The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation

Das, Debanu; Grishin, Nick V.; Kumar, Abhinav; Carlton, Dennis; Bakolitsa, Constantina; Miller, Mitchell D.; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Burra, Prasad; Chen, Connie; Chiu, Hsiu-Ju; Chiu, Michelle; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Ellrott, Kyle; Ernst, Dustin; Farr, Carol L.; Feuerhelm, Julie; Grzechnik, Anna; Grzechnik, Slawomir K.; Grant, Joanna C.; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Johnson, Hope A.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Puckett, Christina; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; van den Bedem, Henry; Weekes, Dana; Wooten, Tiffany; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

doi:10.1107/s1744309109022672

Title: The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation

Abstract

Proteins with the DUF2063 domain constitute a new Pfam family, PF09836. The crystal structure of a member of this family, NGO1945 from Neisseria gonorrhoeae, has been determined and reveals that the N-terminal DUF2063 domain is likely to be a DNA-binding domain. In conjunction with the rest of the protein, NGO1945 is likely to be involved in transcriptional regulation, which is consistent with genomic neighborhood analysis. Of the 216 currently known proteins that contain a DUF2063 domain, the most significant sequence homologs of NGO1945 (40–99% sequence identity) are from various Neisseria and Haemophilus species. As these are important human pathogens, NGO1945 represents an interesting candidate for further exploration via biochemical studies and possible therapeutic intervention.

Authors:

Das, Debanu ^[1]; Grishin, Nick V. ^[2]; Kumar, Abhinav ^[1]; Carlton, Dennis ^[3]; Bakolitsa, Constantina ^[4]; Miller, Mitchell D. ^[1]; Abdubek, Polat ^[5]; Astakhova, Tamara ^[6]; Axelrod, Herbert L. ^[1]; Burra, Prasad ^[4]; Chen, Connie ^[5]; Chiu, Hsiu-Ju ^[1]; Chiu, Michelle ^[5]; Clayton, Thomas ^[3]; Deller, Marc C. ^[3]; Duan, Lian ^[6]; Ellrott, Kyle ^[6]; Ernst, Dustin ^[5]; Farr, Carol L. ^[3]; Feuerhelm, Julie ^[5] more »

Joint Center for Structural Genomics, http://www.jcsg.org (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
Univ. of Texas Southwestern Medical Center, Dallas, TX (United States); Howard Hughes Medical Inst., Dallas, TX (United States)
Joint Center for Structural Genomics, http://www.jcsg.org (United States); The Scripps Research Inst., La Jolla, CA (United States). Dept. of Molecular Biology
Joint Center for Structural Genomics, http://www.jcsg.org (United States); Burnham Inst. for Medical Research, La Jolla, CA (United States). Program on Bioinformatics and Systems Biology
Joint Center for Structural Genomics, http://www.jcsg.org (United States); Genomics Institute of the Novartis Research Foundation, San Diego, CA (United States). Protein Sciences Dept.
Joint Center for Structural Genomics, http://www.jcsg.org (United States); Univ. of California, San Diego, La Jolla, CA (United States). Center for Research in Biological Systems
Joint Center for Structural Genomics, http://www.jcsg.org (United States); Burnham Inst. for Medical Research, La Jolla, CA (United States). Program on Bioinformatics and Systems Biology; Univ. of California, San Diego, La Jolla, CA (United States). Center for Research in Biological Systems
Joint Center for Structural Genomics (United States). http://www.jcsg.org; SLAC National Accelerator Lab., Menlo Park, CA (United States). Photon Science
Joint Center for Structural Genomics, http://www.jcsg.org (United States); The Scripps Research Inst., La Jolla, CA (United States). Dept. of Molecular Biology; Genomics Institute of the Novartis Research Foundation, San Diego, CA (United States). Protein Sciences Dept.

Publication Date:: Tue Oct 27 00:00:00 EDT 2009

Research Org.:: SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1625785

Grant/Contract Number:: AC02-76SF00515

Resource Type:: Accepted Manuscript

Journal Name:: Acta Crystallographica. Section F

Additional Journal Information:: Journal Volume: 66; Journal Issue: 10; Journal ID: ISSN 1744-3091

Publisher:: International Union of Crystallography

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; biochemistry & molecular biology; biophysics; crystallography; NGO1945; PF09836; DUF2063; putative DNA-binding proteins; putative transcription regulators; structural genomics

Citation Formats


                    Das, Debanu, Grishin, Nick V., Kumar, Abhinav, Carlton, Dennis, Bakolitsa, Constantina, Miller, Mitchell D., Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L., Burra, Prasad, Chen, Connie, Chiu, Hsiu-Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C., Duan, Lian, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L., Feuerhelm, Julie, Grzechnik, Anna, Grzechnik, Slawomir K., Grant, Joanna C., Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K., Johnson, Hope A., Klock, Heath E., Knuth, Mark W., Kozbial, Piotr, Krishna, S. Sri, Marciano, David, McMullan, Daniel, Morse, Andrew T., Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L., Sefcovic, Natasha, Tien, Henry J., Trame, Christine B., van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Hodgson, Keith O., Wooley, John, Elsliger, Marc-André, Deacon, Ashley M., Godzik, Adam, Lesley, Scott A., and Wilson, Ian A. The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation.  United States: N. p., 2009. 
Web.  doi:10.1107/s1744309109022672.

