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Nudix superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Nudix [ 55810]
Superfamily:   Nudix [ 55811] (7)
Families:   MutT-like [ 55812] (16)
  MutY C-terminal domain-like [ 103211] (2)
  NADH pyrophosphatase [ 103214]
  IPP isomerase-like [ 64369] (3)
  GDP-mannose mannosyl hydrolase NudD [ 111132]
  BT0354 N-terminal domain-like [ 143772] (2)
  mRNA decapping enzyme-like [ 143777]


Superfamily statistics
Genomes (3,128) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 34,107 197,289 44
Proteins 33,579 193,910 43


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular aromatic compound metabolic process0.00000000098950Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.000000023420Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.00054150.000000008322Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.0000000011150Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.00000000045250Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.15911Least InformativeInherited
Biological Process (BP)primary metabolic process0.018290.0006541Least InformativeInherited
Biological Process (BP)biological regulation11Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)single-organism cellular process0.13870.4253Least InformativeInherited
Biological Process (BP)response to stimulus0.10930.9649Least InformativeInherited
Biological Process (BP)biosynthetic process11Least InformativeInherited
Biological Process (BP)nucleoside phosphate metabolic process0.00009880.0000000000002271Moderately InformativeDirect
Biological Process (BP)cellular response to stress0.000000000068750.0000000008244Moderately InformativeDirect
Biological Process (BP)cellular catabolic process0.0009330.00000000001031Moderately InformativeDirect
Biological Process (BP)single-organism catabolic process0.000000026940.00000000005464Moderately InformativeDirect
Biological Process (BP)purine-containing compound metabolic process0.000032460.000000000003698Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process0.00061080.000000000004278Moderately InformativeDirect
Biological Process (BP)positive regulation of cellular process0.63751Moderately InformativeInherited
Biological Process (BP)regulation of response to stimulus0.12441Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.048681Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process0.20711Moderately InformativeInherited
Biological Process (BP)gene expression0.97211Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.054910.01499Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.016110.0000159Moderately InformativeInherited
Biological Process (BP)lipid metabolic process0.88060.7032Moderately InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.0058530.02835Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.62031Moderately InformativeInherited
Biological Process (BP)DNA metabolic process0.00000000057980.0000000008657InformativeDirect
Biological Process (BP)cellular response to DNA damage stimulus0.00034880.00002807InformativeDirect
Biological Process (BP)nucleobase-containing compound catabolic process0.000000025310InformativeDirect
Biological Process (BP)regulation of cellular component biogenesis0.00051610.0004702InformativeDirect
Biological Process (BP)organophosphate catabolic process00InformativeDirect
Biological Process (BP)carbohydrate derivative catabolic process0.000005710.0000000000225InformativeDirect
Biological Process (BP)negative regulation of gene expression0.0090480.01023InformativeInherited
Biological Process (BP)alcohol metabolic process0.0000065780.00479InformativeInherited
Biological Process (BP)cellular macromolecule catabolic process0.11250.001834InformativeInherited
Biological Process (BP)RNA modification0.00073220.001218InformativeInherited
Biological Process (BP)isoprenoid metabolic process0.0021420.00002963InformativeInherited
