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1016  structures 9162  species 0  interactions 105053  sequences 951  architectures

Family: NUDIX (PF00293)

Summary: NUDIX domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Nudix family". More...

Nudix family Edit Wikipedia article

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

NUDIX domain Provide feedback

No Pfam abstract.

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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000086

The Nudix superfamily is widespread among eukaryotes, bacteria, archaea and viruses and consists mainly of pyrophosphohydrolases that act upon substrates of general structure NUcleoside DIphosphate linked to another moiety, X (NDP-X) to yield NMP plus P-X. Such substrates include (d)NTPs (both canonical and oxidised derivatives), nucleotide sugars and alcohols, dinucleoside polyphosphates (NpnN), dinucleotide coenzymes and capped RNAs. However, phosphohydrolase activity, including activity towards NDPs themselves, and non-nucleotide substrates such as diphosphoinositol polyphosphates (DIPs), 5-phosphoribosyl 1-pyrophosphate (PRPP), thiamine pyrophosphate (TPP) and dihydroneopterin triphosphate (DHNTP) have also been described. Some superfamily members, such as Escherichia coli mutT, have the ability to degrade potentially mutagenic, oxidised nucleotides while others control the levels of metabolic intermediates and signalling compounds. In procaryotes and simple eucaryotes, the number of Nudix genes varies from 0 to over 30, reflecting the metabolic complexity and adaptability of the organism. Nudix hydrolases are typically small proteins, larger ones having additional domains with interactive or other catalytic functions [ PUBMED:16378245 ].

The Nudix domain formed by two beta-sheets packed between alpha-helices [ PUBMED:8810257 , PUBMED:17698004 ]. It can accomodate sequences of different lengths in the connecting loops and in the amtiparallel beta-sheet. Catalysis depends on the conserved 23-amino acid Nudix motif (Nudix box), G-x(5)-E-x(5)-[UA]-x-R-E-x(2)-E-E-x-G-U, where U is an aliphatic, hydrophobic residue. This sequence is located in a loop-helix-loop structural motif and the Glu residues in the core of the motif, R-E-x(2)-E-E, play an important role in binding essential divalent cations [ PUBMED:16378245 ]. The substrate specificity is determined by other residues outside the Nudix box. For example, CoA pyrophosphatases share the NuCoA motif L-L-T-x-R-[SA]-x(3)-R-x(3)-G-x(3)-F-P-G-G that is located N-terminal of the Nudix box and is involved in CoA recognition [ PUBMED:19340986 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan NUDIX (CL0261), which has the following description:

This superfamily contains the NUDIX family and one related family.

The clan contains the following 10 members:

DUF4743 DUF4916 Hexose_dehydrat MRP-L46 NUDIX NUDIX-like NUDIX_2 NUDIX_4 NUDIX_5 Nudix_hydro


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

Representative proteomes UniProt
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

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Representative proteomes UniProt

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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: mutT;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Finn RD
Number in seed: 127
Number in full: 105053
Average length of the domain: 130.60 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 57.68 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 131
Family (HMM) version: 31
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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The tree shows the occurrence of this domain across different species. More...


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the NUDIX domain has been found. There are 1016 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A024RBG1 View 3D Structure Click here
A0A0G2JYZ4 View 3D Structure Click here
A0A0G2K7J8 View 3D Structure Click here
A0A0G2K9B5 View 3D Structure Click here
A0A0G2QC37 View 3D Structure Click here
A0A0P0WGN9 View 3D Structure Click here
A0A0R0EHG3 View 3D Structure Click here
A0A0R0EPX0 View 3D Structure Click here
A0A0R0FR01 View 3D Structure Click here
A0A0R0G8N1 View 3D Structure Click here
A0A0R0GGY3 View 3D Structure Click here
A0A0R0GRC9 View 3D Structure Click here
A0A0R0GTG6 View 3D Structure Click here
A0A0R0I796 View 3D Structure Click here
A0A0R0IVX2 View 3D Structure Click here
A0A0R0J1H1 View 3D Structure Click here
A0A0R0JBP7 View 3D Structure Click here
A0A0R0JPF1 View 3D Structure Click here
A0A0R0JS08 View 3D Structure Click here
A0A0R0K0C4 View 3D Structure Click here
A0A0R0KE69 View 3D Structure Click here
A0A0R0L5J3 View 3D Structure Click here
A0A0R0LDV8 View 3D Structure Click here
A0A0R4IIN8 View 3D Structure Click here
A0A0R4ISD4 View 3D Structure Click here
A0A0R4J4I4 View 3D Structure Click here
A0A1D6E436 View 3D Structure Click here
A0A1D6H9C2 View 3D Structure Click here
A0A1D6HW16 View 3D Structure Click here
A0A1D6HXL6 View 3D Structure Click here
A0A1D6I1Y6 View 3D Structure Click here
A0A1D6LN55 View 3D Structure Click here
A0A1D6LP98 View 3D Structure Click here
A0A1D6LR33 View 3D Structure Click here
A0A1D6LVA3 View 3D Structure Click here
A0A1D6M4E9 View 3D Structure Click here
A0A1D6MJ98 View 3D Structure Click here
A0A1D6NVT0 View 3D Structure Click here
A0A1D6P2Y7 View 3D Structure Click here
A0A1D6P4C1 View 3D Structure Click here