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161  structures 4518  species 3  interactions 20885  sequences 130  architectures

Family: ACT (PF01842)

Summary: ACT domain

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This is the Wikipedia entry entitled "ACT domain". More...

ACT domain Edit Wikipedia article

ACT
PDB 2j0w EBI.jpg
Crystal structure of E. coli aspartokinase iii in complex with aspartate and adp (r-state)
Identifiers
Symbol ACT
Pfam PF01842
Pfam clan CL0070
InterPro IPR002912
SCOP 1psd
SUPERFAMILY 1psd
CDD cd02116

In molecular biology, the ACT domain is a protein domain that is found in a variety of proteins involved in metabolism. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The ACT domain is named after three of the proteins that contain it: aspartate kinase, chorismate mutase and TyrA. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure.[1]

The ACT domain was discovered by Aravind and Koonin using iterative sequence searches.[2]

References[edit]

  1. ^ Chipman DM, Shaanan B (December 2001). "The ACT domain family". Curr. Opin. Struct. Biol. 11 (6): 694–700. doi:10.1016/S0959-440X(01)00272-X. PMID 11751050. 
  2. ^ Aravind L, Koonin EV (April 1999). "Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches". J. Mol. Biol. 287 (5): 1023–40. doi:10.1006/jmbi.1999.2653. PMID 10222208. 

This article incorporates text from the public domain Pfam and InterPro IPR002912

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.

ACT domain Provide feedback

This family of domains generally have a regulatory role. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. The ACT domain is found in: D-3-phosphoglycerate dehydrogenase EC:1.1.1.95 P08328 which is inhibited by serine [1]. Aspartokinase EC:2.7.2.4 P53553 which is regulated by lysine. Acetolactate synthase small regulatory subunit P00894 which is inhibited by valine. Phenylalanine-4-hydroxylase EC:1.14.16.1 P00439 which is regulated by phenylalanine. Prephenate dehydrogenase EC:4.2.1.51 P21203. formyltetrahydrofolate deformylase EC:3.5.1.10, P37051 which is activated by methionine and inhibited by glycine. GTP pyrophosphokinase EC:2.7.6.5 P11585

Literature references

  1. Schuller DJ, Grant GA, Banaszak LJ; , Nat Struct Biol 1995;2:69-76.: The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase. PUBMED:7719856 EPMC:7719856

  2. Aravind L, Koonin EV; , J Mol Biol 1999;287:1023-1040.: Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. PUBMED:10222208 EPMC:10222208


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002912

The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure [PUBMED:11751050].

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 ACT (CL0070), which has the following description:

These domains are involved in binding to amino-acids and causing allosteric regulation of linked enzyme domains [1]. The relationship between these two families was first noticed in [2].

The clan contains the following 9 members:

ACT ACT_3 ACT_4 ACT_5 ACT_6 ACT_7 DUF493 NikR_C Thr_dehydrat_C

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...

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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
(180)
Full
(20885)
Representative proteomes NCBI
(23355)
Meta
(10616)
RP15
(1838)
RP35
(3898)
RP55
(5060)
RP75
(5944)
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Format an alignment

  Seed
(180)
Full
(20885)
Representative proteomes NCBI
(23355)
Meta
(10616)
RP15
(1838)
RP35
(3898)
RP55
(5060)
RP75
(5944)
Alignment:
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Order:
Sequence:
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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
(180)
Full
(20885)
Representative proteomes NCBI
(23355)
Meta
(10616)
RP15
(1838)
RP35
(3898)
RP55
(5060)
RP75
(5944)
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: Bateman A
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 180
Number in full: 20885
Average length of the domain: 64.10 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 16.98 %

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 20.8 20.2
Trusted cut-off 20.8 20.2
Noise cut-off 20.7 20.1
Model length: 66
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

ACT 2-Hacid_dh ALS_ss_C

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 ACT domain has been found. There are 161 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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