Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864
Letunic et al. (2012) Nucleic Acids Res , doi:10.1093/nar/gkr931

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THUMP

SMART accession number:	SM00981
Description:	The THUMP domain is named after after thiouridine synthases, methylases and PSUSs (PUBMED:11295541). The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains (PUBMED:16343540). It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets (PUBMED:11295541).
Interpro abstract (IPR004114):	The THUMP domain is shared by 4-thiouridine, pseudouridine synthases and RNA methylases [(PUBMED:11295541)] and is probably an RNA-binding domain that adopts an alpha/beta fold similar to that found in the C-terminal domain of translation initiation factor 3 and ribosomal protein S8. The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets [(PUBMED:11295541)]. This domain is found in the thiamine biosynthesis proteins (ThiI) (see IPR003720).
GO function:	RNA binding (GO:0003723)
Family alignment:	View or CHROMA formatCLUSTALW formatMSF formatFASTA formatPIR format

There are 2143 THUMP domains in 2143 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Click on to expand nodes. To display all proteins with a THUMP domain in a specific node, click on it.

  This tree shows only several representative species. The complete taxonomic breakdown of all proteins with THUMP domain is also avaliable.

  Useful shortcuts: Expand all nodes or Collapse tree
  Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes

• Literature (relevant references for this domain)

• Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

  • Waterman DG, Ortiz-Lombardia M, Fogg MJ, Koonin EV, Antson AA
  • Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzymecontaining the predicted RNA-binding THUMP domain.
  • J Mol Biol. 2006; 356: 97-110
  • Display abstract

  • ThiI is an enzyme responsible for the formation of the modified base S(4)U(4-thiouridine) found at position 8 in some prokaryotic tRNAs. This baseacts as a sensitive trigger for the response mechanism to UV exposure,providing protection against its damaging effects. We present the crystalstructure of Bacillus anthracis ThiI in complex with AMP, revealing anextended tripartite architecture in which an N-terminal ferredoxin-likedomain (NFLD) connects the C-terminal catalytic PP-loop pyrophosphatasedomain with a THUMP domain, an ancient predicted RNA-binding domain thatis widespread in all kingdoms of life. We describe the structure of theTHUMP domain, which appears to be unrelated to RNA-binding domains ofknown structure. Mapping the conserved residues of NFLD and the THUMPdomain onto the ThiI structure suggests that these domains jointly formthe tRNA-binding surface. The inaccessibility of U8 in the canonicalL-shaped form of tRNA, and the existence of a glycine-rich linker joiningthe catalytic and RNA-binding moieties of ThiI suggest that structuralchanges may occur in both molecules upon binding.

  • Aravind L, Koonin EV
  • THUMP--a predicted RNA-binding domain shared by 4-thiouridine,pseudouridine synthases and RNA methylases.
  • Trends Biochem Sci. 2001; 26: 215-7
  • Display abstract

  • Sequence profile searches were used to identify an ancient domain inThiI-like thiouridine synthases, conserved RNA methylases, archaealpseudouridine synthases and several uncharacterized proteins. We predictthat this domain is an RNA-binding domain that adopts an alpha/beta foldsimilar to that found in the C-terminal domain of translation initiationfactor 3 and ribosomal protein S8.

• Structure (3D structures containing this domain)

• 3D Structures of THUMP domains in PDB

  PDB code	Main view	Title
  1vbk		Crystal structure of ph1313 from pyrococcus horikoshii ot3
  2c5s		Crystal structure of bacillus anthracis thii, a trna- modifying enzyme containing the predicted rna-binding thump domain
  2dir		Solution structure of the thump domain of thump domain- containing protein 1
  3g8q		A cytidine deaminase edits c-to-u in transfer rnas in archaea
  3k0b		Crystal structure of a predicted n6-adenine-specific dna methylase from listeria monocytogenes str. 4b f2365

• Links (links to other resources describing this domain)

• PFAM	THUMP
  INTERPRO	IPR004114

Send comments to Ivica Letunic