SMART: PUA domain annotation

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

There are 1259 PUA domains in 1259 proteins in SMART's nrdb database.

Click on the following links for more information.

Evolution (species in which this domain is found)
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This tree shows only several representative species. The complete taxonomic breakdown of all proteins with PUA domain is also avaliable.

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Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes
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 (SRS)(SMART) OMIM:300126: Dyskeratosis congenita-1
OMIM:305000: Hoyeraal-Hreidarsson syndrome
OMIM:300240:
Metabolism (metabolic pathways involving proteins which contain this domain)

Structure (3D structures containing this domain)

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

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
3d79
3hax
3hay
3hjw
3hjy

Links (links to other resources describing this domain)
INTERPRO IPR002478