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299  structures 5141  species 3  interactions 30853  sequences 68  architectures

Family: Pribosyltran (PF00156)

Summary: Phosphoribosyl transferase domain

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.

Phosphoribosyl transferase domain Provide feedback

This family includes a range of diverse phosphoribosyl transferase enzymes. This family includes: Adenine phosphoribosyl-transferase EC:2.4.2.7, P07672. Hypoxanthine-guanine-xanthine phosphoribosyl-transferase P51900. Hypoxanthine phosphoribosyl-transferase EC:2.4.2.8 P36766. Ribose-phosphate pyrophosphokinase i EC:2.7.6.1 P09329. Amidophosphoribosyltransferase EC:2.4.2.14 P00496. Orotate phosphoribosyl-transferase EC:2.4.2.10 P11172. Uracil phosphoribosyl-transferase EC:2.4.2.9 P25532. Xanthine-guanine phosphoribosyl-transferase EC:2.4.2.22 P00501. In Arabidopsis, At the very N-terminus of this domain is the P-Loop NTPase domain [1].

Literature references

  1. Islam MR, Kim H, Kang SW, Kim JS, Jeong YM, Hwang HJ, Lee SY, Woo JC, Kim SG;, Plant Mol Biol. 2007;63:465-477.: Functional characterization of a gene encoding a dual domain for uridine kinase and uracil phosphoribosyltransferase in Arabidopsis thaliana. PUBMED:17143579 EPMC:17143579


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000836

The name PRT comes from phosphoribosyltransferase (PRTase) enzymes, which carry out phosphoryl transfer reactions on 5-phosphoribosyl-alpha1-pyrophosphate PRPP, an activated form of ribose-5-phosphate. Members of Phosphoribosyltransferase (PRT) are catalytic and are regulatory proteins involved in nucleotide synthesis and salvage [PUBMED:11751055]. This includes a range of diverse phosphoribosyl transferase enzymes including adenine phosphoribosyltransferase (EC); hypoxanthine-guanine-xanthine phosphoribosyltransferase; hypoxanthine phosphoribosyltransferase (EC); ribose-phosphate pyrophosphokinase (EC); amidophosphoribosyltransferase (EC); orotate phosphoribosyltransferase (EC);uracil phosphoribosyltransferase (EC); and xanthine-guanine phosphoribosyltransferase (EC).

Not all PRT proteins are enzymes. For example, in some bacteria PRT proteins regulate the expression of purine and pyrimidine synthetic genes.

Members of PRT are defined by the protein fold and by a short 13-residue sequence motif, The motif consists of four hydrophobic amino acids, two acidic amino acids and seven amino acids of variable character, usually including glycine and threonine. The motif has been predicted to be a PRPP-binding site in advance of structural information [PUBMED:3009477, PUBMED:3527873]. Apart of this motif, different PRT proteins have a low level of sequence identity, less than 15%. The PRT sequence motif is only found in PRTases from the nucleotide synthesis and salvage pathways. Other PRTases, from the tryptophan, histidine and nicotinamide synthetic and salvage pathways, lack the PRT sequence motif and appear to be unrelated to each other and unrelated to the PRT family.

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 PRTase-like (CL0533), which has the following description:

This superfamily of phosphoribosyl-transferases (PRTases) and phosphoribosyl-pyrophosphate synthetase-like protein families is characterised by a core fold of three layers, a/b/a with a mixed beta-sheet of six strands. In one of the families consists of two domains of this fold.

The clan contains the following 6 members:

Pribosyl_synth Pribosyltran PRTase_1 PRTase_2 PRTase_3 UPRTase

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
(71)
Full
(30853)
Representative proteomes NCBI
(25977)
Meta
(11727)
RP15
(2412)
RP35
(4803)
RP55
(6327)
RP75
(7483)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(71)
Full
(30853)
Representative proteomes NCBI
(25977)
Meta
(11727)
RP15
(2412)
RP35
(4803)
RP55
(6327)
RP75
(7483)
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
(71)
Full
(30853)
Representative proteomes NCBI
(25977)
Meta
(11727)
RP15
(2412)
RP35
(4803)
RP55
(6327)
RP75
(7483)
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: Bateman A
Previous IDs: none
Type: Domain
Author: Bateman A, Sonnhammer ELL, Finn RD
Number in seed: 71
Number in full: 30853
Average length of the domain: 121.40 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 48.82 %

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 26.3 26.3
Trusted cut-off 26.3 26.3
Noise cut-off 26.2 26.2
Model length: 125
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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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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Interactions

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

Pribosyltran PuR_N GATase_2

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 Pribosyltran domain has been found. There are 299 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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