PUA domain-like superfamily

SCOP classification

• Root: SCOP hierarchy in SUPERFAMILY [ 0] (11)
• Class: All beta proteins [ 48724] (174)
• Fold: PUA domain-like [ 88696]
• Superfamily: PUA domain-like [ 88697] (13)
• Families:
  • PUA domain [ 88698] (6)
  • ATP sulfurylase N-terminal domain [ 63801]
  • YggJ N-terminal domain-like [ 89451] (3)
  • Hypothetical protein EF3133 [ 110339]
  • Hypothetical protein TTHA0113 [ 117348]
  • ProFAR isomerase associated domain [ 117351] (2)
  • yqfB-like [ 117356]
  • Atu2648/PH1033-like [ 141703] (6)
  • Hypothetical RNA methyltransferase domain (HRMD) [ 141716] (3)
  • LON domain-like [ 141723] (2)
  • PrgU-like [ 159365]
  • SRA domain-like [ 159368]
  • YtmB-like [ 159372]

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Superfamily statistics

	Genomes (3,218)	Uniprot 2018_03 genome	PDB chains (SCOP 1.75)
Domains	21,175	130,405	56
Proteins	21,042	129,959	56

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Functional annotation

• General category: Regulation
• Detailed category: RNA binding, metabolism and transport

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Enzyme Commission (EC)

Highlighted in gray are those with FDR_all>0.001

	EC term	FDR (all)	IC level	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Transferases	0	0	--	DIRECT
Enzyme Commission (EC)	Intramolecular transferases (mutases)	0	1.259	--	DIRECT
Enzyme Commission (EC)	23S rRNA (cytosine(1962)-C(5))-methyltransferase	0	2.259	--	DIRECT
Enzyme Commission (EC)	Transferring phosphorous-containing groups	0	0.2175	--	DIRECT
Enzyme Commission (EC)	16S rRNA (uracil(1498)-N(3))-methyltransferase	0	2.259	--	DIRECT
Enzyme Commission (EC)	tRNA pseudouridine(55) synthase	0	2.56	--	DIRECT
Enzyme Commission (EC)	Hydrolases	1	0.04271	--	INHERITED FROM: Acting on peptide bonds (peptide hydrolases) || Endopeptidase La || Serine endopeptidases
Enzyme Commission (EC)	Acting on peptide bonds (peptide hydrolases)	0	0.5513	Least Informative	DIRECT
Enzyme Commission (EC)	Isomerases	0	0.5914	Least Informative	DIRECT
Enzyme Commission (EC)	Nucleotidyltransferases	1	0.6105	Least Informative	INHERITED FROM: Sulfate adenylyltransferase
Enzyme Commission (EC)	Transferring one-carbon groups	1	0.7211	Least Informative	INHERITED FROM: Methyltransferases || Histone-lysine N-methyltransferase || 23S rRNA (cytosine(1962)-C(5))-methyltransferase || 16S rRNA (uracil(1498)-N(3))-methyltransferase
Enzyme Commission (EC)	Serine endopeptidases	0	0.9917	Moderately Informative	DIRECT
Enzyme Commission (EC)	Methyltransferases	0.00000008075	0.8609	Moderately Informative	DIRECT
Enzyme Commission (EC)	Phosphotransferases with an alcohol group as accep	1	0.8195	Moderately Informative	INHERITED FROM: Adenylyl-sulfate kinase
Enzyme Commission (EC)	Phosphotransferases with a carboxyl group as accep	0	1.657	Informative	DIRECT
Enzyme Commission (EC)	Transferring other groups	0	1.519	Informative	DIRECT
Enzyme Commission (EC)	Histone-lysine N-methyltransferase	0.000001307	1.384	Informative	DIRECT
Enzyme Commission (EC)	Sulfate adenylyltransferase	0	1.782	Highly Informative	DIRECT
Enzyme Commission (EC)	Endopeptidase La	0	2.083	Highly Informative	DIRECT
Enzyme Commission (EC)	Glutamate 5-kinase	0	2.083	Highly Informative	DIRECT
Enzyme Commission (EC)	Adenylyl-sulfate kinase	0.000000001105	1.958	Highly Informative	DIRECT

