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90  structures 3273  species 1  interaction 7254  sequences 35  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
Identifiers
Symbol Pyridoxal_deC
Pfam PF00282
Pfam clan CL0061
InterPro IPR002129
PROSITE PDOC00329
SCOP 1js3
SUPERFAMILY 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 4.1.1.28, which catalyses the decarboxylation of tryptophan to tryptamine, tyrosine decarboxylase EC 4.1.1.25, which converts tyrosine into tyramine and histidine decarboxylase EC 4.1.1.22, 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

References

  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 53340. 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; 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].

Gene Ontology

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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 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

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
(11)
Full
(7254)
Representative proteomes NCBI
(6947)
Meta
(942)
RP15
(695)
RP35
(1263)
RP55
(1924)
RP75
(2360)
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Format an alignment

  Seed
(11)
Full
(7254)
Representative proteomes NCBI
(6947)
Meta
(942)
RP15
(695)
RP35
(1263)
RP55
(1924)
RP75
(2360)
Alignment:
Format:
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
(11)
Full
(7254)
Representative proteomes NCBI
(6947)
Meta
(942)
RP15
(695)
RP35
(1263)
RP55
(1924)
RP75
(2360)
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.

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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: Prosite
Previous IDs: pyridoxal_deC;
Type: Family
Author: Finn RD
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 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 19.8 19.8
Trusted cut-off 19.8 19.8
Noise cut-off 19.7 19.7
Model length: 373
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Pyridoxal_deC

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 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.

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