Letunic et al. (2017) Nucleic Acids Res doi: 10.1093/nar/gkx922
Letunic et al. (2020) Nucleic Acids Res doi: 10.1093/nar/gkaa937

• HOME
• SETUP
• FAQ
• ABOUT
• GLOSSARY
• WHAT'S NEW
• FEEDBACK

PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase

SMART accession number:	SM00359
Description:	-
Interpro abstract (IPR002478):	The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found [ (PUBMED:10093218) ]. PUA is a highly conserved RNA-binding motif found in a wide range of archaeal, bacterial and eukaryotic proteins, including enzymes that catalyse tRNA and rRNA post-transcriptional modifications, proteins involved in ribosome biogenesis and translation, as well as in enzymes involved in proline biosynthesis [ (PUBMED:16793063) (PUBMED:16407303) ]. The structures of several PUA-RNA complexes reveal a common RNA recognition surface, but also some versatility in the way in which the motif binds to RNA [ (PUBMED:17803682) ]. PUA motifs are involved in dyskeratosis congenita and cancer, pointing to links between RNA metabolism and human diseases [ (PUBMED:16943774) ].
GO function:	RNA binding (GO:0003723)
Family alignment:	View or CHROMA formatHMM/Web logoCLUSTALW formatMSF formatFASTA formatPIR format

There are 27311 PUA domains in 27309 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Taxonomic distribution of proteins containing PUA domain.

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

  Click on the protein counts, or double click on taxonomic names to display all proteins containing PUA domain in the selected taxonomic class.

• Cellular role (predicted cellular role)

• Binding / catalysis: RNA-binding

• Literature (relevant references for this domain)

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

  • Aravind L, Koonin EV
  • Novel predicted RNA-binding domains associated with the translation machinery.
  • J Mol Evol. 1999; 48: 291-302
  • Display abstract

  • Two previously undetected domains were identified in a variety of RNA-binding proteins, particularly RNA-modifying enzymes, using methods for sequence profile analysis. A small domain consisting of 60-65 amino acid residues was detected in the ribosomal protein S4, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. Another novel domain, designated PUA domain, after PseudoUridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes. We propose that the S4 domain and the PUA domain bind RNA molecules with complex folded structures, adding to the growing collection of nucleic acid-binding domains associated with DNA and RNA modification enzymes. The evolution of the translation machinery components containing the S4, PUA, and SUI1 domains must have included several events of lateral gene transfer and gene loss as well as lineage-specific domain fusions.

• Disease (disease genes where sequence variants are found in this domain)

• SwissProt sequences and OMIM curated human diseases associated with missense mutations within the PUA domain.

  Protein	Disease
  H/ACA ribonucleoprotein complex subunit 4 (O60832) (SMART)	OMIM:300126: Dyskeratosis congenita-1 OMIM:305000: Hoyeraal-Hreidarsson syndrome OMIM:300240:

• Metabolism (metabolic pathways involving proteins which contain this domain)

• Click the image to view the interactive version of the map in iPath

  % proteins involved KEGG pathway ID Description 84.48 map00220 Urea cycle and metabolism of amino groups 3.58 map00240 Pyrimidine metabolism 1.79 map00380 Tryptophan metabolism 1.79 map00450 Selenoamino acid metabolism 1.49 map00350 Tyrosine metabolism 1.49 map00440 Aminophosphonate metabolism 1.49 map00150 Androgen and estrogen metabolism 1.49 map00626 Naphthalene and anthracene degradation 1.49 map00340 Histidine metabolism 0.60 map00920 Sulfur metabolism 0.30 map00230 Purine metabolism This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with PUA domain which could be assigned to a KEGG orthologous group, and not all proteins containing PUA domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of PUA domains in PDB

  PDB code	Main view	Title
  1iq8		Crystal Structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii
  1it7		Crystal structure of archaeosine tRNA-guanine transglycosylase complexed with guanine
  1it8		Crystal structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii complexed with archaeosine precursor, preQ0
  1j2b		Crystal Structure Of Archaeosine tRNA-Guanine Transglycosylase Complexed With lambda-form tRNA(Val)
  1q7h		Structure of a Conserved PUA Domain Protein from Thermoplasma acidophilum
  1r3e		Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit
  1sqw		Crystal structure of KD93, a novel protein expressed in the human pro
  1t5y		Crystal Structure of Northeast Structural Genomics Consortium Target HR2118: A Human Homolog of Saccharomyces cerevisiae Nip7p
  1ze1		Conformational Change of Pseudouridine 55 Synthase upon Its Association with RNA Substrate
  1ze2		Conformational change of pseudouridine 55 synthase upon its association with RNA substrate
  1zs7		The structure of gene product APE0525 from Aeropyrum pernix
  2ab4		Dissecting the Roles of a Strictly Conserved Tyrosine in Substrate Recognition and Catalysis by Pseudouridine 55 Synthase
  2apo		Crystal Structure of the Methanococcus jannaschii Cbf5 Nop10 Complex
  2as0		Crystal Structure of PH1915 (APC 5817): A Hypothetical RNA Methyltransferase
  2aus		Crystal structure of the archaeal box H/ACA sRNP Nop10-Cbf5 complex
  2cx0		Crystal structure of a PUA domain (APE0525) from the Aeropyrum pernix K1 (sulfate complex)
  2cx1		Crystal structure of a PUA domain (APE0525) from the Aeropyrum pernix K1 (tartrate complex)
  2ey4		Crystal Structure of a Cbf5-Nop10-Gar1 Complex
  2hvy		Crystal structure of an H/ACA box RNP from Pyrococcus furiosus
  2j5t		Glutamate 5-kinase from Escherichia coli complexed with glutamate
  2j5v		GLUTAMATE 5-KINASE FROM ESCHERICHIA COLI COMPLEXED WITH GLUTAMYL-5-PHOSPHATE AND PYROGLUTAMIC ACID
  2q07		Crystal structure of AF0587, a protein of unknown function
  2rfk		Substrate RNA Positioning in the Archaeal H/ACA Ribonucleoprotein Complex
  3c0k		Crystal Structure of a ribosomal RNA methyltranferase
  3d79		Crystal structure of hypothetical protein PH0734.1 from hyperthermophilic archaea Pyrococcus horikoshii OT3
  3hax		Crystal structure of a substrate-bound Gar1-minus H/ACA RNP from Pyrococcus furiosus
  3hay		Crystal structure of a substrate-bound full H/ACA RNP from Pyrococcus furiosus
  3hjw		Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA
  3hjy		Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA
  3lwo		Structure of H/ACA RNP bound to a substrate RNA containing 5BrU
  3lwp		Structure of H/ACA RNP bound to a substrate RNA containing 5BrdU
  3lwq		Structure of H/ACA RNP bound to a substrate RNA containing 3MU
  3lwr		Structure of H/ACA RNP bound to a substrate RNA containing 4SU
  3lwv		Structure of H/ACA RNP bound to a substrate RNA containing 2'-deoxyuridine
  3mqk		Cbf5-Nop10-Gar1 complex binding with 17mer RNA containing ACA trinucleotide
  3r90		Crystal structure of Malignant T cell-amplified sequence 1 protein
  3u28		Crystal structure of a Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae
  3uai		Structure of the Shq1-Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae
  3zv0		Structure of the SHQ1P-CBF5P complex
  4dmg		Thermus thermophilus m5C1942 methyltransferase RlmO
  4q1t		Crystal structure of a glutamate 5-kinase from Burkholderia thailandensis

• Links (links to other resources describing this domain)

• INTERPRO	IPR002478

Send comments to Ivica Letunic