Biological Process (BP)isoprenoid biosynthetic process0.00019130.0000001297Highly InformativeDirect
Biological Process (BP)nucleoside triphosphate catabolic process0.00000031210.0000002346Highly InformativeDirect
Biological Process (BP)nucleotide catabolic process0.00000000081930Highly InformativeDirect
Biological Process (BP)deoxyribonucleoside triphosphate metabolic process0.00000048240.00000000007153Highly InformativeDirect
Biological Process (BP)deoxyribonucleotide metabolic process0.00000002570.000000000007595Highly InformativeDirect
Biological Process (BP)deoxyribose phosphate metabolic process0.000000024510Highly InformativeDirect
Biological Process (BP)regulation of DNA metabolic process0.000000012410.0002595Highly InformativeDirect
Biological Process (BP)purine-containing compound catabolic process0.0000000030680Highly InformativeDirect
Biological Process (BP)negative regulation of RNA metabolic process0.0010520.8653Highly InformativeInherited
Biological Process (BP)polyol metabolic process0.032920.09818Highly InformativeInherited
Biological Process (BP)RNA catabolic process0.019990.0000001858Highly InformativeInherited
Biological Process (BP)mRNA processing0.058661Highly InformativeInherited
Biological Process (BP)regulation of cellular response to stress0.00000036660.001903Highly InformativeInherited
Molecular Function (MF)hydrolase activity0.0000000000000027270Least InformativeDirect
Molecular Function (MF)binding0.00087420.9482Least InformativeInherited
Molecular Function (MF)hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides00Moderately InformativeDirect
Molecular Function (MF)metal ion binding0.00000000010930.000000000002322Moderately InformativeDirect
Molecular Function (MF)small molecule binding0.59710.1397Moderately InformativeInherited
Molecular Function (MF)carbohydrate derivative binding0.22270.3571Moderately InformativeInherited
Molecular Function (MF)anion binding11Moderately InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds11Moderately InformativeInherited
Molecular Function (MF)isomerase activity0.040460.006027Moderately InformativeInherited
Molecular Function (MF)nucleic acid binding0.0000000000000013860.01044Moderately InformativeInherited
Molecular Function (MF)magnesium ion binding0.00000000000058840.00000000000001678InformativeDirect
Molecular Function (MF)RNA binding00.00000000001492InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity0.0000014290.00000000001834InformativeDirect
Molecular Function (MF)purine nucleotide binding0.0067210.7807InformativeInherited
Molecular Function (MF)ribonucleotide binding0.0095510.3707InformativeInherited
Molecular Function (MF)purine ribonucleoside triphosphate binding0.0032220.05927InformativeInherited
Molecular Function (MF)phosphatase activity0.9020.993InformativeInherited
Molecular Function (MF)peptidase activity, acting on L-amino acid peptides0.005620.3003InformativeInherited
Molecular Function (MF)metallopeptidase activity0.000000077730.0007735Highly InformativeDirect
Molecular Function (MF)exopeptidase activity0.00000069110.0005766Highly InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity, transposing C=C bonds0.000000000059110Highly InformativeDirect
Molecular Function (MF)nucleoside-diphosphatase activity0.0000017270Highly InformativeDirect
Molecular Function (MF)manganese ion binding0.00000000000081930.0000000000004804Highly InformativeDirect
Molecular Function (MF)nucleoside-triphosphate diphosphatase activity0.000000000079320.000000000000003188Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.02030.005965Least InformativeInherited
Cellular Component (CC)protein complex0.76471Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.95761Least InformativeInherited
Cellular Component (CC)nuclear part0.0082010.8363Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.0071940.313Moderately InformativeInherited
Cellular Component (CC)nucleoplasm part0.02170.4088InformativeInherited

