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99  structures 4744  species 1  interaction 7983  sequences 48  architectures

Family: ACPS (PF01648)

Summary: 4'-phosphopantetheinyl transferase superfamily

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This is the Wikipedia entry entitled "4'-phosphopantetheinyl transferase". More...

4'-phosphopantetheinyl transferase Edit Wikipedia article

ACPS
PDB 1qr0 EBI.jpg
crystal structure of the 4'-phosphopantetheinyl transferase sfp-coenzyme a complex
Identifiers
Symbol ACPS
Pfam PF01648
InterPro IPR008278
SCOP 1qr0
SUPERFAMILY 1qr0

In molecular biology, the 4'-phosphopantetheinyl transferase superfamily of proteins transfer a 4'-phosphopantetheine (4'-PP) moiety from coenzyme A (CoA) to an invariant serine in an acyl carrier protein (ACP), a small protein responsible for acyl group activation in fatty acid biosynthesis. This post-translational modification renders holo-ACP capable of acyl group activation via thioesterification of the cysteamine thiol of 4'-PP.[1] This superfamily consists of two subtypes: The ACPS type such as E. coli ACPS and the Sfp type such as B. subtilis SFP. The structure of the Sfp type is known,[2] which shows the active site accommodates a magnesium ion. The most highly conserved regions of the protein are involved in binding the magnesium ion.

References[edit]

  1. ^ Lambalot RH, Walsh CT (October 1995). "Cloning, overproduction, and characterization of the Escherichia coli holo-acyl carrier protein synthase". J. Biol. Chem. 270 (42): 24658–61. doi:10.1074/jbc.270.42.24658. PMID 7559576. 
  2. ^ Reuter K, Mofid MR, Marahiel MA, Ficner R (December 1999). "Crystal structure of the surfactin synthetase-activating enzyme sfp: a prototype of the 4'-phosphopantetheinyl transferase superfamily". EMBO J. 18 (23): 6823–31. doi:10.1093/emboj/18.23.6823. PMC 1171745. PMID 10581256. 

This article incorporates text from the public domain Pfam and InterPro IPR008278

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.

4'-phosphopantetheinyl transferase superfamily Provide feedback

Members of this family transfers the 4'-phosphopantetheine (4'-PP) moiety from coenzyme A (CoA) to the invariant serine of PF00550. This post-translational modification renders holo-ACP capable of acyl group activation via thioesterification of the cysteamine thiol of 4'-PP [1]. This superfamily consists of two subtypes: The ACPS type such as P24224 and the Sfp type such as P39135. The structure of the Sfp type is known [3] which shows the active site accommodates a magnesium ion. The most highly conserved regions of the alignment are involved in binding the magnesium ion.

Literature references

  1. Lambalot RH, Walsh CT; , J Biol Chem 1995;270:24658-24661.: Cloning, overproduction, and characterization of the Escherichia coli holo-acyl carrier protein synthase. PUBMED:7559576 EPMC:7559576

  2. Lambalot RH, Gehring AM, Flugel RS, Zuber P, LaCelle M, Marahiel MA, Reid R, Khosla C, Walsh CT; , Chem Biol 1996;3:923-936.: A new enzyme superfamily - the phosphopantetheinyl transferases. PUBMED:8939709 EPMC:8939709

  3. Reuter K, Mofid MR, Marahiel MA, Ficner R; , EMBO J 1999;18:6823-6831.: Crystal structure of the surfactin synthetase-activating enzyme sfp: a prototype of the 4'-phosphopantetheinyl transferase superfamily [In Process Citation] PUBMED:10581256 EPMC:10581256


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008278

These proteins transfer the 4'-phosphopantetheine (4'-PP) moiety from coenzyme A (CoA) to the invariant serine of pp-binding. This post-translational modification renders holo-ACP capable of acyl group activation via thioesterification of the cysteamine thiol of 4'-PP [PUBMED:7559576]. This superfamily consists of two subtypes: The ACPS type such as ACPS_ECOLI and the Sfp type such as SFP_BACSU. The structure of the Sfp type is known [PUBMED:10581256], which shows the active site accommodates a magnesium ion. The most highly conserved regions of the alignment are involved in binding the magnesium ion.

Gene Ontology

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Domain organisation

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Alignments

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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
(7983)
Representative proteomes NCBI
(5342)
Meta
(1894)
RP15
(622)
RP35
(1194)
RP55
(1612)
RP75
(1916)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(154)
Full
(7983)
Representative proteomes NCBI
(5342)
Meta
(1894)
RP15
(622)
RP35
(1194)
RP55
(1612)
RP75
(1916)
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
(154)
Full
(7983)
Representative proteomes NCBI
(5342)
Meta
(1894)
RP15
(622)
RP35
(1194)
RP55
(1612)
RP75
(1916)
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.

Pfam alignments:

HMM logo

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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_1679 (release 4.1) & Pfam-B_3672 (Release 7.5)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 154
Number in full: 7983
Average length of the domain: 110.90 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 48.33 %

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 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 115
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...

ACPS

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 ACPS domain has been found. There are 99 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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