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

Autor: 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, Kyle Ellrott
Jazyk: angličtina
Rok vydání: 2010
Předmět:
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
Zdroj: Acta Crystallographica Section F: Structural Biology and Crystallization Communications
Acta crystallographica. Section F, Structural biology and crystallization communications, vol 66, iss Pt 10
ISSN: 1744-3091
Popis: 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.
Databáze: OpenAIRE
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