The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role

Krishna, S. Sri; Aravind, L.; Bakolitsa, Constantina; Caruthers, Jonathan; Carlton, Dennis; Miller, Mitchell D.; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Feuerhelm, Julie; Grant, Joanna C.; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kumar, Abhinav; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Reyes, Ron; Rife, Christopher L.; van den Bedem, Henry; Weekes, Dana; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

doi:10.1107/s1744309110002514

Title: The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role

Abstract

SSO2064 is the first structural representative of PF01796 (DUF35), a large prokaryotic family with a wide phylogenetic distribution. The structure reveals a novel two-domain architecture comprising an N-terminal, rubredoxin-like, zinc ribbon and a C-terminal, oligonucleotide/oligosaccharide-binding (OB) fold domain. Additional N-terminal helical segments may be involved in protein–protein interactions. Domain architectures, genomic context analysis and functional evidence from certain bacterial representatives of this family suggest that these proteins form a novel fatty-acid-binding component that is involved in the biosynthesis of lipids and polyketide antibiotics and that they possibly function as acyl-CoA-binding proteins. This structure has led to a reevaluation of the DUF35 family, which has now been split into two entries in the latest Pfam release (v.24.0).

Authors:

Krishna, S. Sri ^[1]; Aravind, L. ^[2]; Bakolitsa, Constantina ^[3]; Caruthers, Jonathan ^[4]; Carlton, Dennis ^[5]; Miller, Mitchell D. ^[4]; Abdubek, Polat ^[6]; Astakhova, Tamara ^[7]; Axelrod, Herbert L. ^[4]; Chiu, Hsiu-Ju ^[4]; Clayton, Thomas ^[5]; Deller, Marc C. ^[5]; Duan, Lian ^[7]; Feuerhelm, Julie ^[6]; Grant, Joanna C. ^[6]; Han, Gye Won ^[5]; Jaroszewski, Lukasz ^[1]; Jin, Kevin K. ^[4]; Klock, Heath E. ^[6]; Knuth, Mark W. ^[6] more »

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
National Institutes of Health (NIH), Bethesda, MD (United States)
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); SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
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); 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 Laboratory (SLAC), 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); National Center for Research Resources (NCRR); USDOE Office of Science (SC), Basic Energy Sciences (BES)

OSTI Identifier:: 1625792

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

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; structural genomics; domains of unknown function; acyl-carrier proteins; acyl-coA; polyketide biosynthesis

Citation Formats


                    Krishna, S. Sri, Aravind, L., Bakolitsa, Constantina, Caruthers, Jonathan, Carlton, Dennis, Miller, Mitchell D., Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L., Chiu, Hsiu-Ju, Clayton, Thomas, Deller, Marc C., Duan, Lian, Feuerhelm, Julie, Grant, Joanna C., Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K., Klock, Heath E., Knuth, Mark W., Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T., Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Rife, Christopher L., van den Bedem, Henry, Weekes, Dana, 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 SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role.  United States: N. p., 2010. 
Web.  doi:10.1107/s1744309110002514.

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                    Krishna, S. Sri, Aravind, L., Bakolitsa, Constantina, Caruthers, Jonathan, Carlton, Dennis, Miller, Mitchell D., Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L., Chiu, Hsiu-Ju, Clayton, Thomas, Deller, Marc C., Duan, Lian, Feuerhelm, Julie, Grant, Joanna C., Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K., Klock, Heath E., Knuth, Mark W., Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T., Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Rife, Christopher L., van den Bedem, Henry, Weekes, Dana, Xu, Qingping, Hodgson, Keith O., Wooley, John, Elsliger, Marc-André, Deacon, Ashley M., Godzik, Adam, Lesley, Scott A., & Wilson, Ian A. The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role.  United States.  https://doi.org/10.1107/s1744309110002514

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                    Krishna, S. Sri, Aravind, L., Bakolitsa, Constantina, Caruthers, Jonathan, Carlton, Dennis, Miller, Mitchell D., Abdubek, Polat, Astakhova, Tamara, Axelrod, Herbert L., Chiu, Hsiu-Ju, Clayton, Thomas, Deller, Marc C., Duan, Lian, Feuerhelm, Julie, Grant, Joanna C., Han, Gye Won, Jaroszewski, Lukasz, Jin, Kevin K., Klock, Heath E., Knuth, Mark W., Kumar, Abhinav, Marciano, David, McMullan, Daniel, Morse, Andrew T., Nigoghossian, Edward, Okach, Linda, Reyes, Ron, Rife, Christopher L., van den Bedem, Henry, Weekes, Dana, 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 SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role".  United States.  https://doi.org/10.1107/s1744309110002514.  https://www.osti.gov/servlets/purl/1625792.

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@article{osti_1625792,

  title        = {The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role},

  author       = {Krishna, S. Sri and Aravind, L. and Bakolitsa, Constantina and Caruthers, Jonathan and Carlton, Dennis and Miller, Mitchell D. and Abdubek, Polat and Astakhova, Tamara and Axelrod, Herbert L. and Chiu, Hsiu-Ju and Clayton, Thomas and Deller, Marc C. and Duan, Lian and Feuerhelm, Julie and Grant, Joanna C. and Han, Gye Won and Jaroszewski, Lukasz and Jin, Kevin K. and Klock, Heath E. and Knuth, Mark W. and Kumar, Abhinav and Marciano, David and McMullan, Daniel and Morse, Andrew T. and Nigoghossian, Edward and Okach, Linda and Reyes, Ron and Rife, Christopher L. and van den Bedem, Henry and Weekes, Dana 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 = {SSO2064 is the first structural representative of PF01796 (DUF35), a large prokaryotic family with a wide phylogenetic distribution. The structure reveals a novel two-domain architecture comprising an N-terminal, rubredoxin-like, zinc ribbon and a C-terminal, oligonucleotide/oligosaccharide-binding (OB) fold domain. Additional N-terminal helical segments may be involved in protein–protein interactions. Domain architectures, genomic context analysis and functional evidence from certain bacterial representatives of this family suggest that these proteins form a novel fatty-acid-binding component that is involved in the biosynthesis of lipids and polyketide antibiotics and that they possibly function as acyl-CoA-binding proteins. This structure has led to a reevaluation of the DUF35 family, which has now been split into two entries in the latest Pfam release (v.24.0).},

  doi          = {10.1107/s1744309110002514},

  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 SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role

Abstract

Citation Formats

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