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968  structures 8951  species 0  interactions 99500  sequences 935  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.

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 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 9 members:

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

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
(99500)
Representative proteomes UniProt
(401774)
RP15
(12454)
RP35
(45146)
RP55
(96394)
RP75
(163638)
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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.

Format an alignment

  Seed
(127)
Full
(99500)
Representative proteomes UniProt
(401774)
RP15
(12454)
RP35
(45146)
RP55
(96394)
RP75
(163638)
Alignment:
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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
(99500)
Representative proteomes UniProt
(401774)
RP15
(12454)
RP35
(45146)
RP55
(96394)
RP75
(163638)
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: 99500
Average length of the domain: 130.60 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 57.79 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -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: 30
Download: download the raw HMM for this family

Species distribution

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

Selections

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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 968 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
A0A0R0G8N1 View 3D Structure Click here
A0A0R0GGY3 View 3D Structure Click here
A0A0R0GRC9 View 3D Structure Click here
A0A0R0GTG6 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
A0A1D6Q2F0 View 3D Structure Click here
A0A1D6QCD2 View 3D Structure Click here
A0A1D8PHM2 View 3D Structure Click here
A0A1D8PLI2 View 3D Structure Click here
A0A1D8PPW7 View 3D Structure Click here
A0A1D8PTQ2 View 3D Structure Click here
A0A1D8PU14 View 3D Structure Click here
A0A2R8QKR4 View 3D Structure Click here
A0A2R8RL21 View 3D Structure Click here
A4HSD8 View 3D Structure Click here
A4HT52 View 3D Structure Click here
A4I7A0 View 3D Structure Click here
A4I7W9 View 3D Structure Click here
A4ICV7 View 3D Structure Click here
A4ID31 View 3D Structure Click here
B4F8F0 View 3D Structure Click here
B4F8J7 View 3D Structure Click here
B4FG54 View 3D Structure Click here
B4FGD4 View 3D Structure Click here
B4FPF6 View 3D Structure Click here
B4FX37 View 3D Structure Click here
B4FYW7 View 3D Structure Click here
B4G1X5 View 3D Structure Click here
B6T9Z2 View 3D Structure Click here
B7EII4 View 3D Structure Click here
C0H4F3 View 3D Structure Click here
C0P7W5 View 3D Structure Click here
C0VXV6 View 3D Structure Click here
C6SXU5 View 3D Structure Click here
C6SYK7 View 3D Structure Click here
C6T3J9 View 3D Structure Click here
C6TEN2 View 3D Structure Click here
C6TF29 View 3D Structure Click here
C6TGP5 View 3D Structure Click here
C6THS8 View 3D Structure Click here
D3ZCD3 View 3D Structure Click here
D3ZCT0 View 3D Structure Click here
D3ZEH6 View 3D Structure Click here
D3ZH27 View 3D Structure Click here
D3ZKQ0 View 3D Structure Click here
D3ZV74 View 3D Structure Click here
D3ZVY0 View 3D Structure Click here
D3ZYH3 View 3D Structure Click here
D4A1D4 View 3D Structure Click here
D4A2H8 View 3D Structure Click here
D4AEN4 View 3D Structure Click here
E7FAS2 View 3D Structure Click here
F1Q9N4 View 3D Structure Click here
F1QFB9 View 3D Structure Click here
F1QIX4 View 3D Structure Click here
F1QL34 View 3D Structure Click here
F1QVG2 View 3D Structure Click here
G3V7P6 View 3D Structure Click here
G5EFQ1 View 3D Structure Click here
I1J6S8 View 3D Structure Click here
I1JD09 View 3D Structure Click here
I1JHV6 View 3D Structure Click here
I1JJJ8 View 3D Structure Click here
I1JNL1 View 3D Structure Click here
I1K5L3 View 3D Structure Click here
I1KDB2 View 3D Structure Click here
I1L038 View 3D Structure Click here
I1L435 View 3D Structure Click here
I1L4F2 View 3D Structure Click here
I1L6A2 View 3D Structure Click here
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I1M039 View 3D Structure Click here
