!!

Powering down the Pfam website
On October 5th, we will start redirecting the traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will be available at pfam-legacy.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in our blog post.

Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
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

Redirect to:

  • From a page move: This is a redirect from a page that has been moved (renamed). This page was kept as a redirect to avoid breaking links, both internal and external, that may have been made to the old page name.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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

Nudix hydrolase Edit Wikipedia article

The Nudix family is a protein family of phosphohydrolases. Using water-mediated catalysis they break a phosphate bond in their substrate to create two products. Nudix stands for Nucleotide Diphosphate linked to X. There are two components to the Nudix family, the so-called Nudix fold of a beta sheet with alpha helices on each side and the Nudix motif which contains catalytic and metal-binding amino acids. The Nudix motif is GXXXXXEXXXXXXXREUXEEXGU where U is Isoleucine, Leucine, or Valine and X is any amino acid. This forms a short helix which (usually) contains the catalytic amino acids. Nudix family enzymes include Dcp2 of the decapping complex, ADP-ribose diphosphatase, MutT, ADPRase, Ap4A, RppH, and many others.[1]

References

  1. ^ Mildvan, A.S.; Xia, Z.; Azurmendi, H.F.; Saraswat, V.; Legler, P.M.; Massiah, M.A.; Gabelli, S.B.; Bianchet, M.A.; Kang, L.W.; Amzel, L.M. (2005), "Structures and mechanisms of Nudix hydrolases", Archives of Biochemistry and Biophysics, 433 (1): 129–143, doi:10.1016/j.abb.2004.08.017

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Internal database links

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...

Loading domain graphics...

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

Alignments

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...

View options

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.

  Seed
(127)
Full
(105053)
Representative proteomes UniProt
(428498)
RP15
(13477)
RP35
(48216)
RP55
(103570)
RP75
(176405)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(127)
Full
(105053)
Representative proteomes UniProt
(428498)
RP15
(13477)
RP35
(48216)
RP55
(103570)
RP75
(176405)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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.

  Seed
(127)
Full
(105053)
Representative proteomes UniProt
(428498)
RP15
(13477)
RP35
(48216)
RP55
(103570)
RP75
(176405)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download    

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...

Trees

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: 130.6 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

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

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

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Structures

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.

Loading structure mapping...

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
A0A044RTQ6 View 3D Structure Click here
A0A044SHQ4 View 3D Structure Click here
A0A044TV93 View 3D Structure Click here
A0A044UZ04 View 3D Structure Click here
A0A044V8E0 View 3D Structure Click here
A0A044VFQ0 View 3D Structure Click here
A0A044VGM4 View 3D Structure Click here
A0A077YWF3 View 3D Structure Click here
A0A077YYA5 View 3D Structure Click here
A0A077Z122 View 3D Structure Click here
A0A077Z336 View 3D Structure Click here
A0A077Z8T9 View 3D Structure Click here
A0A077ZAF1 View 3D Structure Click here
A0A077ZG86 View 3D Structure Click here
A0A077ZGU6 View 3D Structure Click here
A0A077ZH97 View 3D Structure Click here
A0A077ZKJ3 View 3D Structure Click here
A0A077ZKM7 View 3D Structure Click here
A0A0A2V6Q3 View 3D Structure Click here
A0A0D2DI59 View 3D Structure Click here
A0A0D2DNL9 View 3D Structure Click here
A0A0D2DXQ3 View 3D Structure Click here
A0A0D2E112 View 3D Structure Click here
A0A0D2E4C8 View 3D Structure Click here
A0A0D2E4L0 View 3D Structure Click here
A0A0D2E8G5 View 3D Structure Click here
A0A0D2ER91 View 3D Structure Click here
A0A0D2FHB2 View 3D Structure Click here
A0A0D2FIG2 View 3D Structure Click here
A0A0D2G791 View 3D Structure Click here
A0A0D2G9Y2 View 3D Structure Click here
A0A0D2GLT4 View 3D Structure Click here
A0A0D2GND0 View 3D Structure Click here
A0A0D2GQZ8 View 3D Structure Click here
A0A0D2GT50 View 3D Structure Click here
A0A0D2H5M4 View 3D Structure Click here
A0A0D2HJK6 View 3D Structure Click here
A0A0G2JYZ4 View 3D Structure Click here
A0A0G2K7J8 View 3D Structure Click here