Summary: NUDIX domain
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This is the Wikipedia entry entitled "Nudix family". More...
Nudix family Edit Wikipedia article
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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
- ^ 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.
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No Pfam abstract.
Internal database links
| SCOOP: | DUF4916 NUDIX_2 NUDIX_4 |
| Similarity to PfamA using HHSearch: | NUDIX_4 |
External database links
| HOMSTRAD: | mutT |
| PROSITE: | PDOC00695 |
| SCOP: | 1mut |
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_hydroAlignments
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.
| Seed (127) |
Full (105053) |
Representative proteomes | UniProt (428498) |
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| RP15 (13477) |
RP35 (48216) |
RP55 (103570) |
RP75 (176405) |
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| PP/heatmap | 1 | ||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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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.
| Seed (127) |
Full (105053) |
Representative proteomes | UniProt (428498) |
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|---|---|---|---|---|---|---|---|
| RP15 (13477) |
RP35 (48216) |
RP55 (103570) |
RP75 (176405) |
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| Raw Stockholm | |||||||
| Gzipped | |||||||
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
| Seed source: | Prosite |
| Previous IDs: | mutT; |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Bateman A  , Finn RD
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| 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
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 131 | ||||||||||||
| Family (HMM) version: | 31 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
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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.
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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.