I1M0Q4 View 3D Structure Click here
I1M666 View 3D Structure Click here
I1MFS0 View 3D Structure Click here
I1MIP6 View 3D Structure Click here
I1MUA9 View 3D Structure Click here
I1MZF1 View 3D Structure Click here
I1N095 View 3D Structure Click here
I1N3Z3 View 3D Structure Click here
I1N989 View 3D Structure Click here
I1NDT8 View 3D Structure Click here
I6X235 View 3D Structure Click here
I6XHX8 View 3D Structure Click here
I6YDV4 View 3D Structure Click here
K7K749 View 3D Structure Click here
K7K829 View 3D Structure Click here
K7KN13 View 3D Structure Click here
K7KRE3 View 3D Structure Click here
K7L281 View 3D Structure Click here
K7L547 View 3D Structure Click here
K7LD64 View 3D Structure Click here
K7LMW3 View 3D Structure Click here
K7LQN0 View 3D Structure Click here
K7M4C3 View 3D Structure Click here
K7M8E1 View 3D Structure Click here
K7MQH8 View 3D Structure Click here
K7VFM9 View 3D Structure Click here
M0R515 View 3D Structure Click here
M0RBQ1 View 3D Structure Click here
M0RBU2 View 3D Structure Click here
O06597 View 3D Structure Click here
O13717 View 3D Structure Click here
O13828 View 3D Structure Click here
O22951 View 3D Structure Click here
O35760 View 3D Structure Click here
O45830 View 3D Structure Click here
O61902 View 3D Structure Click here
O62255 View 3D Structure Click here
O69700 View 3D Structure Click here
O95848 View 3D Structure Click here
O95989 View 3D Structure Click here
P08337 View 3D Structure Click here
P0A776 View 3D Structure Click here
P0AEI6 View 3D Structure Click here
P0AFC0 View 3D Structure Click here
P0C024 View 3D Structure Click here
P0C025 View 3D Structure Click here
P0C026 View 3D Structure Click here
P0C027 View 3D Structure Click here
P0C028 View 3D Structure Click here
P15496 View 3D Structure Click here
P32056 View 3D Structure Click here
P32664 View 3D Structure Click here
P36639 View 3D Structure Click here
P37128 View 3D Structure Click here
P41888 View 3D Structure Click here
P43337 View 3D Structure Click here
P45799 View 3D Structure Click here
P47173 View 3D Structure Click here
P50583 View 3D Structure Click here
P52006 View 3D Structure Click here
P53164 View 3D Structure Click here
P53368 View 3D Structure Click here
P53369 View 3D Structure Click here
P53370 View 3D Structure Click here
P53550 View 3D Structure Click here
P56380 View 3D Structure Click here
P58044 View 3D Structure Click here
P65556 View 3D Structure Click here
P70563 View 3D Structure Click here
P77788 View 3D Structure Click here
P91148 View 3D Structure Click here
P93740 View 3D Structure Click here
P9WIX5 View 3D Structure Click here
P9WIX7 View 3D Structure Click here
P9WIX9 View 3D Structure Click here
P9WIY1 View 3D Structure Click here
P9WIY3 View 3D Structure Click here
P9WKK5 View 3D Structure Click here
Q01976 View 3D Structure Click here
Q09297 View 3D Structure Click here
Q09790 View 3D Structure Click here
Q0IZS1 View 3D Structure Click here
Q0JB97 View 3D Structure Click here
Q0JDJ5 View 3D Structure Click here
Q10132 View 3D Structure Click here
Q12524 View 3D Structure Click here
Q13907 View 3D Structure Click here
Q19427 View 3D Structure Click here
Q1L8L1 View 3D Structure Click here
Q1LYN2 View 3D Structure Click here
Q23236 View 3D Structure Click here
Q2FVC2 View 3D Structure Click here
Q2FXQ3 View 3D Structure Click here
Q2FY72 View 3D Structure Click here
Q2G0U7 View 3D Structure Click here
Q2G2V5 View 3D Structure Click here
Q2R391 View 3D Structure Click here
Q38929 View 3D Structure Click here
Q3U2V3 View 3D Structure Click here
Q42553 View 3D Structure Click here
Q46822 View 3D Structure Click here
Q4D1W8 View 3D Structure Click here
Q4D5V9 View 3D Structure Click here
Q4D8Y8 View 3D Structure Click here
Q4DB19 View 3D Structure Click here
Q4DBF8 View 3D Structure Click here
Q4DDM6 View 3D Structure Click here
Q4DN64 View 3D Structure Click here
Q4DRF4 View 3D Structure Click here
Q4E0V3 View 3D Structure Click here
Q4V6M1 View 3D Structure Click here
Q4V8V2 View 3D Structure Click here
Q52K88 View 3D Structure Click here
Q54BB8 View 3D Structure Click here
Q54FR0 View 3D Structure Click here
