Summary: Phosphopantetheine attachment site
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Phosphopantetheine attachment site Provide feedback
A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of P19828 has the attachment serine replaced by an alanine.
Internal database links
SCOOP: | DUF1493 PP-binding_2 Ribosomal_L50 |
External database links
HOMSTRAD: | pp-binding |
PROSITE: | PDOC00012 |
SCOP: | 1acp |
This tab holds annotation information from the InterPro database.
InterPro entry IPR009081
Acyl carrier protein (ACP) is an essential cofactor in the synthesis of fatty acids by the fatty acid synthetases systems in bacteria and plants. In addition to fatty acid synthesis, ACP is also involved in many other reactions that require acyl transfer steps, such as the synthesis of polyketide antibiotics, biotin precursor, membrane-derived oligosaccharides, and activation of toxins, and functions as an essential cofactor in lipoylation of pyruvate and alpha-ketoglutarate dehydrogenase complexes [PUBMED:12057197]. Phosphopantetheine (or pantetheine 4' phosphate) is the prosthetic group of acyl carrier proteins (ACP) in some multienzyme complexes where it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups [PUBMED:18551496]. Phosphopantetheine is attached to a serine residue in these proteins. The core structure of ACP consists of a four-helical bundle, where helix three is shorter than the others.
Several other proteins share structural homology with ACP, such as the bacterial apo-D-alanyl carrier protein, which facilitates the incorporation of D-alanine into lipoteichoic acid by a ligase, necessary for the growth and development of Gram-positive organisms [PUBMED:11434765]; and the thioester domain of the bacterial peptide carrier protein (PCP) found within large modular non-ribosomal peptide synthetases, which are responsible for the synthesis of a variety of microbial bioactive peptides [PUBMED:10801488].
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 PP-binding (CL0314), which has the following description:
The clan contains the following 4 members:
DUF1493 PP-binding PP-binding_2 Ribosomal_L50Alignments
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 (154) |
Full (90917) |
Representative proteomes | UniProt (338843) |
NCBI (707631) |
Meta (2940) |
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RP15 (5557) |
RP35 (27188) |
RP55 (63890) |
RP75 (122475) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (154) |
Full (90917) |
Representative proteomes | UniProt (338843) |
NCBI (707631) |
Meta (2940) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (5557) |
RP35 (27188) |
RP55 (63890) |
RP75 (122475) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | SCOP |
Previous IDs: | pp-binding; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 154 |
Number in full: | 90917 |
Average length of the domain: | 66.40 aa |
Average identity of full alignment: | 22 % |
Average coverage of the sequence by the domain: | 6.68 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 67 | ||||||||||||
Family (HMM) version: | 26 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 14 interactions for this family. More...
ACPS FA_desaturase_2 Thioesterase tRNA-synt_2b PP-binding p450 AMP-binding STAS Condensation AMP-binding_C AMP-binding AMP-binding_C Abhydrolase_6 CondensationStructures
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 PP-binding domain has been found. There are 348 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 sequence.
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