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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 (3,215) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 21,098 85,864 56
Proteins 20,965 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) macromolecule metabolic process 0.00004603 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00005285 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00003122 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.00893 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.003792 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.08595 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.00352 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) cellular component organization or biogenesis 0.004204 Least Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.0001184 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.4025 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.06569 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.8193 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate biosynthetic process 0.06486 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.03771 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.1287 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.8444 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.1521 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.6766 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.6381 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.007756 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.3372 Moderately Informative Inherited
Biological Process (BP) gene expression 0.1106 Moderately Informative Inherited
Biological Process (BP) peptide metabolic process 0.7703 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.2891 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.0001928 Informative Direct
Biological Process (BP) proteolysis 0.000008144 Informative Direct
Biological Process (BP) glutamine family amino acid metabolic process 0.0008409 Informative Direct
Biological Process (BP) RNA modification 0.000002571 Informative Direct
Biological Process (BP) ncRNA processing 0.0000002422 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.000002012 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.0005761 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.0009479 Informative Direct
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.5402 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.01362 Informative Inherited
Biological Process (BP) chromosome organization 0.01336 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.003552 Informative Inherited
Biological Process (BP) translational initiation 0.0005195 Highly Informative Direct
Biological Process (BP) rRNA metabolic process 0.0009583 Highly Informative Direct
Biological Process (BP) histone modification 0.0005168 Highly Informative Direct
Biological Process (BP) protein modification by small protein conjugation 0 Highly Informative Direct
Biological Process (BP) ribonucleoside bisphosphate biosynthetic process 0.00000000792 Highly Informative Direct
Biological Process (BP) purine nucleoside bisphosphate biosynthetic process 0.00000000792 Highly Informative Direct
Biological Process (BP) macromolecule methylation 0.0000006322 Highly Informative Direct
Biological Process (BP) DNA methylation or demethylation 0.0000000001302 Highly Informative Direct
Biological Process (BP) proteolysis involved in cellular protein catabolic process 0.0001904 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.005563 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.000000000003612 Least Informative Direct
Molecular Function (MF) binding 0.8731 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) small molecule binding 0.0000474 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.04111 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.7066 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.1206 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.23 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.6559 Moderately Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) DNA binding 0.9989 Informative Inherited
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.04598 Informative Inherited
Molecular Function (MF) purine nucleotide binding 1 Informative Inherited
Molecular Function (MF) ribonucleotide binding 0.8523 Informative Inherited
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.2889 Informative Inherited
Molecular Function (MF) ATPase activity 0.2241 Informative Inherited
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 0.9007 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 0.1454 Informative Inherited
Molecular Function (MF) ATP binding 0.000889 Highly Informative Direct
Molecular Function (MF) translation factor activity, RNA binding 0.0006236 Highly Informative Direct
Molecular Function (MF) ubiquitin-like protein transferase activity 0.0001302 Highly Informative Direct
Molecular Function (MF) double-stranded DNA binding 0.1368 Highly Informative Inherited
Molecular Function (MF) sequence-specific DNA binding 0.4902 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.0003618 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) macromolecular complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.2166 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.03958 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.000001461 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.04357 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.002858 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 0.0001568 Informative Direct
Cellular Component (CC) microbody 0.0003027 Informative Direct
Cellular Component (CC) plastid 0.02296 Informative Inherited
Cellular Component (CC) chromosome 0.0369 Informative Inherited
Cellular Component (CC) chromatin 0.008398 Highly Informative Inherited
Cellular Component (CC) nuclear chromosome part 0.006646 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

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the eye0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of limbs0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the vertebral column0Moderately InformativeDirect
Phenotypic Abnormality (PA)Growth abnormality0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormal genital system morphology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of body height0InformativeDirect
Phenotypic Abnormality (PA)Growth delay0InformativeDirect

Document: HP 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)gonad0Least InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage0.8792Least InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage0.9344Least InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage 5 (16-cell)0.0003135Highly InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptidases)0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Acyltransferases1Moderately 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 transferases0InformativeDirect
Enzyme Commission (EC)Histone-lysine N-methyltransferase0.0001017InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.0001871InformativeDirect
Enzyme Commission (EC)Pentosyltransferases0.4218InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a carboxy 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 biosynthesis0.000000000002405Highly InformativeDirect
Biological processGrowth regulation0.000002706Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPeroxisome0.00000000003161InformativeDirect
Cellular componentChromosome0.0001187InformativeDirect
Cellular componentCentromere0.0000000000005758Highly InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionS-adenosyl-L-methionine0.000007282InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.4268Least InformativeInherited
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.00000008149Moderately InformativeDirect
Post-translational modificationSerine protease0InformativeDirect
Post-translational modificationChromatin regulator0.0000000004286InformativeDirect

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 ubiquitination0.0005499Moderately InformativeDirect
UniPathway (UP)hydrogen sulfide biosynthesis0.0000000001211InformativeDirect
UniPathway (UP)tRNA modification0.04972InformativeInherited
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) · Human Phenotype (HP) · 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) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]