Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
20  structures 137  species 1  interaction 362  sequences 4  architectures

Family: GMP_PDE_delta (PF05351)

Summary: GMP-PDE, delta subunit

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

This is the Wikipedia entry entitled "GMP phosphodiesterase, delta subunit". More...

GMP phosphodiesterase, delta subunit Edit Wikipedia article

GMP-PDE, delta subunit
1ksg opm.gif
Membrane-bound ADP ribosylation factor-like protein 2 (ARL2 mouse, red), complex with phosphodiesterase delta (yellow) (1ksg) Blue dots show hydrocarbon boundary of the lipid bilayer
Identifiers
Symbol GMP_PDE_delta
Pfam PF05351
InterPro IPR008015
SCOP 1ksj
SUPERFAMILY 1ksj
OPM protein 1ksg

GMP-PDE delta subunit was originally identified as a fourth subunit of rod cell-specific cGMP phosphodiesterase (PDE) (EC 3.1.4.35). The precise function of PDE delta subunit in the rod specific GMP-PDE complex is unclear. In addition, PDE delta subunit is not confined to photoreceptor cells but is widely distributed in different tissues. PDE delta subunit is thought to be a specific soluble transport factor for certain prenylated proteins and Arl2-GTP a regulator of PDE-mediated transport.[1]

Human proteins containing this domain[edit]

PDE6D; UNC119;

References[edit]

  1. ^ Wittinghofer A, Renault L, Hanzal-bayer M, Roversi P, Hillig RC (2002). "The complex of Arl2-GTP and PDE delta: from structure to function". EMBO J. 21 (9): 2095–2106. doi:10.1093/emboj/21.9.2095. PMC 125981. PMID 11980706. 

This article incorporates text from the public domain Pfam and InterPro IPR008015

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

GMP-PDE, delta subunit Provide feedback

GMP-PDE delta subunit was originally identified as a fourth subunit of rod-specific cGMP phosphodiesterase (PDE)( EC:3.1.4.35). The precise function of PDE delta subunit in the rod specific GMP-PDE complex is unclear. In addition, PDE delta subunit is not confined to photoreceptor cells but is widely distributed in different tissues. PDE delta subunit is thought to be a specific soluble transport factor for certain prenylated proteins and Arl2-GTP a regulator of PDE-mediated transport [1].

Literature references

  1. Hanzal-Bayer M, Renault L, Roversi P, Wittinghofer A, Hillig RC; , EMBO J 2002;21:2095-2106.: The complex of Arl2-GTP and PDE delta: from structure to function. PUBMED:11980706 EPMC:11980706


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008015

GMP-PDE delta subunit was originally identified as a fourth subunit of rod-specific cGMP phosphodiesterase (PDE) (EC). The precise function of PDE delta subunit in the rod specific GMP-PDE complex is unclear. In addition, PDE delta subunit is not confined to photoreceptor cells but is widely distributed in different tissues. PDE delta subunit is thought to be a specific soluble transport factor for certain prenylated proteins and Arl2-GTP a regulator of PDE-mediated transport [PUBMED:11980706].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

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
(23)
Full
(362)
Representative proteomes NCBI
(325)
Meta
(4)
RP15
(80)
RP35
(100)
RP55
(155)
RP75
(215)
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(23)
Full
(362)
Representative proteomes NCBI
(325)
Meta
(4)
RP15
(80)
RP35
(100)
RP55
(155)
RP75
(215)
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
(23)
Full
(362)
Representative proteomes NCBI
(325)
Meta
(4)
RP15
(80)
RP35
(100)
RP55
(155)
RP75
(215)
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_13828 (release 7.8)
Previous IDs: none
Type: Family
Author: Finn RD
Number in seed: 23
Number in full: 362
Average length of the domain: 144.60 aa
Average identity of full alignment: 44 %
Average coverage of the sequence by the domain: 72.54 %

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 25.0 25.0
Trusted cut-off 30.2 30.1
Noise cut-off 18.2 18.1
Model length: 157
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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...

Loading sunburst data...

Tree controls

Hide

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

Loading...

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.

Interactions

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

Arf

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 GMP_PDE_delta domain has been found. There are 20 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.

Loading structure mapping...