Taxonomic distribution of proteins containing FDF domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing FDF domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

Structural basis for the mutually exclusive anchoring of P body components EDC3and Tral to the DEAD box protein DDX6/Me31B.

Tritschler F, Braun JE, Eulalio A, Truffault V, Izaurralde E, Weichenrieder O
Mol Cell. 2009; 33: 661-8

The DEAD box helicase DDX6/Me31B functions in translational repression and mRNAdecapping. How particular RNA helicases are recruited specifically to distinctfunctional complexes is poorly understood. We present the crystal structure ofthe DDX6 C-terminal RecA-like domain bound to a highly conserved FDF sequencemotif in the decapping activator EDC3. The FDF peptide adopts an alpha-helicalconformation upon binding to DDX6, occupying a shallow groove opposite to theDDX6 surface involved in RNA binding and ATP hydrolysis. Mutagenesis of Me31Bshows the relevance of the FDF interaction surface both for Me31B's accumulation in P bodies and for its ability to repress the expression of bound mRNAs. Thetranslational repressor Tral contains a similar FDF motif. Together withmutational and competition studies, the structure reveals why the interactions ofMe31B with EDC3 and Tral are mutually exclusive and how the respective decapping and translational repressor complexes might hook onto an mRNA substrate.

Novel Sm-like proteins with long C-terminal tails and associatedmethyltransferases.

Albrecht M, Lengauer T
FEBS Lett. 2004; 569: 18-26

Sm and Sm-like proteins of the Lsm (like Sm) domain family are generallyinvolved in essential RNA-processing tasks. While recent research hasfocused on the function and structure of small family members, little isknown about Lsm domain proteins carrying additional domains. Using anintegrative bioinformatics approach, we discovered five novel groups ofLsm domain proteins (Lsm12-16) with long C-terminal tails and investigatedtheir functions. All of them are evolutionarily conserved in eukaryoteswith an N-terminal Lsm domain to bind nucleic acids followed by as yetuncharacterized C-terminal domains and sequence motifs. Based on knownyeast interaction partners, Lsm12-16 may play important roles in RNAmetabolism. Particularly, Lsm12 is possibly involved in mRNA degradationor tRNA splicing, and Lsm13-16 in the regulation of the mitotic G2/Mphase. Lsm16 proteins have an additional C-terminal YjeF_N domain of asyet unknown function. The identification of an additionalmethyltransferase domain at the C-terminus of one of the Lsm12 proteinsalso led to the recognition of three new groups of methyltransferases,presumably dependent on S-adenosyl-l-methionine. Further computationalanalyses revealed that some methyltransferases contain putativeRNA-binding helix-turn-helix domains and zinc fingers.

Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycleregulation, decapping and RNA stability.

Anantharaman V, Aravind L
BMC Genomics. 2004; 5: 45-45

BACKGROUND: The emergence of eukaryotes was characterized by the expansion anddiversification of several ancient RNA-binding domains and the apparent de novoinnovation of new RNA-binding domains. The identification of these RNA-bindingdomains may throw light on the emergence of eukaryote-specific systems of RNAmetabolism. RESULTS: Using sensitive sequence profile searches, homology-basedfold recognition and sequence-structure superpositions, we identified novel,divergent versions of the Sm domain in the Scd6p family of proteins. This family of Sm-related domains shares certain features of conventional Sm domains, whichare required for binding RNA, in addition to possessing some unique conservedfeatures. We also show that these proteins contain a second previouslyuncharacterized C-terminal domain, termed the FDF domain (after a conservedsequence motif in this domain). The FDF domain is also found in the fungalDcp3p-like and the animal FLJ22128-like proteins, where it fused to a C-terminal domain of the YjeF-N domain family. In addition to the FDF domains, theFLJ22128-like proteins contain yet another divergent version of the Sm domain at their extreme N-terminus. We show that the YjeF-N domains represent a novelversion of the Rossmann fold that has acquired a set of catalytic residues andstructural features that distinguish them from the conventional dehydrogenases.CONCLUSIONS: Several lines of contextual information suggest that the Scd6pfamily and the Dcp3p-like proteins are conserved components of the eukaryotic RNAmetabolism system. We propose that the novel domains reported here, namely thedivergent versions of the Sm domain and the FDF domain may mediate specificRNA-protein and protein-protein interactions in cytoplasmic ribonucleoproteincomplexes. More specifically, the protein complexes containing Sm-like domains ofthe Scd6p family are predicted to regulate the stability of mRNA encodingproteins involved in cell cycle progression and vesicular assembly. The Dcp3p andFLJ22128 proteins may localize to the cytoplasmic processing bodies and possibly catalyze a specific processing step in the decapping pathway. The explosivediversification of Sm domains appears to have played a role in the emergence ofseveral uniquely eukaryotic ribonucleoprotein complexes, including those involvedin decapping and mRNA stability.