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325  structures 5206  species 3  interactions 43912  sequences 282  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

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

References

  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/j.abb.2004.08.017. 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/j.abb.2004.08.017. PMID 15581572 

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NUDIX domain Provide feedback

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Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000086

The generic name 'NUDIX hydrolases' (NUcleoside DIphosphate linked to some other moiety X) has been coined for this domain family [PUBMED:8810257]. The family can be divided into a number of subgroups, of which MutT anti- mutagenic activity represents only one type; most of the rest hydrolyse diverse nucleoside diphosphate derivatives (including ADP-ribose, GDP- mannose, TDP-glucose, NADH, UDP-sugars, dNTP and NTP).

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 5 members:

DBC1 NUDIX NUDIX-like NUDIX_2 NUDIX_4

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(197)
Full
(43912)
Representative proteomes NCBI
(31604)
Meta
(9218)
RP15
(3648)
RP35
(7193)
RP55
(9734)
RP75
(11753)
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Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(197)
Full
(43912)
Representative proteomes NCBI
(31604)
Meta
(9218)
RP15
(3648)
RP35
(7193)
RP55
(9734)
RP75
(11753)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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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
(197)
Full
(43912)
Representative proteomes NCBI
(31604)
Meta
(9218)
RP15
(3648)
RP35
(7193)
RP55
(9734)
RP75
(11753)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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
Author: Bateman A, Finn RD
Number in seed: 197
Number in full: 43912
Average length of the domain: 130.90 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 65.32 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -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: 23
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

DCP2 NUDIX-like NUDIX

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 325 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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