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Human Phenotype (HP)

Highlighted in gray are those with FDR_all>0.001

	HP term	FDR (all)	IC level	SDHP level	Annotation (direct or inherited)
Phenotypic Abnormality (PA)	Abnormality of the skeletal system	0	0.4621	--	DIRECT
Phenotypic Abnormality (PA)	Abnormal axial skeleton morphology	0	0.7344	--	DIRECT
Phenotypic Abnormality (PA)	Abnormality of skeletal morphology	0	0.472	Least Informative	DIRECT

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Worm Phenotype (WP)

Highlighted in gray are those with FDR_all>0.001

	WP term	FDR (all)	IC level	SDWP level	Annotation (direct or inherited)
Worm Phenotype (WP)	postembryonic development variant	0	0.3347	--	DIRECT
Worm Phenotype (WP)	embryonic lethal	0	0.07108	--	DIRECT
Worm Phenotype (WP)	lethal	0	0.01121	--	DIRECT
Worm Phenotype (WP)	fertility variant	0	0.08329	--	DIRECT
Worm Phenotype (WP)	development variant	0	0.001706	--	DIRECT
Worm Phenotype (WP)	morphology variant	0	0.06117	--	DIRECT
Worm Phenotype (WP)	organism development variant	0	0.004279	--	DIRECT
Worm Phenotype (WP)	organism morphology variant	0	0.2011	--	DIRECT
Worm Phenotype (WP)	organ system physiology variant	0	0.05921	--	DIRECT
Worm Phenotype (WP)	organism physiology variant	0	0.1405	--	DIRECT
Worm Phenotype (WP)	reproductive system physiology variant	0	0.07209	--	DIRECT
Worm Phenotype (WP)	maternal sterile	0	0.171	--	DIRECT
Worm Phenotype (WP)	hermaphrodite sterile	0	0.1685	--	DIRECT
Worm Phenotype (WP)	embryonic development variant	0	0.06709	--	DIRECT
Worm Phenotype (WP)	hermaphrodite fertility variant	0	0.1278	--	DIRECT
Worm Phenotype (WP)	hermaphrodite fertility reduced	0	0.1672	--	DIRECT
Worm Phenotype (WP)	fertility reduced	0	0.09267	--	DIRECT
Worm Phenotype (WP)	physiology variant	1	0	--	INHERITED FROM: hermaphrodite fertility variant || reproductive system physiology variant || lethal || organism physiology variant || development variant || hermaphrodite sterile || hermaphrodite fertility reduced || embryonic development variant || embryonic lethal || fertility variant || postembryonic development variant || organ system physiology variant || maternal sterile || organism development variant || fertility reduced
Worm Phenotype (WP)	sterile	1	0.161	--	INHERITED FROM: hermaphrodite sterile || maternal sterile

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Yeast Phenotype (YP)

Highlighted in gray are those with FDR_all>0.001

	YP term	FDR (all)	IC level	SDYP level	Annotation (direct or inherited)
Yeast Phenotype (YP)	cellular processes	0	0.1328	--	DIRECT

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Xenopus Anatomy (XA)

Highlighted in gray are those with FDR_all>0.001

	XA term	FDR (all)	IC level	SDXA level	Annotation (direct or inherited)
Xenopus ANatomical entity (XAN)	anatomical structure	0	0	--	DIRECT
Xenopus ANatomical entity (XAN)	multicellular anatomical structure	0	0.1217	--	DIRECT
Xenopus ANatomical entity (XAN)	whole organism	1	0.09747	--	INHERITED FROM: multicellular anatomical structure
Xenopus DEvelopment stage (XDE)	NF stage	0	0.02327	--	DIRECT

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Enzyme Commission (EC)