Document: GO annotation of SCOP domains

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 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0006541 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.000000008322 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.9649 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.4253 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.0000000000002271 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0000000008244 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.00000000001031 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.00000000005464 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.000000000003698 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0000159 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.000000000004278 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.1609 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.01157 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.7032 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.02835 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.01499 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.0000000008657 Informative Direct
Biological Process (BP) isoprenoid metabolic process 0.00002963 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.00002807 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.0004702 Informative Direct
Biological Process (BP) organophosphate catabolic process 0 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0.0000000000225 Informative Direct
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.9617 Informative Inherited
Biological Process (BP) alcohol metabolic process 0.00479 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.001834 Informative Inherited
Biological Process (BP) RNA modification 0.001218 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.01023 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.006002 Informative Inherited
Biological Process (BP) RNA catabolic process 0.0000001858 Highly Informative Direct
Biological Process (BP) isoprenoid biosynthetic process 0.0000001297 Highly Informative Direct
Biological Process (BP) nucleoside triphosphate catabolic process 0.0000002346 Highly Informative Direct
Biological Process (BP) nucleotide catabolic process 0 Highly Informative Direct
Biological Process (BP) deoxyribonucleoside triphosphate metabolic process 0.00000000007153 Highly Informative Direct
Biological Process (BP) deoxyribonucleotide metabolic process 0.000000000007595 Highly Informative Direct
Biological Process (BP) coenzyme A metabolic process 0.00000001664 Highly Informative Direct
Biological Process (BP) deoxyribose phosphate metabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.0002595 Highly Informative Direct
Biological Process (BP) purine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.001903 Highly Informative Inherited
Biological Process (BP) negative regulation of RNA metabolic process 0.8653 Highly Informative Inherited
Biological Process (BP) polyol metabolic process 0.09818 Highly Informative Inherited
Biological Process (BP) mRNA processing 1 Highly Informative Inherited
Biological Process (BP) gene silencing 0.008817 Highly Informative Inherited
Biological Process (BP) regulation of gene expression, epigenetic 0.01244 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.9482 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0.000000000002322 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.1397 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.3571 Moderately Informative Inherited
Molecular Function (MF) anion binding 1 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 1 Moderately Informative Inherited
Molecular Function (MF) isomerase activity 0.006027 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.01044 Moderately Informative Inherited
Molecular Function (MF) magnesium ion binding 0.00000000000001678 Informative Direct
Molecular Function (MF) RNA binding 0.00000000001492 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.00000000001834 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.7807 Informative Inherited
Molecular Function (MF) ribonucleotide binding 0.3707 Informative Inherited
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.05927 Informative Inherited
Molecular Function (MF) phosphatase activity 0.993 Informative Inherited
Molecular Function (MF) hydrolase activity, acting on glycosyl bonds 0.815 Informative Inherited
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 0.3003 Informative Inherited
Molecular Function (MF) metallopeptidase activity 0.0007735 Highly Informative Direct
Molecular Function (MF) exopeptidase activity 0.0005766 Highly Informative Direct
Molecular Function (MF) thiolester hydrolase activity 0.0000002335 Highly Informative Direct
Molecular Function (MF) hydrolase activity, hydrolyzing N-glycosyl compounds 0.0000001668 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, transposing C=C bonds 0 Highly Informative Direct
Molecular Function (MF) nucleoside-diphosphatase activity 0 Highly Informative Direct
Molecular Function (MF) manganese ion binding 0.0000000000004804 Highly Informative Direct
Molecular Function (MF) nucleoside-triphosphate diphosphatase activity 0.000000000000003188 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.00001733 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.005965 Least Informative Inherited
Cellular Component (CC) ribosome 0.07433 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.8363 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.313 Moderately Informative Inherited
Cellular Component (CC) large ribosomal subunit 0.0003642 Informative Direct
Cellular Component (CC) ribonucleoprotein granule 0.0000001648 Informative Direct
Cellular Component (CC) microbody 0.0000000000004592 Informative Direct
Cellular Component (CC) nucleoplasm part 0.4088 Informative Inherited
Cellular Component (CC) mitochondrial ribosome 0.001461 Informative Inherited
Cellular Component (CC) P-body 0.00009688 Highly Informative Direct
Cellular Component (CC) mitochondrial large ribosomal subunit 0.00007729 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 acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0Moderately InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Transposing C==C bonds0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism0.9608Moderately InformativeInherited
Biological processSteroid metabolism0.00000000002644InformativeDirect
Biological processLipid biosynthesis0.4456InformativeInherited
Biological processIsoprene biosynthesis0Highly InformativeDirect
Biological processSterol biosynthesis2.442e-16Highly InformativeDirect
Biological processSteroid biosynthesis0.0000000000000168Highly InformativeDirect
Biological processChlorophyll biosynthesis0.00000000001333Highly InformativeDirect
Biological processNonsense-mediated mRNA decay0.0000001012Highly InformativeDirect
Cellular componentPeroxisome0InformativeDirect
Cellular componentHost endoplasmic reticulum0.00002693Highly InformativeDirect
DomainTransit peptide0.0001449Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionNAD0.0000000000001307Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR015797 SSF55811 Protein matches
Abstract MutT is a small bacterial protein (~12-15Kd) involved in the GO system [PubMed1328155] responsible for removing an oxidatively damaged form of guanine (8-hydroxy- guanine or 7,8-dihydro-8-oxoguanine) from DNA and the nucleotide pool. 8-oxo-dGTP is inserted opposite dA and dC residues of template DNA with near equal efficiency, leading to A-T to G-C transversions. MutT specifically degrades 8-oxo-dGTP to the monophosphate, with the concomitant release of pyrophosphate. A short conserved N-terminal region of mutT (designated the MutT domain) is also found in a variety of other prokaryotic, viral and eukaryotic proteins [PubMed8233837, PubMed8170394, PubMed8226881, PubMed10373642].

The generic name `NUDIX hydrolases' (NUcleoside DIphosphate linked to some other moiety X) has been coined for this domain family [PubMed8810257]. The family can be divided into a number of subgroups, of which MutT anti- mutagenic activity represents only one type; most of the rest hydrolyse diverse nucleoside diphosphate derivatives (including ADP-ribose, GDP- mannose, TDP-glucose, NADH, UDP-sugars, dNTP and NTP).


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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

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 31 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 Nudix 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 31 hidden Markov models representing the Nudix 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]