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34  structures 2021  species 1  interaction 4764  sequences 83  architectures

Family: Phosphodiest (PF01663)

Summary: Type I phosphodiesterase / nucleotide pyrophosphatase

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Type I phosphodiesterase / nucleotide pyrophosphatase Provide feedback

This family consists of phosphodiesterases, including human plasma-cell membrane glycoprotein PC-1 / alkaline phosphodiesterase i / nucleotide pyrophosphatase (nppase). These enzymes catalyse the cleavage of phosphodiester and phosphosulfate bonds in NAD, deoxynucleotides and nucleotide sugars [1]. Also in this family is ATX an autotaxin, tumour cell motility-stimulating protein which exhibits type I phosphodiesterases activity [4]. The alignment encompasses the active site [3,4]. Also present with in this family is 60-kDa Ca2+-ATPase form F. odoratum [2].

Literature references

  1. Jin-Hua P, Goding JW, Nakamura H, Sano K; , Genomics 1997;45:412-415.: Molecular cloning and chromosomal localization of PD-Ibeta (PDNP3), a new member of the human phosphodiesterase I genes. PUBMED:9344668 EPMC:9344668

  2. Peiffer WE, Desrosiers MG, Menick DR; , J Biol Chem 1996;271:5095-5100.: Cloning and expression of the unique Ca2+-ATPase from Flavobacterium odoratum. PUBMED:8617788 EPMC:8617788

  3. Deissler H, Lottspeich F, Rajewsky MF; , J Biol Chem 1995;270:9849-9855.: Affinity purification and cDNA cloning of rat neural differentiation and tumor cell surface antigen gp130RB13-6 reveals relationship to human and murine PC-1. PUBMED:7730366 EPMC:7730366

  4. Murata J, Lee HY, Clair T, Krutzsch HC, Arestad AA, Sobel ME, Liotta LA, Stracke ML; , J Biol Chem 1994;269:30479-30484.: cDNA cloning of the human tumor motility-stimulating protein, autotaxin, reveals a homology with phosphodiesterases. PUBMED:7982964 EPMC:7982964


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002591

This family consists of phosphodiesterases, including human plasma-cell membrane glycoprotein PC-1 / alkaline phosphodiesterase I / nucleotide pyrophosphatase (nppase). These enzymes catalyse the cleavage of phosphodiester and phosphosulphate bonds in NAD, deoxynucleotides and nucleotide sugars [PUBMED:9344668]. Another member of this family is ATX an autotaxin, tumor cell motility-stimulating protein which exhibits type I phosphodiesterases activity [PUBMED:7982964]. The alignment encompasses the active site [PUBMED:7730366, PUBMED:7982964]. Also present within this family is 60 kDa Ca2+-ATPase from Myroides odoratus [PUBMED:8617788].

This signature also hits a number of ethanolamine phosphate transferase involved in glycosylphosphatidylinositol-anchor biosynthesis.

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 Alk_phosphatase (CL0088), which has the following description:

The members of this clan all share a common structure of their catalytic domains, which contain conserved metal binding residues [1].

The clan contains the following 9 members:

Alk_phosphatase DUF1501 DUF229 Metalloenzyme PglZ Phosphodiest Phosphoesterase Sulfatase Sulfatase_C

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
(70)
Full
(4764)
Representative proteomes NCBI
(12839)
Meta
(5667)
RP15
(703)
RP35
(1239)
RP55
(1744)
RP75
(2144)
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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
(70)
Full
(4764)
Representative proteomes NCBI
(12839)
Meta
(5667)
RP15
(703)
RP35
(1239)
RP55
(1744)
RP75
(2144)
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
(70)
Full
(4764)
Representative proteomes NCBI
(12839)
Meta
(5667)
RP15
(703)
RP35
(1239)
RP55
(1744)
RP75
(2144)
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: Pfam-B_994 (release 4.1) & Pfam-B_6150 (Release 8.0)
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A
Number in seed: 70
Number in full: 4764
Average length of the domain: 283.30 aa
Average identity of full alignment: 14 %
Average coverage of the sequence by the domain: 54.15 %

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 19.9 19.9
Trusted cut-off 19.9 19.9
Noise cut-off 19.8 19.8
Model length: 365
Family (HMM) version: 17
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 is 1 interaction for this family. More...

Phosphodiest

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 Phosphodiest domain has been found. There are 34 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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