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57  structures 838  species 0  interactions 5547  sequences 68  architectures

Family: 5_nucleotid (PF05761)

Summary: 5' nucleotidase family

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

5' nucleotidase family Provide feedback

This family of eukaryotic proteins includes 5' nucleotidase enzymes, such as purine 5'-nucleotidase EC:3.1.3.5.

Literature references

  1. Allegrini S, Pesi R, Tozzi MG, Fiol CJ, Johnson RB, Eriksson S; , Biochem J 1997;328:483-487.: Bovine cytosolic IMP/GMP-specific 5'-nucleotidase: cloning and expression of active enzyme in Escherichia coli. PUBMED:9371705 EPMC:9371705


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008380

This family includes a 5'-nucleotidase, EC , specific for purines (IMP and GMP) [ PUBMED:9371705 ]. These enzymes are members of the Haloacid Dehalogenase (HAD) superfamily. HAD members are recognised by three short motifs {hhhhDxDx(T/V)}, {hhhh(T/S)}, and either {hhhh(D/E)(D/E)x(3-4)(G/N)} or {hhhh(G/N)(D/E)x(3-4)(D/E)} (where "h" stands for a hydrophobic residue). Crystal structures of many HAD enzymes has verified PSI-PRED predictions of secondary structural elements which show each of the "hhhh" sequences of the motifs as part of beta sheets. This subfamily of enzymes is part of "Subfamily I" of the HAD superfamily by virtue of a "cap" domain in between motifs 1 and 2. This subfamily's cap domain has a different predicted secondary structure than all other known HAD enzymes and thus has been designated "subfamily IG", the domain appears to consist of a mixed alpha/beta fold.

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 HAD (CL0137), which has the following description:

This clan represents the haloacid dehalogenase (HAD) superfamily that includes a diverse range of enzymes that use an asp carboxylate as a nucleophile [1].

The clan contains the following 25 members:

5_nucleotid Acid_phosphat_B Acid_PPase APP1_cat Cation_ATPase DHH DUF2608 DUF705 HAD HAD_2 Hydrolase Hydrolase_3 Hydrolase_6 Hydrolase_like LNS2 NIF NT5C PGP_phosphatase PhoLip_ATPase_C PMM PNK3P Put_Phosphatase S6PP Trehalose_PPase UMPH-1

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
(85)
Full
(5547)
Representative proteomes UniProt
(9404)
RP15
(990)
RP35
(2195)
RP55
(4421)
RP75
(5771)
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
(85)
Full
(5547)
Representative proteomes UniProt
(9404)
RP15
(990)
RP35
(2195)
RP55
(4421)
RP75
(5771)
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
(85)
Full
(5547)
Representative proteomes UniProt
(9404)
RP15
(990)
RP35
(2195)
RP55
(4421)
RP75
(5771)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: Pfam-B_2948 (release 8.0)
Previous IDs: 5_nucleotidase;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 85
Number in full: 5547
Average length of the domain: 352.5 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 79.17 %

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 28.5 28.5
Trusted cut-off 28.5 28.5
Noise cut-off 28.3 28.3
Model length: 461
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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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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...

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Tree controls

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

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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 5_nucleotid domain has been found. There are 57 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
A0A077Z560 View 3D Structure Click here
A0A077ZG40 View 3D Structure Click here
A0A0K0EH52 View 3D Structure Click here
A0A0K0EJA1 View 3D Structure Click here
A0A0K0EP61 View 3D Structure Click here
A0A0K0J2M0 View 3D Structure Click here
A0A0N4U443 View 3D Structure Click here
A0A0N4U831 View 3D Structure Click here
A0A0P0Y7Q4 View 3D Structure Click here
A0A0R0JG80 View 3D Structure Click here
A0A158N850 View 3D Structure Click here
A0A178VR03 View 3D Structure Click here
A0A1D6FC88 View 3D Structure Click here
A0A1D6GM41 View 3D Structure Click here
A0A1D6I4N4 View 3D Structure Click here
A0A1D6K8W9 View 3D Structure Click here
A0A1D6K9J7 View 3D Structure Click here
A0A1D6L6B8 View 3D Structure Click here
A0A1X7YIW7 View 3D Structure Click here
A0A2I3BR81 View 3D Structure Click here
A0A2K6W2I5 View 3D Structure Click here
A0A3P7DW83 View 3D Structure Click here
A0A3P7EJJ3 View 3D Structure Click here
A0A3P7GF41 View 3D Structure Click here
A0A3Q0KP95 View 3D Structure Click here
A0A5K4F9F8 View 3D Structure Click here
A0A5K4FA53 View 3D Structure Click here
A0A5K4FBN5 View 3D Structure Click here
A0A5K4FCK7 View 3D Structure Click here
A0A5K4FCL2 View 3D Structure Click here
A0A5K4FDW5 View 3D Structure Click here
A0A7I4K7G9 View 3D Structure Click here
A0A7I4K9W8 View 3D Structure Click here
A1Z7V9 View 3D Structure Click here
A4IHT9 View 3D Structure Click here
A8PGL7 View 3D Structure Click here
B1WC66 View 3D Structure Click here
D3ZAI6 View 3D Structure Click here
D3ZMY7 View 3D Structure Click here
E7FC21 View 3D Structure Click here