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218  structures 4781  species 0  interactions 22160  sequences 206  architectures

Family: Pyridoxal_deC (PF00282)

Summary: Pyridoxal-dependent decarboxylase conserved domain

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This is the Wikipedia entry entitled "Group II pyridoxal-dependent decarboxylases". More...

Group II pyridoxal-dependent decarboxylases Edit Wikipedia article

Pyridoxal-dependent decarboxylase conserved domain
PDB 1es0 EBI.jpg
crystal structure of the murine class ii allele i-a(g7) complexed with the glutamic acid decarboxylase (gad65) peptide 207-220
Symbol Pyridoxal_deC
Pfam PF00282
Pfam clan CL0061
InterPro IPR002129
SCOP 1js3

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, which catalyses the decarboxylation of tryptophan to tryptamine, tyrosine decarboxylase EC, which converts tyrosine into tyramine and histidine decarboxylase EC, which catalyses the decarboxylation of histidine to histamine.[1][2]

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.[3]

See also


  1. ^ 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. 
  2. ^ 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 53340Freely accessible. PMID 2300558. 
  3. ^ 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 article incorporates text from the public domain Pfam and InterPro IPR002129

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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Pyridoxal-dependent decarboxylase conserved domain Provide feedback

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Literature references

  1. 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

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; histidine decarboxylase, which catalyses the decarboxylation of histidine to histamine [ PUBMED:2300558 ]; L-aspartate decarboxylase, which converts aspartate to beta-alanine [ PUBMED:24415726 ]; and phenylacetaldehyde synthase that catalyses the decarboxylation of L-phenylalanine to 2-phenylethylamine [ PUBMED:16766535 ]. These enzymes belong to the group II decarboxylases [ PUBMED:8181483 , PUBMED:8889823 ].

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 PLP_aminotran (CL0061), which has the following description:

This superfamily contains a variety of PLP-dependent enzymes.

The clan contains the following 16 members:

Alliinase_C Aminotran_1_2 Aminotran_3 Aminotran_5 Asp_aminotransf Beta_elim_lyase ComK Cys_Met_Meta_PP DegT_DnrJ_EryC1 GDC-P Met_gamma_lyase OKR_DC_1 Pyridoxal_deC SelA SepSecS SHMT


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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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.

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Curation and family details

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Seed source: Prosite
Previous IDs: pyridoxal_deC;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 9
Number in full: 22160
Average length of the domain: 309.00 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 63.15 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 375
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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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 218 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0A2IDH4 View 3D Structure Click here
A0A0P0WPH7 View 3D Structure Click here
A0A0P0Y215 View 3D Structure Click here
A0A0R0ELZ8 View 3D Structure Click here
A0A0R0I4X1 View 3D Structure Click here
A0A1D6E9M9 View 3D Structure Click here
A0A1D6FCD5 View 3D Structure Click here
A0A1D6HA12 View 3D Structure Click here
A0A1D6JQY5 View 3D Structure Click here
A0A1D6JQY7 View 3D Structure Click here
A0A1D6KL56 View 3D Structure Click here
A0A1D6PWC9 View 3D Structure Click here
A0A1D6Q2W6 View 3D Structure Click here
A0A1D8PF79 View 3D Structure Click here
A0A1D8PJQ9 View 3D Structure Click here
A0A2R8Q3N8 View 3D Structure Click here
A0B9M9 View 3D Structure Click here
A0PA85 View 3D Structure Click here
A1Z6N2 View 3D Structure Click here
A1Z6N4 View 3D Structure Click here
A2STQ3 View 3D Structure Click here
A4HWU0 View 3D Structure Click here
A4I5R3 View 3D Structure Click here
A6QM00 View 3D Structure Click here
A6UVR4 View 3D Structure Click here
A7IAB9 View 3D Structure Click here
A7MBC2 View 3D Structure Click here
A8C8H5 View 3D Structure Click here
B0V1P2 View 3D Structure Click here
B4F972 View 3D Structure Click here
B4G0K6 View 3D Structure Click here
B6SWT3 View 3D Structure Click here
B6TV07 View 3D Structure Click here
B8A0V8 View 3D Structure Click here
B8GDM7 View 3D Structure Click here
C0HHT5 View 3D Structure Click here
C0PCE9 View 3D Structure Click here
C6T8E8 View 3D Structure Click here
C6TF12 View 3D Structure Click here
E7FDZ2 View 3D Structure Click here