Summary: Pyridoxal-dependent decarboxylase conserved domain
This is the Wikipedia entry entitled "Group II pyridoxal-dependent decarboxylases". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at email@example.com and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
Group II pyridoxal-dependent decarboxylases Edit Wikipedia article
|Pyridoxal-dependent decarboxylase conserved domain|
crystal structure of the murine class ii allele i-a(g7) complexed with the glutamic acid decarboxylase (gad65) peptide 207-220
In molecular biology, group II pyridoxal-dependent decarboxylases are family of enzymes including aromatic-L-amino-acid decarboxylase (L-dopa decarboxylase or tryptophan decarboxylase) EC 22.214.171.124, which catalyses the decarboxylation of tryptophan to tryptamine, tyrosine decarboxylase EC 126.96.36.199, which converts tyrosine into tyramine and histidine decarboxylase EC 188.8.131.52, which catalyses the decarboxylation of histidine to histamine.
Pyridoxal-5'-phosphate-dependent amino acid decarboxylases can be divided into four groups based on amino acid sequence. Group II includes glutamate, histidine, tyrosine, and aromatic-L-amino-acid decarboxylases.
- Group I pyridoxal-dependent decarboxylases
- Group III pyridoxal-dependent decarboxylases
- Group IV pyridoxal-dependent decarboxylases
- Ishii S, Mizuguchi H, Nishino J, Hayashi H, Kagamiyama H (August 1996). "Functionally important residues of aromatic L-amino acid decarboxylase probed by sequence alignment and site-directed mutagenesis". J. Biochem. 120 (2): 369–76. doi:10.1093/oxfordjournals.jbchem.a021422. PMID 8889823.
- Joseph DR, Sullivan PM, Wang YM, Kozak C, Fenstermacher DA, Behrendsen ME, Zahnow CA (January 1990). "Characterization and expression of the complementary DNA encoding rat histidine decarboxylase". Proc. Natl. Acad. Sci. U.S.A. 87 (2): 733–7. doi:10.1073/pnas.87.2.733. PMC 53340. PMID 2300558.
- Sandmeier E, Hale TI, Christen P (May 1994). "Multiple evolutionary origin of pyridoxal-5'-phosphate-dependent amino acid decarboxylases". Eur. J. Biochem. 221 (3): 997–1002. doi:10.1111/j.1432-1033.1994.tb18816.x. PMID 8181483.
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.
Pyridoxal-dependent decarboxylase conserved domain Provide feedback
No Pfam abstract.
Viguera E, Trelles O, Urdiales JL, Mates JM, Sanchez-Jimenez F; , Trends Biochem Sci 1994;19:318-319.: Mammalian L-amino acid decarboxylases producing 1,4-diamines: analogies among differences. PUBMED:7940675 EPMC:7940675
Internal database links
|Similarity to PfamA using HHSearch:||Aminotran_1_2 Aminotran_5 Beta_elim_lyase DegT_DnrJ_EryC1 SLA_LP_auto_ag|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR002129
Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). Pyridoxal 5'-phosphate (PLP) is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination [PUBMED:8690703, PUBMED:7748903, PUBMED:15189147]. PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors [PUBMED:17109392]. Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy [PUBMED:16763894].
PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalysed reactions, enzymatic and non-enzymatic [PUBMED:15581583].A number of pyridoxal-dependent decarboxylases share regions of sequence similarity, particularly in the vicinity of a conserved lysine residue, which provides the attachment site for the pyridoxal-phosphate (PLP) group [PUBMED:8181483, PUBMED:2124279]. Among these enzymes are aromatic-L-amino-acid decarboxylase (L-dopa decarboxylase or tryptophan decarboxylase), which catalyses the decarboxylation of tryptophan to tryptamine [PUBMED:8889823]; tyrosine decarboxylase, which converts tyrosine into tyramine; and histidine decarboxylase, which catalyses the decarboxylation of histidine to histamine [PUBMED:2300558]. These enzymes belong to the group II decarboxylases [PUBMED:8181483, PUBMED:8889823].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||carboxy-lyase activity (GO:0016831)|
|pyridoxal phosphate binding (GO:0030170)|
|Biological process||carboxylic acid metabolic process (GO:0019752)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
This superfamily contains a variety of PLP-dependent enzymes.
The clan contains the following 15 members:Alliinase_C Aminotran_1_2 Aminotran_3 Aminotran_5 Aminotran_MocR Beta_elim_lyase Cys_Met_Meta_PP DegT_DnrJ_EryC1 GDC-P Met_gamma_lyase OKR_DC_1 Pyridoxal_deC SelA SHMT SLA_LP_auto_ag
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Number in seed:||11|
|Number in full:||7254|
|Average length of the domain:||298.70 aa|
|Average identity of full alignment:||24 %|
|Average coverage of the sequence by the domain:||67.83 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Pyridoxal_deC domain has been found. There are 90 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...