Summary: Pyridoxal-dependent decarboxylase conserved domain
This is the Wikipedia entry entitled "Group II pyridoxal-dependent decarboxylases". More...
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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 188.8.131.52, which catalyses the decarboxylation of tryptophan to tryptamine, tyrosine decarboxylase EC 184.108.40.206, which converts tyrosine into tyramine and histidine decarboxylase EC 220.127.116.11, 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.
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
|SCOOP:||Late_protein_L1 DegT_DnrJ_EryC1 Cys_Met_Meta_PP Beta_elim_lyase OKR_DC_1 SelA SepSecS LdpA_C TMEM213 PRTase_3 QIL1|
|Similarity to PfamA using HHSearch:||Aminotran_1_2 Aminotran_5 DegT_DnrJ_EryC1 Beta_elim_lyase SepSecS|
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
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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 SepSecS SHMT
We make a range of alignments for each Pfam-A family:
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- 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
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Curation and family details
|Number in seed:||9|
|Number in full:||21776|
|Average length of the domain:||290.00 aa|
|Average identity of full alignment:||26 %|
|Average coverage of the sequence by the domain:||68.81 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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There are 2 interactions 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 132 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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