardeep, Nair, Mridul, Otto, Thomas D., Rawlings, Neil D., Rivailler, Pierre, Sanchez-Flores, Alejandro, Sanders, Mandy, Subramaniam, Chandra, Tay, Yea-Ling, Woo, Yong, Wu, Xikun, Barrell, Bart, Dear, Paul H., Doerig, Christian, Gruber, Arthur, Ivens, Alasdair C., Parkinson, John, Rajandream, Marie-Adèle, Shirley, Martin W., Wan, Kiew-Lian, Berriman, Matthew, Tomley, Fiona M., Pain, Arnab, Reid, Adam J., Blake, Damer P., Ansari, Hifzur R., Billington, Karen, Browne, Hilary P., Bryant, Josephine, Dunn, Matt, Hung, Stacy S., Kawahara, Fumiya, Miranda-Saavedra, Diego, Malas, Tareq B., Mourier, Tobias, Naghra, Hardeep, Nair, Mridul, Otto, Thomas D., Rawlings, Neil D., Rivailler, Pierre, Sanchez-Flores, Alejandro, Sanders, Mandy, Subramaniam, Chandra, Tay, Yea-Ling, Woo, Yong, Wu, Xikun, Barrell, Bart, Dear, Paul H., Doerig, Christian, Gruber, Arthur, Ivens, Alasdair C., Parkinson, John, Rajandream, Marie-Adèle, Shirley, Martin W., Wan, Kiew-Lian, Berriman, Matthew, Tomley, Fiona M., and Pain, Arnab

Abstract

Global production of chickens has trebled in the past two decades and they are now the most important source of dietary animal protein worldwide. Chickens are subject to many infectious diseases that reduce their performance and productivity. Coccidiosis, caused by apicomplexan protozoa of the genus Eimeria, is one of the most important poultry diseases. Understanding the biology of Eimeria parasites underpins development of new drugs and vaccines needed to improve global food security. We have produced annotated genome sequences of all seven species of Eimeria that infect domestic chickens, which reveal the full extent of previously described repeat-rich and repeat-poor regions and show that these parasites possess the most repeat-rich proteomes ever described. Furthermore, while no other apicomplexan has been found to possess retrotransposons, Eimeria is home to a family of chromoviruses. Analysis of Eimeria genes involved in basic biology and host-parasite interaction highlights adaptations to a relatively simple developmental life cycle and a complex array of co-expressed surface proteins involved in host cell binding.

Published
2014

15. LUD, a new protein domain associated with lactate utilization.

Author

Hwang, William C, Hwang, William C, Bakolitsa, Constantina, Punta, Marco, Coggill, Penelope C, Bateman, Alex, Axelrod, Herbert L, Rawlings, Neil D, Sedova, Mayya, Peterson, Scott N, Eberhardt, Ruth Y, Aravind, L, Pascual, Jaime, Godzik, Adam, Hwang, William C, Hwang, William C, Bakolitsa, Constantina, Punta, Marco, Coggill, Penelope C, Bateman, Alex, Axelrod, Herbert L, Rawlings, Neil D, Sedova, Mayya, Peterson, Scott N, Eberhardt, Ruth Y, Aravind, L, Pascual, Jaime, and Godzik, Adam

Abstract

BackgroundA novel highly conserved protein domain, DUF162 [Pfam: PF02589], can be mapped to two proteins: LutB and LutC. Both proteins are encoded by a highly conserved LutABC operon, which has been implicated in lactate utilization in bacteria. Based on our analysis of its sequence, structure, and recent experimental evidence reported by other groups, we hereby redefine DUF162 as the LUD domain family.ResultsJCSG solved the first crystal structure [PDB:2G40] from the LUD domain family: LutC protein, encoded by ORF DR_1909, of Deinococcus radiodurans. LutC shares features with domains in the functionally diverse ISOCOT superfamily. We have observed that the LUD domain has an increased abundance in the human gut microbiome.ConclusionsWe propose a model for the substrate and cofactor binding and regulation in LUD domain. The significance of LUD-containing proteins in the human gut microbiome, and the implication of lactate metabolism in the radiation-resistance of Deinococcus radiodurans are discussed.