Q54JI0 View 3D Structure Click here
Q54L59 View 3D Structure Click here
Q54N32 View 3D Structure Click here
Q54QJ4 View 3D Structure Click here
Q54R87 View 3D Structure Click here
Q54S89 View 3D Structure Click here
Q54U83 View 3D Structure Click here
Q557E3 View 3D Structure Click here
Q55A74 View 3D Structure Click here
Q55BE3 View 3D Structure Click here
Q55D56 View 3D Structure Click here
Q55GI4 View 3D Structure Click here
Q566C7 View 3D Structure Click here
Q568Q0 View 3D Structure Click here
Q58549 View 3D Structure Click here
Q59VP4 View 3D Structure Click here
Q5ADP5 View 3D Structure Click here
Q5AGF0 View 3D Structure Click here
Q5U127 View 3D Structure Click here
Q5VSC2 View 3D Structure Click here
Q5XIG0 View 3D Structure Click here
Q5XJC2 View 3D Structure Click here
Q5Z802 View 3D Structure Click here
Q641Y7 View 3D Structure Click here
Q656M7 View 3D Structure Click here
Q66JN9 View 3D Structure Click here
Q6AUB0 View 3D Structure Click here
Q6AY63 View 3D Structure Click here
Q6DG97 View 3D Structure Click here
Q6H4N6 View 3D Structure Click here
Q6IQ66 View 3D Structure Click here
Q6K683 View 3D Structure Click here
Q6K837 View 3D Structure Click here
Q6NPD7 View 3D Structure Click here
Q6P3D0 View 3D Structure Click here
Q6PEC0 View 3D Structure Click here
Q6Z2I1 View 3D Structure Click here
Q6ZVK8 View 3D Structure Click here
Q71RX2 View 3D Structure Click here
Q75IK6 View 3D Structure Click here
Q7F188 View 3D Structure Click here
Q7JVG2 View 3D Structure Click here
Q7KWR0 View 3D Structure Click here
Q7PLS1 View 3D Structure Click here
Q7ZWC3 View 3D Structure Click here
Q803B9 View 3D Structure Click here
Q86X67 View 3D Structure Click here
Q8BFZ6 View 3D Structure Click here
Q8BG93 View 3D Structure Click here
Q8BVU5 View 3D Structure Click here
Q8CH40 View 3D Structure Click here
Q8GVZ0 View 3D Structure Click here
Q8GW31 View 3D Structure Click here
Q8GYB1 View 3D Structure Click here
Q8H4U7 View 3D Structure Click here
Q8IDK8 View 3D Structure Click here
Q8IEM5 View 3D Structure Click here
Q8IU60 View 3D Structure Click here
Q8JZU0 View 3D Structure Click here
Q8L7W2 View 3D Structure Click here
Q8L831 View 3D Structure Click here
Q8LET2 View 3D Structure Click here
Q8NFP7 View 3D Structure Click here
Q8R2U6 View 3D Structure Click here
Q8VXZ0 View 3D Structure Click here
Q8VY81 View 3D Structure Click here
Q8WV74 View 3D Structure Click here
Q92350 View 3D Structure Click here
Q93K97 View 3D Structure Click here
Q93ZY7 View 3D Structure Click here
Q94A82 View 3D Structure Click here
Q94B74 View 3D Structure Click here
Q95XC4 View 3D Structure Click here
Q96DE0 View 3D Structure Click here
Q96G61 View 3D Structure Click here
Q99321 View 3D Structure Click here
Q99MY2 View 3D Structure Click here
Q99P30 View 3D Structure Click here
Q9BQG2 View 3D Structure Click here
Q9BW91 View 3D Structure Click here
Q9BXS1 View 3D Structure Click here
Q9C6Z2 View 3D Structure Click here
Q9CA40 View 3D Structure Click here
Q9CAF2 View 3D Structure Click here
Q9CR24 View 3D Structure Click here
Q9CWD3 View 3D Structure Click here
Q9CYC6 View 3D Structure Click here
Q9D142 View 3D Structure Click here
Q9DCN1 View 3D Structure Click here
Q9FNH4 View 3D Structure Click here
Q9JI46 View 3D Structure Click here
Q9JKX6 View 3D Structure Click here
Q9LE73 View 3D Structure Click here
Q9LHK1 View 3D Structure Click here
Q9LQU5 View 3D Structure Click here
Q9NA25 View 3D Structure Click here
Q9NH02 View 3D Structure Click here
Q9NV35 View 3D Structure Click here
Q9NZJ9 View 3D Structure Click here
Q9P791 View 3D Structure Click here
Q9SJC4 View 3D Structure Click here
Q9SJC6 View 3D Structure Click here
Q9SNS9 View 3D Structure Click here
Q9SU14 View 3D Structure Click here
Q9SZ63 View 3D Structure Click here
Q9U2M7 View 3D Structure Click here
Q9UKK9 View 3D Structure Click here
Q9VB64 View 3D Structure Click here
Q9VDC2 View 3D Structure Click here
Q9VGM4 View 3D Structure Click here
Q9VV83 View 3D Structure Click here
Q9VXR9 View 3D Structure Click here
Q9VY79 View 3D Structure Click here
Q9W086 View 3D Structure Click here
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Q9ZU95 View 3D Structure Click here