SUPERFAMILY 1.75 HMM library and genome assignments server

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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 2018_03 genome PDB chains (SCOP 1.75)
Domains 34,107 259,735 44
Proteins 33,579 255,481 43


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

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

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)nervous system disease0.1559Least InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.03063Moderately InformativeInherited
Disease Ontology (DO)motor neuron disease0.0002231InformativeDirect
Disease Ontology (DO)lateral sclerosis0.00003772Highly InformativeDirect
Disease Ontology (DO)amyotrophic lateral sclerosis0.0001305Highly InformativeDirect

Document: DO 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) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Glycosylases1Moderately InformativeInherited
Enzyme Commission (EC)In phosphorus-containing anhydrides0InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0InformativeDirect
Enzyme Commission (EC)Hydrolyzing N-glycosyl compounds0.000000002379InformativeDirect
Enzyme Commission (EC)Transposing C=C bonds0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Post-translational modificationHydrolase0Least 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 · Enzyme Commission (EC) · Disease Ontology (DO) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 · Enzyme Commission (EC) · Disease Ontology (DO) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]