Published
2013

16. Handbook of proteolytic enzymes

Author

Rawlings, Neil D., editor, Salvesen, G., editor, Rawlings, Neil D., editor, and Salvesen, G., editor

Published
2013

17. Handbook of proteolytic enzymes

Author

Rawlings, Neil D., editor, Salvesen, G., editor, Rawlings, Neil D., editor, and Salvesen, G., editor

Published
2013

18. LUD, a new protein domain associated with lactate utilization.

Author

Hwang, William C, Hwang, William C, Bakolitsa, Constantina, Punta, Marco, Coggill, Penelope C, Bateman, Alex, Axelrod, Herbert L, Rawlings, Neil D, Sedova, Mayya, Peterson, Scott N, Eberhardt, Ruth Y, Aravind, L, Pascual, Jaime, Godzik, Adam, Hwang, William C, Hwang, William C, Bakolitsa, Constantina, Punta, Marco, Coggill, Penelope C, Bateman, Alex, Axelrod, Herbert L, Rawlings, Neil D, Sedova, Mayya, Peterson, Scott N, Eberhardt, Ruth Y, Aravind, L, Pascual, Jaime, and Godzik, Adam

Abstract

BackgroundA novel highly conserved protein domain, DUF162 [Pfam: PF02589], can be mapped to two proteins: LutB and LutC. Both proteins are encoded by a highly conserved LutABC operon, which has been implicated in lactate utilization in bacteria. Based on our analysis of its sequence, structure, and recent experimental evidence reported by other groups, we hereby redefine DUF162 as the LUD domain family.ResultsJCSG solved the first crystal structure [PDB:2G40] from the LUD domain family: LutC protein, encoded by ORF DR_1909, of Deinococcus radiodurans. LutC shares features with domains in the functionally diverse ISOCOT superfamily. We have observed that the LUD domain has an increased abundance in the human gut microbiome.ConclusionsWe propose a model for the substrate and cofactor binding and regulation in LUD domain. The significance of LUD-containing proteins in the human gut microbiome, and the implication of lactate metabolism in the radiation-resistance of Deinococcus radiodurans are discussed.

Published
2013

19. Handbook of proteolytic enzymes

Author

Rawlings, Neil D., editor, Salvesen, G., editor, Rawlings, Neil D., editor, and Salvesen, G., editor

Published
2013

20. Saccharopepsin

Author

Rawlings, Neil D., Salvesen, Guy, Winther, Jakob R., Webb, Helen, Kay, John, Rawlings, Neil D., Salvesen, Guy, Winther, Jakob R., Webb, Helen, and Kay, John

Published
2013

21. Saccharopepsin

Author

Rawlings, Neil D., Salvesen, Guy, Winther, Jakob R., Webb, Helen, Kay, John, Rawlings, Neil D., Salvesen, Guy, Winther, Jakob R., Webb, Helen, and Kay, John

Published
2013

22. Handbook of proteolytic enzymes

Author

Rawlings, Neil D., editor, Salvesen, G., editor, Rawlings, Neil D., editor, and Salvesen, G., editor

Published
2013

23. Sindbis Virus nsP2 Endopeptidase

Author

Rawlings, Neil D., Salvesen, Guy, Strauss, Ellen G., Strauss, James H., Rawlings, Neil D., Salvesen, Guy, Strauss, Ellen G., and Strauss, James H.

Abstract

The third edition of the Handbook of Proteolytic Enzymes aims to be a comprehensive reference work for the enzymes that cleave proteins and peptides, and contains over 800 chapters. Each chapter is organized into sections describing the name and history, activity and specificity, structural chemistry, preparation, biological aspects, and distinguishing features for a specific peptidase. The subject of Chapter 494 is Sindbis Virus nsP2 Endopeptidase.

Published
2012

24. Structural and sequence analysis of imelysin-like proteins implicated in bacterial iron uptake.

Author

Xu, Qingping, Xu, Qingping, Rawlings, Neil D, Farr, Carol L, Chiu, Hsiu-Ju, Grant, Joanna C, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Weekes, Dana, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Xu, Qingping, Xu, Qingping, Rawlings, Neil D, Farr, Carol L, Chiu, Hsiu-Ju, Grant, Joanna C, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Weekes, Dana, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Abstract

Imelysin-like proteins define a superfamily of bacterial proteins that are likely involved in iron uptake. Members of this superfamily were previously thought to be peptidases and were included in the MEROPS family M75. We determined the first crystal structures of two remotely related, imelysin-like proteins. The Psychrobacter arcticus structure was determined at 2.15 Å resolution and contains the canonical imelysin fold, while higher resolution structures from the gut bacteria Bacteroides ovatus, in two crystal forms (at 1.25 Å and 1.44 Å resolution), have a circularly permuted topology. Both structures are highly similar to each other despite low sequence similarity and circular permutation. The all-helical structure can be divided into two similar four-helix bundle domains. The overall structure and the GxHxxE motif region differ from known HxxE metallopeptidases, suggesting that imelysin-like proteins are not peptidases. A putative functional site is located at the domain interface. We have now organized the known homologous proteins into a superfamily, which can be separated into four families. These families share a similar functional site, but each has family-specific structural and sequence features. These results indicate that imelysin-like proteins have evolved from a common ancestor, and likely have a conserved function.

Published
2011

25. Structural analysis of papain-like NlpC/P60 superfamily enzymes with a circularly permuted topology reveals potential lipid binding sites.