Highlighted in gray are those with FDR_all>0.001

	EC term	FDR (all)	IC level	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Transferases	0	0.3035	--	DIRECT
Enzyme Commission (EC)	23S rRNA (cytosine(1962)-C(5))-methyltransferase	0	2.651	--	DIRECT
Enzyme Commission (EC)	16S rRNA (uracil(1498)-N(3))-methyltransferase	0	2.651	--	DIRECT
Enzyme Commission (EC)	tRNA-guanine(15) transglycosylase	0	2.475	--	DIRECT
Enzyme Commission (EC)	Glutamate 5-kinase	0	2.475	--	DIRECT
Enzyme Commission (EC)	Endopeptidase La	0	2.475	--	DIRECT
Enzyme Commission (EC)	Transferring other groups	0	1.673	--	DIRECT
Enzyme Commission (EC)	tRNA pseudouridine(55) synthase	0	2.651	--	DIRECT
Enzyme Commission (EC)	Adenylyl-sulfate kinase	0.000000001164	2.35	--	DIRECT
Enzyme Commission (EC)	Methyltransferases	0.0003359	1.181	--	DIRECT
Enzyme Commission (EC)	Acyltransferases	1	0.8446	--	INHERITED FROM: RING-type E3 ubiquitin transferase
Enzyme Commission (EC)	Transferring phosphorus-containing groups	0	0.5453	Least Informative	DIRECT
Enzyme Commission (EC)	Hydrolases	0.719	0.3541	Least Informative	INHERITED FROM: Serine endopeptidases || Acting on peptide bonds (peptidases) || Endopeptidase La
Enzyme Commission (EC)	Acting on peptide bonds (peptidases)	0	0.8949	Moderately Informative	DIRECT
Enzyme Commission (EC)	Isomerases	0	0.8446	Moderately Informative	DIRECT
Enzyme Commission (EC)	Aminoacyltransferases	0.09541	1.166	Moderately Informative	INHERITED FROM: RING-type E3 ubiquitin transferase
Enzyme Commission (EC)	Transferring one-carbon groups	1	1.054	Moderately Informative	INHERITED FROM: 23S rRNA (cytosine(1962)-C(5))-methyltransferase || Methyltransferases || 16S rRNA (uracil(1498)-N(3))-methyltransferase
Enzyme Commission (EC)	Glycosyltransferases	1	1.204	Moderately Informative	INHERITED FROM: tRNA-guanine(15) transglycosylase
Enzyme Commission (EC)	Phosphotransferases with an alcohol group as acceptor	1	1.119	Moderately Informative	INHERITED FROM: Adenylyl-sulfate kinase
Enzyme Commission (EC)	Nucleotidyltransferases	1	0.9432	Moderately Informative	INHERITED FROM: Sulfate adenylyltransferase
Enzyme Commission (EC)	Serine endopeptidases	0	1.35	Informative	DIRECT
Enzyme Commission (EC)	Intramolecular transferases	0	1.408	Informative	DIRECT
Enzyme Commission (EC)	RING-type E3 ubiquitin transferase	0.0006178	1.384	Informative	DIRECT
Enzyme Commission (EC)	Pentosyltransferases	0.5143	1.447	Informative	INHERITED FROM: tRNA-guanine(15) transglycosylase
Enzyme Commission (EC)	Phosphotransferases with a carboxy group as acceptor	0	2.049	Highly Informative	DIRECT
Enzyme Commission (EC)	Sulfate adenylyltransferase	0	2.174	Highly Informative	DIRECT

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InterPro annotation

• Cross references: IPR015947 SSF88697 Protein matches
• Abstract:

  This entry represents domains with a PUA-like structure, consisting of a pseudo-barrel composed of mixed folded sheets of five strands. This structural motif is found in:

  • PUA-containing proteins.
  • The N-terminal of ATP sulphurylases, which contains extra structures, some similar to the PK beta-barrel domain [11157739].
  • Several bacterial hypothetical proteins, such as the N-terminal domain of YggJ [14517985].

  The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found [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 []. 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. PUA motifs are involved in dyskeratosis congenita and cancer, pointing to links between RNA metabolism and human diseases.

InterPro database

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