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                    Das, Debanu, Grishin, Nick V., Kumar, Abhinav, Carlton, Dennis, Bakolitsa, Constantina, Miller, Mitchell D., Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L., Burra, Prasad, Chen, Connie, Chiu, Hsiu-Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C., Duan, Lian, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L., Feuerhelm, Julie, Grzechnik, Anna, Grzechnik, Slawomir K., Grant, Joanna C., Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K., Johnson, Hope A., Klock, Heath E., Knuth, Mark W., Kozbial, Piotr, Krishna, S. Sri, Marciano, David, McMullan, Daniel, Morse, Andrew T., Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L., Sefcovic, Natasha, Tien, Henry J., Trame, Christine B., van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Hodgson, Keith O., Wooley, John, Elsliger, Marc-André, Deacon, Ashley M., Godzik, Adam, Lesley, Scott A., & Wilson, Ian A. The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation.  United States.  https://doi.org/10.1107/s1744309109022672

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                    Das, Debanu, Grishin, Nick V., Kumar, Abhinav, Carlton, Dennis, Bakolitsa, Constantina, Miller, Mitchell D., Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L., Burra, Prasad, Chen, Connie, Chiu, Hsiu-Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C., Duan, Lian, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L., Feuerhelm, Julie, Grzechnik, Anna, Grzechnik, Slawomir K., Grant, Joanna C., Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K., Johnson, Hope A., Klock, Heath E., Knuth, Mark W., Kozbial, Piotr, Krishna, S. Sri, Marciano, David, McMullan, Daniel, Morse, Andrew T., Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Oommachen, Silvya, Paulsen, Jessica, Puckett, Christina, Reyes, Ron, Rife, Christopher L., Sefcovic, Natasha, Tien, Henry J., Trame, Christine B., van den Bedem, Henry, Weekes, Dana, Wooten, Tiffany, Xu, Qingping, Hodgson, Keith O., Wooley, John, Elsliger, Marc-André, Deacon, Ashley M., Godzik, Adam, Lesley, Scott A., and Wilson, Ian A. Tue .  
"The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation".  United States.  https://doi.org/10.1107/s1744309109022672.  https://www.osti.gov/servlets/purl/1625785.

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@article{osti_1625785,

  title        = {The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation},

  author       = {Das, Debanu and Grishin, Nick V. and Kumar, Abhinav and Carlton, Dennis and Bakolitsa, Constantina and Miller, Mitchell D. and Abdubek, Polat and Astakhova, Tamara and Axelrod, Herbert L. and Burra, Prasad and Chen, Connie and Chiu, Hsiu-Ju and Chiu, Michelle and Clayton, Thomas and Deller, Marc C. and Duan, Lian and Ellrott, Kyle and Ernst, Dustin and Farr, Carol L. and Feuerhelm, Julie and Grzechnik, Anna and Grzechnik, Slawomir K. and Grant, Joanna C. and Han, Gye Won and Jaroszewski, Lukasz and Jin, Kevin K. and Johnson, Hope A. and Klock, Heath E. and Knuth, Mark W. and Kozbial, Piotr and Krishna, S. Sri and Marciano, David and McMullan, Daniel and Morse, Andrew T. and Nigoghossian, Edward and Nopakun, Amanda and Okach, Linda and Oommachen, Silvya and Paulsen, Jessica and Puckett, Christina and Reyes, Ron and Rife, Christopher L. and Sefcovic, Natasha and Tien, Henry J. and Trame, Christine B. and van den Bedem, Henry and Weekes, Dana and Wooten, Tiffany and Xu, Qingping and Hodgson, Keith O. and Wooley, John and Elsliger, Marc-André and Deacon, Ashley M. and Godzik, Adam and Lesley, Scott A. and Wilson, Ian A.},

  abstractNote = {Proteins with the DUF2063 domain constitute a new Pfam family, PF09836. The crystal structure of a member of this family, NGO1945 from Neisseria gonorrhoeae, has been determined and reveals that the N-terminal DUF2063 domain is likely to be a DNA-binding domain. In conjunction with the rest of the protein, NGO1945 is likely to be involved in transcriptional regulation, which is consistent with genomic neighborhood analysis. Of the 216 currently known proteins that contain a DUF2063 domain, the most significant sequence homologs of NGO1945 (40–99% sequence identity) are from various Neisseria and Haemophilus species. As these are important human pathogens, NGO1945 represents an interesting candidate for further exploration via biochemical studies and possible therapeutic intervention.},

  doi          = {10.1107/s1744309109022672},

  journal      = {Acta Crystallographica. Section F},

  number       = 10,

  volume       = 66,

  place        = {United States},

  year         = {Tue Oct 27 00:00:00 EDT 2009},

  month        = {Tue Oct 27 00:00:00 EDT 2009}

}

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Scientific Reports, Vol. 6, Issue 1
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Title: The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation

Abstract

Citation Formats

Bph32, a novel gene encoding an unknown SCR domain-containing protein, confers resistance against the brown planthopper in rice journal, November 2016

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