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59  structures 2463  species 1  interaction 7067  sequences 222  architectures

Family: GDPD (PF03009)

Summary: Glycerophosphoryl diester phosphodiesterase family

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Glycerophosphoryl diester phosphodiesterase family Provide feedback

E. coli has two sequence related isozymes of glycerophosphoryl diester phosphodiesterase (GDPD) - periplasmic and cytosolic. This family also includes agrocinopine synthase, the similarity to GDPD has been noted [1]. This family appears to have weak but not significant matches to mammalian phospholipase C PF00388 which suggests that this family may adopt a TIM barrel fold.

Literature references

  1. Kim H, Farrand SK; , J Bacteriol 1997;179:7559-7572.: Characterization of the acc operon from the nopaline-type Ti plasmid pTiC58, which encodes utilization of agrocinopines A and B and susceptibility to agrocin 84. PUBMED:9393724 EPMC:9393724


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR030395

This entry represents the GP-PDE domain.

The glycerophosphodiester phosphodiesterases (GD-PDEs) were initially characterised in bacteria, where they have functional roles for production of metabolic carbon and phosphate sources from glycerophosphodiesters and in adherence to and degradation of mammalian host-cell membranes. Mammalian GP- GDEs have been identified more recently and shown to be implicated in several physiological functions. GD-PDEs are involved in glycerol metabolism and catalyze the reaction of glycerophosphodiester and water to alcohol and sn-glycerol-3-phosphate. They display broad specificity for glycerophosphodiesters, such as glycerophosphocholine, glycerophosphoethanolamine, glycerophosphoglycerol and bis(glycerophosphoglycerol).

The GP-PDE domain adopts the ubiquitous triosephosphate isomerase (TIM) barrel alpha/beta fold. The TIM barrel is comprised of an eight-stranded parallel beta-sheet barrel surrounded by eight alpha-helices. There is a small insertion to the conventional TIM barrel structure referred to as the GDPD-insertion (GDPD-I). The GDPD-I is comprised of beta strands, alpha-helices (H3 and H4), and 3/10 helices. Although the TIM barrel and a small insertion are unique for GP-PDE family, there are subtle differences in size and topology of each domain [PUBMED:15162496, PUBMED:16909422].

Some proteins known to contain a GP-PDE domain are listed below:

  • Bacterial glycerophosphoryl diester phosphodiesterase GlpQ (EC 3.1.4.46).
  • Bacterial gylcerophosphoryl diester phosphodiesterase UgpQ (EC 3.1.4.46).
  • Mammalian glycerophosphodiester phosphodiesterase 1 (GDE1) (EC 3.1.4.44) (or MMIR16) [PUBMED:12576545], an integral membrane glycoprotein that interacts with regulator of G protein signaling proteins. It hydrolyzes glycerophosphoinositols (GPIs) producing inositol and glycerol 3-phosphate.
  • Mammalian glycerophosphodiester phosphodiesterase domain-containing protein 5 (GDPD5) (EC 3.1.-.-) (or GDE2) [PUBMED:15276213].
  • Mammalian glycerophosphoinositol inositolphosphodiesterase GDPD2 (or GDE3) (EC 3.1.4.43) [PUBMED:12933806], up-regulated during osteoblast differentiation and can affect cell morpholgy. It hydrolyzes glycerophosphoinositol (GroPIns), producing inositol 1-phosphate and glycerol.
  • Mammalian glycerophosphodiester phosphodiesterase domain-containing protein 1 (GDPD1) (EC 3.1.-.-) (or GDE4) [PUBMED:18991142].
  • Mammalian glycerophosphocholine phosphodiesterase GPCPD1 (EC 3.1.4.2) (or GDE5), selectively hydrolyzes glycerophosphocholine (GroPCho) and controls skeletal muscle development [PUBMED:20576599].
  • Mammalian glycerophosphodiester phosphodiesterase domain-containing protein 4 (GDPD4) (EC 3.1.-.-) (or GDE6) [PUBMED:15276213].

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 PLC (CL0384), which has the following description:

Superfamily consists of Glycerophosphoryl diester phosphodiesterase and phosphatidylinositol-specific phospholipase C families.

The clan contains the following 4 members:

GDPD GDPD_2 PI-PLC-X PI-PLC-Y

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(30)
Full
(7067)
Representative proteomes UniProt
(25717)
NCBI
(39674)
Meta
(2555)
RP15
(1481)
RP35
(4575)
RP55
(8287)
RP75
(13005)
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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
(30)
Full
(7067)
Representative proteomes UniProt
(25717)
NCBI
(39674)
Meta
(2555)
RP15
(1481)
RP35
(4575)
RP55
(8287)
RP75
(13005)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(30)
Full
(7067)
Representative proteomes UniProt
(25717)
NCBI
(39674)
Meta
(2555)
RP15
(1481)
RP35
(4575)
RP55
(8287)
RP75
(13005)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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_4008 (release 6.4)
Previous IDs: none
Type: Family
Author: Griffiths-Jones SR
Number in seed: 30
Number in full: 7067
Average length of the domain: 234.00 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 57.33 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.6 23.6
Trusted cut-off 23.6 23.6
Noise cut-off 23.5 23.5
Model length: 259
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

GDPD

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 GDPD domain has been found. There are 59 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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