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

Herbert L. Axelrod, Debanu Das, Polat Abdubek, Tamara Astakhova, Constantina Bakolitsa, Dennis Carlton, Connie Chen, Hsiu Ju Chiu, Thomas Clayton, Marc C. Deller, Lian Duan, Kyle Ellrott, Carol L. Farr, Julie Feuerhelm, Joanna C. Grant, Anna Grzechnik, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. KlockMark W. Knuth, Piotr Kozbial, S. Sri Krishna, Abhinav Kumar, Winnie W. Lam, David Marciano, Daniel McMullan, Mitchell D. Miller, Andrew T. Morse, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Christina Puckett, Ron Reyes, Natasha Sefcovic, Henry J. Tien, Christine B. Trame, Henry Van Den Bedem, Dana Weekes, Tiffany Wooten, Qingping Xu, Keith O. Hodgson, John Wooley, Marc André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson

Research output: Contribution to journalArticle

5 Scopus citations

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 Desulfito-bacterium 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 α+Β core domain (NTD) consisting of a five-stranded, mixed Β-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.

Original languageEnglish (US)
Pages (from-to)1335-1346
Number of pages12
JournalActa Crystallographica Section F: Structural Biology and Crystallization Communications
Volume66
Issue number10
DOIs
StatePublished - Oct 1 2010

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Keywords

  • Pfam family PF02663
  • domain swapping
  • metalloproteins
  • methanogenesis
  • structural genomics

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Biochemistry
  • Genetics
  • Condensed Matter Physics

Cite this

Axelrod, H. L., Das, D., Abdubek, P., Astakhova, T., Bakolitsa, C., Carlton, D., Chen, C., Chiu, H. J., Clayton, T., Deller, M. C., Duan, L., Ellrott, K., Farr, C. L., Feuerhelm, J., Grant, J. C., Grzechnik, A., Han, G. W., Jaroszewski, L., Jin, K. K., ... Wilson, I. A. (2010). 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. Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 66(10), 1335-1346. https://doi.org/10.1107/S1744309110020166