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Title: Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger

Abstract

Examination of the genomic context for members of the FmdE Pfam family (PF02663), such as the protein encoded by the fmdE gene from the methanogenic archaeon Methanobacterium thermoautotrophicum, indicates that 13 of them are co-transcribed with genes encoding subunits of molybdenum formylmethanofuran dehydrogenase (EC 1.2.99.5), an enzyme that is involved in microbial methane production. Here, the first crystal structures from PF02663 are described, representing two bacterial and one archaeal species: B8FYU2_ DESHY from the anaerobic dehalogenating bacterium Desulfitobacterium hafniense DCB-2, Q2LQ23_SYNAS from the syntrophic bacterium Syntrophus aciditrophicus SB and Q9HJ63_THEAC from the thermoacidophilic archaeon Thermoplasma acidophilum. Two of these proteins, Q9HJ63_THEAC and Q2LQ23_SYNAS, contain two domains: an N-terminal thioredoxin-like + core domain (NTD) consisting of a five-stranded, mixed -sheet flanked by several -helices and a C-terminal zinc-finger domain (CTD). B8FYU2_ DESHY, on the other hand, is composed solely of the NTD. The CTD of Q9HJ63_THEAC and Q2LQ23_SYNAS is best characterized as a treble-clef zinc finger. Two significant structural differences between Q9HJ63_THEAC and Q2LQ23_SYNAS involve their metal binding. First, zinc is bound to the putative active site on the NTD of Q9HJ63_THEAC, but is absent from the NTD of Q2LQ23_SYNAS. Second, whereas the structure of the CTD of Q2LQ23_SYNAS shows fourmore » Cys side chains within coordination distance of the Zn atom, the structure of Q9HJ63_THEAC is atypical for a treble-cleft zinc finger in that three Cys side chains and an Asp side chain are within coordination distance of the zinc.« less

Authors:
 [1];  [1];  [2];  [3];  [4];  [5];  [2];  [1];  [5];  [5];  [3];  [3];  [5];  [2];  [2];  [5];  [5];  [6];  [1];  [2] more »;  [2];  [4];  [6];  [1];  [1];  [5];  [7];  [1];  [3];  [2];  [5];  [2];  [2];  [1];  [4];  [5];  [1];  [1];  [4];  [2];  [1];  [8];  [3];  [5];  [1];  [6];  [9];  [5] « less
+ Show Author Affiliations
  1. 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)
  2. 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.
  3. 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
  4. Joint Center for Structural Genomics, http://www.jcsg.org (United States); Sanford–Burnham Medical Research Institute, La Jolla, CA (United States). Program on Bioinformatics and Systems Biology
  5. Joint Center for Structural Genomics, http://www.jcsg.org (United States); The Scripps Research Inst., La Jolla, CA (United States). Dept. of Molecular Biology
  6. 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; Sanford–Burnham Medical Research Institute, La Jolla, CA (United States). Program on Bioinformatics and Systems Biology
  7. Joint Center for Structural Genomics, http://www.jcsg.org (United States); Genomics Institute of the Novartis Research Foundation, San Diego, CA (United States). Protein Therapeutics Dept.
  8. Joint Center for Structural Genomics, http://www.jcsg.org (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States). Photon Science
  9. 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.; Sanford–Burnham Medical Research Institute, La Jolla, CA (United States). Program on Bioinformatics and Systems Biology
Publication Date:
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:
1625797
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; fam family PF02663; metalloproteins; domain swapping; structural genomics; methanogenesis