Author

Xu, Qingping, Xu, Qingping, Rawlings, Neil D, Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Elsliger, Marc-Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Xu, Qingping, Xu, Qingping, Rawlings, Neil D, Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Elsliger, Marc-Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Abstract

NlpC/P60 superfamily papain-like enzymes play important roles in all kingdoms of life. Two members of this superfamily, LRAT-like and YaeF/YiiX-like families, were predicted to contain a catalytic domain that is circularly permuted such that the catalytic cysteine is located near the C-terminus, instead of at the N-terminus. These permuted enzymes are widespread in virus, pathogenic bacteria, and eukaryotes. We determined the crystal structure of a member of the YaeF/YiiX-like family from Bacillus cereus in complex with lysine. The structure, which adopts a ligand-induced, "closed" conformation, confirms the circular permutation of catalytic residues. A comparative analysis of other related protein structures within the NlpC/P60 superfamily is presented. Permutated NlpC/P60 enzymes contain a similar conserved core and arrangement of catalytic residues, including a Cys/His-containing triad and an additional conserved tyrosine. More surprisingly, permuted enzymes have a hydrophobic S1 binding pocket that is distinct from previously characterized enzymes in the family, indicative of novel substrate specificity. Further analysis of a structural homolog, YiiX (PDB 2if6) identified a fatty acid in the conserved hydrophobic pocket, thus providing additional insights into possible function of these novel enzymes.

Published
2011

26. Structural analysis of papain-like NlpC/P60 superfamily enzymes with a circularly permuted topology reveals potential lipid binding sites.

Author

Xu, Qingping, Sussman, Joel L1, Xu, Qingping, Rawlings, Neil D, Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Elsliger, Marc-Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Xu, Qingping, Sussman, Joel L1, Xu, Qingping, Rawlings, Neil D, Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Elsliger, Marc-Andre, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Abstract

NlpC/P60 superfamily papain-like enzymes play important roles in all kingdoms of life. Two members of this superfamily, LRAT-like and YaeF/YiiX-like families, were predicted to contain a catalytic domain that is circularly permuted such that the catalytic cysteine is located near the C-terminus, instead of at the N-terminus. These permuted enzymes are widespread in virus, pathogenic bacteria, and eukaryotes. We determined the crystal structure of a member of the YaeF/YiiX-like family from Bacillus cereus in complex with lysine. The structure, which adopts a ligand-induced, "closed" conformation, confirms the circular permutation of catalytic residues. A comparative analysis of other related protein structures within the NlpC/P60 superfamily is presented. Permutated NlpC/P60 enzymes contain a similar conserved core and arrangement of catalytic residues, including a Cys/His-containing triad and an additional conserved tyrosine. More surprisingly, permuted enzymes have a hydrophobic S1 binding pocket that is distinct from previously characterized enzymes in the family, indicative of novel substrate specificity. Further analysis of a structural homolog, YiiX (PDB 2if6) identified a fatty acid in the conserved hydrophobic pocket, thus providing additional insights into possible function of these novel enzymes.

Published
2011

27. Structural and sequence analysis of imelysin-like proteins implicated in bacterial iron uptake.

Author

Xu, Qingping, Rodrigues-Lima, Fernando1, Xu, Qingping, Rawlings, Neil D, Farr, Carol L, Chiu, Hsiu-Ju, Grant, Joanna C, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Weekes, Dana, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, Wilson, Ian A, Xu, Qingping, Rodrigues-Lima, Fernando1, Xu, Qingping, Rawlings, Neil D, Farr, Carol L, Chiu, Hsiu-Ju, Grant, Joanna C, Jaroszewski, Lukasz, Klock, Heath E, Knuth, Mark W, Miller, Mitchell D, Weekes, Dana, Elsliger, Marc-André, Deacon, Ashley M, Godzik, Adam, Lesley, Scott A, and Wilson, Ian A

Abstract

Imelysin-like proteins define a superfamily of bacterial proteins that are likely involved in iron uptake. Members of this superfamily were previously thought to be peptidases and were included in the MEROPS family M75. We determined the first crystal structures of two remotely related, imelysin-like proteins. The Psychrobacter arcticus structure was determined at 2.15 Å resolution and contains the canonical imelysin fold, while higher resolution structures from the gut bacteria Bacteroides ovatus, in two crystal forms (at 1.25 Å and 1.44 Å resolution), have a circularly permuted topology. Both structures are highly similar to each other despite low sequence similarity and circular permutation. The all-helical structure can be divided into two similar four-helix bundle domains. The overall structure and the GxHxxE motif region differ from known HxxE metallopeptidases, suggesting that imelysin-like proteins are not peptidases. A putative functional site is located at the domain interface. We have now organized the known homologous proteins into a superfamily, which can be separated into four families. These families share a similar functional site, but each has family-specific structural and sequence features. These results indicate that imelysin-like proteins have evolved from a common ancestor, and likely have a conserved function.

Published
2011

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