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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]


Superfamily statistics
Genomes (3,216) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 21,108 98,687 56
Proteins 20,975 98,357 56


Functional annotation
General category Regulation
Detailed category RNA binding, metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) organic cyclic compound metabolic process 0.00002939 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0000471 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0000542 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.003448 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.003261 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.08799 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.00943 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.003173 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.0001044 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.3983 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.8463 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.03638 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.6683 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.1486 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.06156 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.009059 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.6512 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.3363 Moderately Informative Inherited
Biological Process (BP) gene expression 0.1158 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.291 Moderately Informative Inherited
Biological Process (BP) peptide metabolic process 0.766 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.8394 Moderately Informative Inherited
Biological Process (BP) organophosphate biosynthetic process 0.06228 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.1261 Moderately Informative Inherited
Biological Process (BP) ncRNA processing 0.0000001943 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.000002044 Informative Direct
Biological Process (BP) RNA modification 0.000002155 Informative Direct
Biological Process (BP) proteolysis 0.000005137 Informative Direct
Biological Process (BP) DNA metabolic process 0.0001599 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.0005524 Informative Direct
Biological Process (BP) glutamine family amino acid metabolic process 0.000855 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.0009254 Informative Direct
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.5541 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.01314 Informative Inherited
Biological Process (BP) chromosome organization 0.01299 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.003385 Informative Inherited
Biological Process (BP) protein modification by small protein conjugation 0 Highly Informative Direct
Biological Process (BP) DNA methylation or demethylation 0.000000000113 Highly Informative Direct
Biological Process (BP) ribonucleoside bisphosphate biosynthetic process 0.000000006947 Highly Informative Direct
Biological Process (BP) purine nucleoside bisphosphate biosynthetic process 0.000000006947 Highly Informative Direct
Biological Process (BP) cellular protein catabolic process 0.00000001423 Highly Informative Direct
Biological Process (BP) macromolecule methylation 0.0000005002 Highly Informative Direct
Biological Process (BP) histone modification 0.0004669 Highly Informative Direct
Biological Process (BP) translational initiation 0.0004826 Highly Informative Direct
Biological Process (BP) rRNA metabolic process 0.0009255 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.005076 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.00000000000403 Least Informative Direct
Molecular Function (MF) binding 0.9328 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) small molecule binding 0.00004364 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.04817 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.09251 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.6926 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.2323 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.6555 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.04382 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) RNA binding 0.1251 Informative Inherited
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.2732 Informative Inherited
Molecular Function (MF) ribonucleotide binding 0.9088 Informative Inherited
Molecular Function (MF) purine nucleotide binding 1 Informative Inherited
Molecular Function (MF) ATPase activity 0.2249 Informative Inherited
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 0.8922 Informative Inherited
Molecular Function (MF) kinase activity 1 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 1 Informative Inherited
Molecular Function (MF) ubiquitin-like protein transferase activity 0.0001271 Highly Informative Direct
Molecular Function (MF) translation factor activity, RNA binding 0.0005451 Highly Informative Direct
Molecular Function (MF) ATP binding 0.0008143 Highly Informative Direct
Molecular Function (MF) double-stranded DNA binding 0.1617 Highly Informative Inherited
Molecular Function (MF) sequence-specific DNA binding 0.528 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.0002657 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.0341 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.2673 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.000002713 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.005559 Moderately Informative Inherited
Cellular Component (CC) transferase complex 0.03248 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 0.0001498 Informative Direct
Cellular Component (CC) microbody 0.0003093 Informative Direct
Cellular Component (CC) plastid 0.02218 Informative Inherited
Cellular Component (CC) chromosome 0.04303 Informative Inherited
Cellular Component (CC) chromatin 0.008807 Highly Informative Inherited
Cellular Component (CC) nuclear chromosome part 0.005672 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups1Least InformativeInherited
Enzyme Commission (EC)Serine endopeptidases0Moderately InformativeDirect
Enzyme Commission (EC)Methyltransferases0.00000008075Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep1Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a carboxyl group as accep0InformativeDirect
Enzyme Commission (EC)Transferring other groups0InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0.000001307InformativeDirect
Enzyme Commission (EC)Sulfate adenylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Endopeptidase La0Highly InformativeDirect
Enzyme Commission (EC)Glutamate 5-kinase0Highly InformativeDirect
Enzyme Commission (EC)Adenylyl-sulfate kinase0.000000001105Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processStress response0InformativeDirect
Biological processrRNA processing0InformativeDirect
Biological processtRNA processing0InformativeDirect
Biological processCysteine biosynthesis0.000000000002881Highly InformativeDirect
Biological processGrowth regulation0.000002802Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPeroxisome0.00000000003079InformativeDirect
Cellular componentChromosome0.0001189InformativeDirect
Cellular componentCentromere0.000000000000595Highly InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionS-adenosyl-L-methionine0.000007226InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.4225Least InformativeInherited
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.00000007612Moderately InformativeDirect
Post-translational modificationSerine protease0InformativeDirect
Post-translational modificationChromatin regulator0.0000000004142InformativeDirect

Document: KW annotation of SCOP domains

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 [PubMed11157739].
  • Several bacterial hypothetical proteins, such as the N-terminal domain of YggJ [PubMed14517985].

The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found [PubMed10093218]. 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


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 38 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a PUA domain-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 38 hidden Markov models representing the PUA domain-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]