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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 (3,211) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 21,062 85,864 56
Proteins 20,929 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 0.00001779 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0007025 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0003376 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.07302 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.006015 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.006175 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.01345 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) organonitrogen compound metabolic process 0.9926 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.0003828 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.00005874 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.02725 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.9761 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.7096 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.0543 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.5751 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.2149 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.3214 Moderately Informative Inherited
Biological Process (BP) gene expression 0.2641 Moderately Informative Inherited
Biological Process (BP) peptide metabolic process 0.2794 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.1888 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.000254 Informative Direct
Biological Process (BP) proteolysis 0.00002091 Informative Direct
Biological Process (BP) glutamine family amino acid metabolic process 0.0008052 Informative Direct
Biological Process (BP) RNA modification 0.00001325 Informative Direct
Biological Process (BP) ribonucleoprotein complex biogenesis 0.00000000005279 Informative Direct
Biological Process (BP) ncRNA processing 0.000001303 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.000001669 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.4239 Informative Inherited
Biological Process (BP) translational initiation 0.0006017 Highly Informative Direct
Biological Process (BP) rRNA metabolic process 0.00003843 Highly Informative Direct
Biological Process (BP) histone modification 0.0007675 Highly Informative Direct
Biological Process (BP) protein modification by small protein conjugation 0 Highly Informative Direct
Biological Process (BP) macromolecule methylation 0.000000515 Highly Informative Direct
Biological Process (BP) DNA methylation or demethylation 0.000000000131 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.004636 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.000000000004216 Least Informative Direct
Molecular Function (MF) binding 0.9728 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) small molecule binding 0.0001971 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.008172 Moderately Informative Inherited
Molecular Function (MF) protein binding 1 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 0.152 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.6443 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.2366 Moderately Informative Inherited
Molecular Function (MF) zinc ion binding 0.0008594 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.04178 Informative Inherited
Molecular Function (MF) DNA binding 0.8579 Informative Inherited
Molecular Function (MF) RNA binding 0.2653 Informative Inherited
Molecular Function (MF) ATPase activity 0.2111 Informative Inherited
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 0.8948 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) translation factor activity, RNA binding 0.0003183 Highly Informative Direct
Molecular Function (MF) ubiquitin-like protein transferase activity 0.0001095 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding 0.3484 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.0003454 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.1127 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.03507 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.0000003726 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.05658 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.002046 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 0.0001295 Informative Direct
Cellular Component (CC) microbody 0.0002337 Informative Direct
Cellular Component (CC) chromosome 0.004555 Informative Inherited
Cellular Component (CC) chromatin 0.00007684 Highly Informative Direct
Cellular Component (CC) nucleolus 0.0009723 Highly Informative Direct
Cellular Component (CC) nuclear chromosome 0.0024 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)Abnormal joint morphology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Growth abnormality0Moderately InformativeDirect
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving the skeleton0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of digit0Moderately 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 stage0.8795Least InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage0.9345Least InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage 5 (16-cell)0.0003251Highly 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)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-methyltransferase0.00009668InformativeDirect
Enzyme Commission (EC)Pentosyltransferases0.3477InformativeInherited
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 biosynthesis0.000000000001272Highly InformativeDirect
Biological processGrowth regulation0.000002213Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPeroxisome0.00000000002793InformativeDirect
Cellular componentChromosome0.00009061InformativeDirect
Cellular componentCentromere0.0000000000004596Highly InformativeDirect
DomainTransit peptide0.0002373Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionS-adenosyl-L-methionine0.00000001421InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationHydrolase0.6979Least InformativeInherited
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.00000003927Moderately InformativeDirect
Post-translational modificationSerine protease0InformativeDirect
Post-translational modificationChromatin regulator0.0000000009354InformativeDirect

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 ubiquitination0.000509Moderately InformativeDirect
UniPathway (UP)hydrogen sulfide biosynthesis0.0000000002165InformativeDirect
UniPathway (UP)tRNA modification0.05281InformativeInherited
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 ]