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 (3,210) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 21,057 85,864 56
Proteins 20,925 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 0.000002159 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000004089 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00000519 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0003383 Least Informative Direct
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.1817 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.06603 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.032 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.1842 Least Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.000001503 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.04166 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.05048 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.5105 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.02908 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.6058 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.9723 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.6655 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.6615 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.061 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.06443 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.001989 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.137 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.03469 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.9037 Moderately Informative Inherited
Biological Process (BP) gene expression 0.2624 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.002432 Moderately Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 0 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.000000001014 Informative Direct
Biological Process (BP) proteolysis 0.000000001787 Informative Direct
Biological Process (BP) protein catabolic process 0.0000000045 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0000006383 Informative Direct
Biological Process (BP) RNA modification 0.000001213 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 0.00002954 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.00003175 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.00003493 Informative Direct
Biological Process (BP) chromosome organization 0.0002151 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.0005075 Informative Direct
Biological Process (BP) purine ribonucleotide metabolic process 0.4905 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.001248 Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0.002347 Informative Inherited
Biological Process (BP) RNA processing 0.003653 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.006303 Informative Inherited
Biological Process (BP) protein ubiquitination 0 Highly Informative Direct
Biological Process (BP) ribonucleoside bisphosphate biosynthetic process 0.0000000001101 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.0000002751 Highly Informative Direct
Biological Process (BP) purine nucleoside bisphosphate biosynthetic process 0.0000004177 Highly Informative Direct
Biological Process (BP) histone modification 0.000008863 Highly Informative Direct
Biological Process (BP) DNA modification 0.0003631 Highly Informative Direct
Biological Process (BP) rRNA processing 0.006158 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.0000000002122 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0006847 Moderately Informative Direct
Molecular Function (MF) cation binding 0.1257 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.2547 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.239 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.002349 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) nucleotide binding 0.0002428 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.0003129 Informative Direct
Molecular Function (MF) zinc ion binding 0.0005086 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.06077 Informative Inherited
Molecular Function (MF) DNA binding 0.9881 Informative Inherited
Molecular Function (MF) peptidase activity 0.0258 Informative Inherited
Molecular Function (MF) nucleoside-triphosphatase activity 0.3132 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 1 Informative Inherited
Molecular Function (MF) kinase activity 1 Informative Inherited
Molecular Function (MF) RNA binding 0.1486 Informative Inherited
Molecular Function (MF) adenylyltransferase activity 0.0000000001139 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 0.0000008452 Highly Informative Direct
Molecular Function (MF) methyltransferase activity 0.00004872 Highly Informative Direct
Molecular Function (MF) ubiquitin-protein transferase activity 0.00005473 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding 0.2225 Highly Informative Inherited
Molecular Function (MF) translation factor activity, nucleic acid binding 0.01897 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.1552 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.03487 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.008287 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.0000001607 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.0001651 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.01198 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 0.000007744 Informative Direct
Cellular Component (CC) microbody 0.0004561 Informative Direct
Cellular Component (CC) chromosome 0.01235 Informative Inherited
Cellular Component (CC) chromatin 0.00004704 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.0007947 Highly Informative Direct

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-methyltransferase0.0000975InformativeDirect
Enzyme Commission (EC)Pentosyltransferases0.4018InformativeInherited
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 biosynthesis0.000000000001135Highly InformativeDirect
Biological processGrowth regulation0.000001046Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPeroxisome0.00000000001806InformativeDirect
Cellular componentChromosome0.00006376InformativeDirect
Cellular componentCentromere0.0000000000001388Highly InformativeDirect
DomainTransit peptide0.0001193Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionS-adenosyl-L-methionine0.00000001685InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.5434Least InformativeInherited
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.00000008109Moderately InformativeDirect
Post-translational modificationSerine protease0InformativeDirect
Post-translational modificationChromatin regulator0.0000000008219InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0Least InformativeDirect
UniPathway (UP)biopolymer metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)energy metabolism0Moderately InformativeDirect
UniPathway (UP)protein ubiquitination0.0003063Moderately InformativeDirect
UniPathway (UP)hydrogen sulfide biosynthesis0.0000000008373InformativeDirect
UniPathway (UP)tRNA modification0.05537InformativeInherited
UniPathway (UP)L-proline biosynthesis0Highly InformativeDirect
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 ]