SUPERFAMILY 1.75 HMM library and genome assignments server


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 (3,168) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 20,270 40,263 56
Proteins 20,146 39,942 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) cellular aromatic compound metabolic process 0.0005363 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 7.477e-07 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 8.995e-06 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 2.086e-06 Least Informative Direct
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.07246 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.2142 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.1226 Least Informative Inherited
Biological Process (BP) sulfur compound metabolic process 2.53e-08 Moderately Informative Direct
Biological Process (BP) macromolecule catabolic process 1.214e-05 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.08795 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.02819 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.04302 Moderately Informative Inherited
Biological Process (BP) gene expression 0.398 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.6582 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.3934 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.003617 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.05604 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.4847 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.03273 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.7957 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) organic cyclic compound biosynthetic process 0.8843 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.7626 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.4678 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.0009869 Informative Direct
Biological Process (BP) proteolysis 2.728e-10 Informative Direct
Biological Process (BP) RNA modification 9.727e-07 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 2.47e-07 Informative Direct
Biological Process (BP) protein catabolic process 1.184e-09 Informative Direct
Biological Process (BP) ncRNA metabolic process 6.369e-05 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 3.407e-07 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0.0004581 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.000994 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.0005122 Informative Direct
Biological Process (BP) chromosome organization 0.0003639 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 3.551e-05 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 1.61e-05 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0.4549 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.007572 Informative Inherited
Biological Process (BP) RNA processing 0.003331 Informative Inherited
Biological Process (BP) DNA modification 1.028e-11 Highly Informative Direct
Biological Process (BP) protein ubiquitination 0 Highly Informative Direct
Biological Process (BP) histone modification 0.0003567 Highly Informative Direct
Biological Process (BP) ribonucleoside bisphosphate biosynthetic process 4.637e-11 Highly Informative Direct
Biological Process (BP) purine nucleoside bisphosphate biosynthetic process 2.415e-07 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 4.102e-14 Highly Informative Direct
Biological Process (BP) purine ribonucleotide biosynthetic process 0.001995 Highly Informative Inherited
Biological Process (BP) rRNA processing 0.01268 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0008879 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.2118 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.001927 Moderately Informative Inherited
Molecular Function (MF) cation binding 0.09527 Moderately Informative Inherited
Molecular Function (MF) nucleotide binding 0.0001618 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.0001391 Informative Direct
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 1.267e-08 Informative Direct
Molecular Function (MF) DNA binding 0.9882 Informative Inherited
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.01606 Informative Inherited
Molecular Function (MF) transition metal ion binding 0.02724 Informative Inherited
Molecular Function (MF) peptidase activity 0.02146 Informative Inherited
Molecular Function (MF) nucleoside-triphosphatase activity 0.3036 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 0.1319 Informative Inherited
Molecular Function (MF) small conjugating protein ligase activity 3.252e-10 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 7.858e-07 Highly Informative Direct
Molecular Function (MF) adenylyltransferase activity 3.497e-11 Highly Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 0.02104 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 0.3563 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01853 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.02411 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 6.367e-07 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.02713 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 3.607e-06 Informative Direct
Cellular Component (CC) nucleolus 7.015e-06 Informative Direct
Cellular Component (CC) microbody 0.000358 Informative Direct
Cellular Component (CC) chromosome 0.01391 Informative Inherited
Cellular Component (CC) nuclear chromosome part 0.0003122 Highly Informative Direct
Cellular Component (CC) cullin-RING ubiquitin ligase complex 0.1493 Highly Informative Inherited
Cellular Component (CC) chromatin 0.003911 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)Methyltransferases8.075e-08Moderately 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-methyltransferase1.307e-06InformativeDirect
Enzyme Commission (EC)Sulfate adenylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Endopeptidase La0Highly InformativeDirect
Enzyme Commission (EC)Glutamate 5-kinase0Highly InformativeDirect
Enzyme Commission (EC)Adenylyl-sulfate kinase1.105e-09Highly 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-methyltransferase9.158e-07InformativeDirect
Enzyme Commission (EC)Pentosyltransferases0.4149InformativeInherited
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 biosynthesis1.155e-12Highly InformativeDirect
Biological processGrowth regulation4.589e-07Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPeroxisome2.162e-11InformativeDirect
Cellular componentChromosome5.923e-05InformativeDirect
Cellular componentCentromere1.505e-13Highly InformativeDirect
DomainTransit peptide0.0001012Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionS-adenosyl-L-methionine1.865e-10InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.4974Least InformativeInherited
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase1.276e-07Moderately InformativeDirect
Post-translational modificationSerine protease0InformativeDirect
Post-translational modificationChromatin regulator5.806e-10InformativeDirect

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 ubiquitination1.609e-08Moderately InformativeDirect
UniPathway (UP)energy metabolism0.003653Moderately InformativeInherited
UniPathway (UP)hydrogen sulfide biosynthesis0.0002795InformativeDirect
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 ]