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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 (3,209) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 21,020 85,864 56
Proteins 20,890 82,311 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) nitrogen compound metabolic process 0.000003402 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000005872 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.000007841 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0004713 Least Informative Direct
Biological Process (BP) biosynthetic process 1 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) cellular component organization or biogenesis 0.04362 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.1498 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.09941 Least Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.0000001523 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.1384 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.02716 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.04931 Moderately Informative Inherited
Biological Process (BP) gene expression 0.2679 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.4371 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.6817 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.001249 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.06699 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.5318 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.04445 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.8434 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.9234 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.7877 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.4973 Moderately Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 0 Informative Direct
Biological Process (BP) proteolysis 0.000000001722 Informative Direct
Biological Process (BP) protein catabolic process 0.000000004324 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.00000001208 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0000004152 Informative Direct
Biological Process (BP) RNA modification 0.000001008 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 0.00003386 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.00004364 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.00008528 Informative Direct
Biological Process (BP) chromosome organization 0.000357 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0.0005868 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.0006309 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0.454 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.008726 Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0.00123 Informative Inherited
Biological Process (BP) DNA metabolic process 0.001152 Informative Inherited
Biological Process (BP) RNA processing 0.01013 Informative Inherited
Biological Process (BP) protein ubiquitination 0 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.00000000000006059 Highly Informative Direct
Biological Process (BP) DNA modification 0.00000000001202 Highly Informative Direct
Biological Process (BP) nucleoside bisphosphate biosynthetic process 0.00000001533 Highly Informative Direct
Biological Process (BP) purine nucleoside bisphosphate metabolic process 0.0000001994 Highly Informative Direct
Biological Process (BP) histone modification 0.000488 Highly Informative Direct
Biological Process (BP) purine ribonucleotide biosynthetic process 0.002429 Highly Informative Inherited
Biological Process (BP) ribonucleoside bisphosphate metabolic process 1 Highly Informative Inherited
Biological Process (BP) rRNA processing 0.0109 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.0006645 Least Informative Direct
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0007089 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.2311 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.002611 Moderately Informative Inherited
Molecular Function (MF) cation binding 0.1215 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.3832 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 0.000000011 Informative Direct
Molecular Function (MF) nucleotide binding 0.0002256 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.0002569 Informative Direct
Molecular Function (MF) zinc ion binding 0.000477 Informative Direct
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.01313 Informative Inherited
Molecular Function (MF) peptidase activity 0.02403 Informative Inherited
Molecular Function (MF) nucleoside-triphosphatase activity 0.3113 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) RNA binding 0.08263 Informative Inherited
Molecular Function (MF) adenylyltransferase activity 0.0000000001074 Highly Informative Direct
Molecular Function (MF) small conjugating protein ligase activity 0.0000000002256 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.0000007429 Highly Informative Direct
Molecular Function (MF) methyltransferase activity 0.00004209 Highly Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 0.03176 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.1803 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01416 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.03287 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.000001276 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.03384 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 0.000003941 Informative Direct
Cellular Component (CC) microbody 0.0004122 Informative Direct
Cellular Component (CC) chromosome 0.01646 Informative Inherited
Cellular Component (CC) nuclear chromosome part 0.0004209 Highly Informative Direct
Cellular Component (CC) cullin-RING ubiquitin ligase complex 0.1469 Highly Informative Inherited
Cellular Component (CC) chromatin 0.004541 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

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)preweaning lethality0Moderately InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Glycosyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor1Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Serine endopeptidases0InformativeDirect
Enzyme Commission (EC)Intramolecular transferases (mutases)0InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0.00009749InformativeDirect
Enzyme Commission (EC)Pentosyltransferases0.4004InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a carboxyl group as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Sulfate adenylyltransferase0Highly 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 biosynthesis0.000000000001136Highly InformativeDirect
Biological processGrowth regulation0.00000105Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPeroxisome0.00000000001759InformativeDirect
Cellular componentChromosome0.00006377InformativeDirect
Cellular componentCentromere0.000000000000135Highly InformativeDirect
DomainTransit peptide0.0001146Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionS-adenosyl-L-methionine0.00000001845InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.5102Least InformativeInherited
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.00000008617Moderately InformativeDirect
Post-translational modificationSerine protease0InformativeDirect
Post-translational modificationChromatin regulator0.0000000006727InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)protein ubiquitination0.00000003518Moderately InformativeDirect
UniPathway (UP)tRNA modification1InformativeInherited
UniPathway (UP)archaeosine-tRNA biosynthesis0Highly InformativeDirect

Document: UP 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]