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678  structures 322  species 4  interactions 2973  sequences 39  architectures

Family: PPTA (PF01239)

Summary: Protein prenyltransferase alpha subunit repeat

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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.

Protein prenyltransferase alpha subunit repeat Provide feedback

Both farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) recognise a CaaX motif on their substrates where 'a' stands for preferably aliphatic residues, whereas GGT2 recognises a completely different motif. Important substrates for FT include, amongst others, many members of the Ras superfamily. GGT1 substrates include some of the other small GTPases and GGT2 substrates include the Rab family [2].

Literature references

  1. Strickland CL, Windsor WT, Syto R, Wang L, Bond R, Wu Z, Schwartz J, Le HV, Beese LS, Weber PC; , Biochemistry 1998;37:16601-16611.: Crystal structure of farnesyl protein transferase complexed with a CaaX peptide and farnesyl diphosphate analogue. PUBMED:9843427 EPMC:9843427

  2. Maurer-Stroh S, Washietl S, Eisenhaber F; , Genome Biol 2003;4:212.: Protein prenyltransferases. PUBMED:12702202 EPMC:12702202


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002088

Protein prenylation is the posttranslational attachment of either a farnesyl group or a geranylgeranyl group via a thioether linkage (-C-S-C-) to a cysteine at or near the carboxyl terminus of the protein. Farnesyl and geranylgeranyl groups are polyisoprenes, unsaturated hydrocarbons with a multiple of five carbons; the chain is 15 carbons long in the farnesyl moiety and 20 carbons long in the geranylgeranyl moiety. There are three different protein prenyltransferases in humans: farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) share the same motif (the CaaX box) around the cysteine in their substrates, and are thus called CaaX prenyltransferases, whereas geranylgeranyltransferase 2 (GGT2, also called Rab geranylgeranyltransferase) recognises a different motif and is thus called a non-CaaX prenyltransferase. Protein prenyltransferases are currently known only in eukaryotes, but they are widespread, being found in vertebrates, insects, nematodes, plants, fungi and protozoa, including several parasites.

Each protein consists of two subunits, alpha and beta; the alpha subunit of FT and GGT1 is encoded by the same gene, FNTA. The alpha subunit is thought to participate in a stable complex with the isoprenyl substrate; the beta subunit binds the peptide substrate. In the alpha subunits of both types of protein prenyltransferases, seven tetratricopeptide repeats are formed by pairs of helices that are stabilised by conserved intercalating residues. The alpha subunits of GGT2 in mammals and plants also have an immunoglobulin-like domain between the fifth and sixth tetratricopeptide repeat, as well as leucine-rich repeats at the carboxyl terminus. The functions of these additional domains in GGT2 are as yet undefined, but they are apparently not directly involved in the interaction with substrates and Rab escort proteins. The tetratricopeptide repeats of the alpha subunit form a right-handed superhelix, which embraces the (alpha-alpha)6 barrel of the beta subunit [PUBMED:1622936].

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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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
(143)
Full
(2973)
Representative proteomes NCBI
(2958)
Meta
(11)
RP15
(614)
RP35
(1031)
RP55
(1549)
RP75
(1957)
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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
(143)
Full
(2973)
Representative proteomes NCBI
(2958)
Meta
(11)
RP15
(614)
RP35
(1031)
RP55
(1549)
RP75
(1957)
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
(143)
Full
(2973)
Representative proteomes NCBI
(2958)
Meta
(11)
RP15
(614)
RP35
(1031)
RP55
(1549)
RP75
(1957)
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: Prosite
Previous IDs: none
Type: Repeat
Author: Finn RD, Bateman A
Number in seed: 143
Number in full: 2973
Average length of the domain: 30.30 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 27.00 %

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 20.2 20.2
Trusted cut-off 20.2 20.2
Noise cut-off 20.1 20.1
Model length: 31
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 4 interactions for this family. More...

GDI PPTA Prenyltrans RabGGT_insert

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 PPTA domain has been found. There are 678 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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