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400  structures 20069  species 16  interactions 172881  sequences 434  architectures

Family: NUDIX (PF00293)

Summary: NUDIX domain

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

Nudix family Edit Wikipedia article

PDB 1mp2 EBI.jpg
Structure of MT-ADPRase, a Nudix hydrolase from Mycobacterium tuberculosis
Symbol NUDIX
Pfam PF00293
Pfam clan CL0261
InterPro IPR000086
PDB 1vk6 EBI.jpg
Crystal structure of NADH pyrophosphatase (1790429) from Escherichia coli k12 at 2.20 a resolution
Symbol NUDIX-like
Pfam PF09296
Pfam clan CL0261
InterPro IPR015375
SCOP 1vk6

The Nudix family is a protein family of phosphohydrolases.[1][2][3] Using water-mediated catalysis they break a phosphate bond in their substrate to create two products. Nudix stands for Nucleoside 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.[4]


  1. ^ Bessman MJ, Frick DN, O'Handley SF (October 1996). "The MutT proteins or "Nudix" hydrolases, a family of versatile, widely distributed, "housecleaning" enzymes". J. Biol. Chem. 271 (41): 25059–62. doi:10.1074/jbc.271.41.25059. PMID 8810257. 
  2. ^ Mildvan AS, Xia Z, Azurmendi HF; et al. (January 2005). "Structures and mechanisms of Nudix hydrolases". Arch. Biochem. Biophys. 433 (1): 129–43. doi:10.1016/ PMID 15581572. 
  3. ^ McLennan AG (January 2006). "The Nudix hydrolase superfamily". Cell. Mol. Life Sci. 63 (2): 123–43. doi:10.1007/s00018-005-5386-7. PMID 16378245. 
  4. ^ Mildvan, A.S.; Xia, Z.; Azurmendi, H.F.; Saraswat, V.; Legler, P.M.; Massiah, M.A.; Gabelli, S.B.; Bianchet, M.A.; et al. (2005). "Structures and mechanisms of Nudix hydrolases". Archives of Biochemistry and Biophysics 433 (1): 129–143. doi:10.1016/ PMID 15581572 

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This tab holds annotation information from the InterPro database.

InterPro entry IPR000086

The Nudix superfamily is widespread among eucaryotes, 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

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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 4 members:



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Curation and family details

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Seed source: Prosite
Previous IDs: mutT;
Type: Domain
Author: Bateman A, Finn RD
Number in seed: 147
Number in full: 172881
Average length of the domain: 131.60 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 67.55 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 135
Family (HMM) version: 24
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Species distribution

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Archea Archea Eukaryota Eukaryota
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There are 16 interactions for this family. More...

Nudix_N CTP_transf_like NUDIX-like NUDIX zf-NADH-PPase His_Phos_1 Nudix_N_2 Nudix_N_2 DCP2 DCP2 DCP1 NUDIX-like Nudix_N His_Phos_1 zf-NADH-PPase CTP_transf_like


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 400 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 seqence.

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