Citation Formats

Axelrod, Herbert L., Das, Debanu, Abdubek, Polat, Astakhova, Tamara, Bakolitsa, Constantina, Carlton, Dennis, Chen, Connie, Chiu, Hsiu-Ju, Clayton, Thomas, Deller, Marc C., Duan, Lian, Ellrott, Kyle, 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, Lam, Winnie W., Marciano, David, McMullan, Daniel, Miller, Mitchell D., Morse, Andrew T., Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, 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. Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger. United States: N. p., 2010. Web. doi:10.1107/s1744309110020166.
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Axelrod, Herbert L., Das, Debanu, Abdubek, Polat, Astakhova, Tamara, Bakolitsa, Constantina, Carlton, Dennis, Chen, Connie, Chiu, Hsiu-Ju, Clayton, Thomas, Deller, Marc C., Duan, Lian, Ellrott, Kyle, 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, Lam, Winnie W., Marciano, David, McMullan, Daniel, Miller, Mitchell D., Morse, Andrew T., Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, 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. Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger. United States. https://doi.org/10.1107/s1744309110020166
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Axelrod, Herbert L., Das, Debanu, Abdubek, Polat, Astakhova, Tamara, Bakolitsa, Constantina, Carlton, Dennis, Chen, Connie, Chiu, Hsiu-Ju, Clayton, Thomas, Deller, Marc C., Duan, Lian, Ellrott, Kyle, 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, Lam, Winnie W., Marciano, David, McMullan, Daniel, Miller, Mitchell D., Morse, Andrew T., Nigoghossian, Edward, Nopakun, Amanda, Okach, Linda, Puckett, Christina, Reyes, Ron, 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. Wed . "Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger". United States. https://doi.org/10.1107/s1744309110020166. https://www.osti.gov/servlets/purl/1625797.
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@article{osti_1625797,
title = {Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger},
author = {Axelrod, Herbert L. and Das, Debanu and Abdubek, Polat and Astakhova, Tamara and Bakolitsa, Constantina and Carlton, Dennis and Chen, Connie and Chiu, Hsiu-Ju and Clayton, Thomas and Deller, Marc C. and Duan, Lian and Ellrott, Kyle 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 Lam, Winnie W. and Marciano, David and McMullan, Daniel and Miller, Mitchell D. and Morse, Andrew T. and Nigoghossian, Edward and Nopakun, Amanda and Okach, Linda and Puckett, Christina and Reyes, Ron 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 = {Examination of the genomic context for members of the FmdE Pfam family (PF02663), such as the protein encoded by the fmdE gene from the methanogenic archaeon Methanobacterium thermoautotrophicum, indicates that 13 of them are co-transcribed with genes encoding subunits of molybdenum formylmethanofuran dehydrogenase (EC 1.2.99.5), an enzyme that is involved in microbial methane production. Here, the first crystal structures from PF02663 are described, representing two bacterial and one archaeal species: B8FYU2_ DESHY from the anaerobic dehalogenating bacterium Desulfitobacterium hafniense DCB-2, Q2LQ23_SYNAS from the syntrophic bacterium Syntrophus aciditrophicus SB and Q9HJ63_THEAC from the thermoacidophilic archaeon Thermoplasma acidophilum. Two of these proteins, Q9HJ63_THEAC and Q2LQ23_SYNAS, contain two domains: an N-terminal thioredoxin-like + core domain (NTD) consisting of a five-stranded, mixed -sheet flanked by several -helices and a C-terminal zinc-finger domain (CTD). B8FYU2_ DESHY, on the other hand, is composed solely of the NTD. The CTD of Q9HJ63_THEAC and Q2LQ23_SYNAS is best characterized as a treble-clef zinc finger. Two significant structural differences between Q9HJ63_THEAC and Q2LQ23_SYNAS involve their metal binding. First, zinc is bound to the putative active site on the NTD of Q9HJ63_THEAC, but is absent from the NTD of Q2LQ23_SYNAS. Second, whereas the structure of the CTD of Q2LQ23_SYNAS shows four Cys side chains within coordination distance of the Zn atom, the structure of Q9HJ63_THEAC is atypical for a treble-cleft zinc finger in that three Cys side chains and an Asp side chain are within coordination distance of the zinc.},
doi = {10.1107/s1744309110020166},
journal = {Acta Crystallographica. Section F},
number = 10,
volume = 66,
place = {United States},
year = {Wed Aug 04 00:00:00 EDT 2010},
month = {Wed Aug 04 00:00:00 EDT 2010}
}
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https://doi.org/10.1107/s1744309110020166
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Works referencing / citing this record:

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Exploring the evolution of protein function in Archaea
journal, January 2012

  • Goncearenco, Alexander; Berezovsky, Igor N.
  • BMC Evolutionary Biology, Vol. 12, Issue 1
  • DOI: 10.1186/1471-2148-12-75
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