1. 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
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Lukasz Jaroszewski, Polat Abdubek, Sanjay Krishna, Adam Godzik, Henry van den Bedem, Dennis Carlton, Marc-André Elsliger, Natasha Sefcovic, Edward Nigoghossian, Piotr Kozbial, Henry J Tien, Thomas Clayton, Debanu Das, Qingping Xu, Joanna C Grant, Gye Won Han, Heath E. Klock, Carol L. Farr, Ron Reyes, Daniel McMullan, John Wooley, Hsiu-Ju Chiu, Marc C. Deller, Herbert L. Axelrod, Connie Chen, Amanda Nopakun, Tamara Astakhova, Ian A. Wilson, Kevin K. Jin, Christine B Trame, Christina Puckett, Constantina Bakolitsa, David Marciano, Keith O. Hodgson, Winnie W Lam, Ashley M. Deacon, Andrew T. Morse, Mitchell D. Miller, Anna Grzechnik, Julie Feuerhelm, Abhinav Kumar, Tiffany Wooten, Dana Weekes, Lian Duan, Linda Okach, Mark W. Knuth, Scott A. Lesley, and Kyle Ellrott
- Subjects
Pfam family PF02663 ,Models, Molecular ,Secondary ,Ligands That Aid in Function Characterization ,metalloproteins ,Crystallography, X-Ray ,Biochemistry ,Protein Structure, Secondary ,Structural Biology ,Models ,domain swapping ,Zinc finger ,chemistry.chemical_classification ,0303 health sciences ,Crystallography ,biology ,030302 biochemistry & molecular biology ,Thermoplasma acidophilum ,Zinc Fingers ,methanogenesis ,Biological Sciences ,Condensed Matter Physics ,Aldehyde Oxidoreductases ,Methane ,Protein Structure ,Molecular Sequence Data ,Biophysics ,chemistry.chemical_element ,Context (language use) ,Zinc ,Desulfitobacterium ,Formylmethanofuran dehydrogenase ,Structural genomics ,03 medical and health sciences ,Rare Diseases ,Oxidoreductase ,Genetics ,Amino Acid Sequence ,030304 developmental biology ,Structural Homology ,Protein ,Active site ,Molecular ,structural genomics ,biology.organism_classification ,Protein Structure, Tertiary ,chemistry ,Structural Homology, Protein ,Chemical Sciences ,biology.protein ,X-Ray ,Tertiary - Abstract
The first structures from the FmdE Pfam family (PF02663) reveal that some members of this family form tightly intertwined dimers consisting of two domains (N-terminal α+β core and C-terminal zinc-finger domains), whereas others contain only the core domain. The presence of the zinc-finger domain suggests that some members of this family may perform functions associated with transcriptional regulation, protein–protein interaction, RNA binding or metal-ion sensing., 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 α+β core domain (NTD) consisting of a five-stranded, mixed β-sheet flanked by several α-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.
- Published
- 2010