The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function

Das, Debanu; Finn, Robert D.; Carlton, Dennis; Miller, Mitchell D.; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Bakolitsa, Constantina; Chen, Connie; Chiu, Hsiu-Ju; Chiu, Michelle; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Ellrott, Kyle; Ernst, Dustin; Farr, Carol L.; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Kumar, Abhinav; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; 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/s1744309109046788

Title: The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function

Abstract

Proteins that contain the DUF2874 domain constitute a new Pfam family PF11396. Members of this family have predominantly been identified in microbes found in the human gut and oral cavity. The crystal structure of one member of this family, BVU2987 from Bacteroides vulgatus, has been determined, revealing a -lactamase inhibitor protein-like structure with a tandem repeat of domains. Sequence analysis and structural comparisons reveal that BVU2987 and other DUF2874 proteins are related to -lactamase inhibitor protein, PepSY and SmpA_OmlA proteins and hence are likely to function as inhibitory proteins.

Authors:

Das, Debanu ^[1]; Finn, Robert D. ^[2]; Carlton, Dennis ^[3]; Miller, Mitchell D. ^[1]; Abdubek, Polat ^[4]; Astakhova, Tamara ^[5]; Axelrod, Herbert L. ^[1]; Bakolitsa, Constantina ^[6]; Chen, Connie ^[4]; Chiu, Hsiu-Ju ^[1]; Chiu, Michelle ^[4]; Clayton, Thomas ^[3]; Deller, Marc C. ^[3]; Duan, Lian ^[5]; Ellrott, Kyle ^[7]; Ernst, Dustin ^[4]; Farr, Carol L. ^[3]; Feuerhelm, Julie ^[4]; Grant, Joanna C. ^[4]; Grzechnik, Anna ^[3] 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)
Wellcome Trust Sanger Inst., Hinxton (United Kingdom)
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); 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
Joint Center for Structural Genomics, http://www.jcsg.org (United States); Univ. of California, San Diego, La Jolla, CA (United States)
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; 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); 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:: Fri Mar 05 00:00:00 EST 2010

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

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Institute of General Medical Sciences (NIGMS); USDOE Office of Science (SC), Basic Energy Sciences (BES); National Center for Research Resources (NCRR); Wellcome Trust

OSTI Identifier:: 1625789

Grant/Contract Number:: AC02-76SF00515; U54 GM074898; WT077044/Z/05/Z

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; BVU2987; DUF2874; PF11396; human gut microbiome; β-lactamase inhibitor protein-like fold; putative inhibitor proteins.

Citation Formats


                    Das, Debanu, Finn, Robert D., Carlton, Dennis, Miller, Mitchell D., Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L., Bakolitsa, Constantina, Chen, Connie, Chiu, Hsiu-Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C., Duan, Lian, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L., Feuerhelm, Julie, Grant, Joanna C., Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K., Klock, Heath E., Knuth, Mark W., Kozbial, Piotr, Krishna, S. Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T., Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, 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 BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function.  United States: N. p., 2010. 
Web.  doi:10.1107/s1744309109046788.

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                    Das, Debanu, Finn, Robert D., Carlton, Dennis, Miller, Mitchell D., Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L., Bakolitsa, Constantina, Chen, Connie, Chiu, Hsiu-Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C., Duan, Lian, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L., Feuerhelm, Julie, Grant, Joanna C., Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K., Klock, Heath E., Knuth, Mark W., Kozbial, Piotr, Krishna, S. Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T., Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, 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 BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function.  United States.  https://doi.org/10.1107/s1744309109046788

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                    Das, Debanu, Finn, Robert D., Carlton, Dennis, Miller, Mitchell D., Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L., Bakolitsa, Constantina, Chen, Connie, Chiu, Hsiu-Ju, Chiu, Michelle, Clayton, Thomas, Deller, Marc C., Duan, Lian, Ellrott, Kyle, Ernst, Dustin, Farr, Carol L., Feuerhelm, Julie, Grant, Joanna C., Grzechnik, Anna, Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K., Klock, Heath E., Knuth, Mark W., Kozbial, Piotr, Krishna, S. Sri, Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T., Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, 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. Fri .  
"The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function".  United States.  https://doi.org/10.1107/s1744309109046788.  https://www.osti.gov/servlets/purl/1625789.

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@article{osti_1625789,

  title        = {The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function},

  author       = {Das, Debanu and Finn, Robert D. and Carlton, Dennis and Miller, Mitchell D. and Abdubek, Polat and Astakhova, Tamara and Axelrod, Herbert L. and Bakolitsa, Constantina 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 Grant, Joanna C. and Grzechnik, Anna and Han, Gye Won and Jaroszewski, Lukasz and Jin, Kevin K. and Klock, Heath E. and Knuth, Mark W. and Kozbial, Piotr and Krishna, S. Sri and Kumar, Abhinav and Marciano, David and McMullan, Daniel and Morse, Andrew T. and Nigoghossian, Edward and Nopakun, Amanda and Okach, Linda 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 that contain the DUF2874 domain constitute a new Pfam family PF11396. Members of this family have predominantly been identified in microbes found in the human gut and oral cavity. The crystal structure of one member of this family, BVU2987 from Bacteroides vulgatus, has been determined, revealing a -lactamase inhibitor protein-like structure with a tandem repeat of domains. Sequence analysis and structural comparisons reveal that BVU2987 and other DUF2874 proteins are related to -lactamase inhibitor protein, PepSY and SmpA_OmlA proteins and hence are likely to function as inhibitory proteins.},

  doi          = {10.1107/s1744309109046788},

  journal      = {Acta Crystallographica. Section F},

  number       = 10,

  volume       = 66,

  place        = {United States},

  year         = {Fri Mar 05 00:00:00 EST 2010},

  month        = {Fri Mar 05 00:00:00 EST 2010}

}

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Title: The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function

Abstract

Citation Formats

Role of YpeB in Cortex Hydrolysis during Germination of Bacillus anthracis Spores journal, October 2014

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