Summary: Pyridoxal phosphate biosynthetic protein PdxA
Pyridoxal phosphate biosynthetic protein PdxA Provide feedback
In Escherichia coli the coenzyme pyridoxal 5'-phosphate is synthesised de novo by a pathway that is thought to involve the condensation of 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose, catalysed by the enzymes PdxA and PdxJ, to form either pyridoxine (vitamin B6) or pyridoxine 5'-phosphate .
Laber B, Maurer W, Scharf S, Stepusin K, Schmidt FS; , FEBS Lett 1999;449:45-48.: Vitamin B6 biosynthesis: formation of pyridoxine 5'-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein. PUBMED:10225425 EPMC:10225425
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This tab holds annotation information from the InterPro database.
InterPro entry IPR005255
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].
In Escherichia coli, the pdx genes involved in vitamin B6 have been characterised [PUBMED:10225425, PUBMED:15242009, PUBMED:17344055]. This entry represents 4-hydroxythreonine-4-phosphate dehydrogenase (PdxA, EC). PdxA takes part in vitamin B6 biosynthesis, forming pyridoxine 5'-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate.
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|Molecular function||4-hydroxythreonine-4-phosphate dehydrogenase activity (GO:0050570)|
|NAD binding (GO:0051287)|
|Biological process||pyridoxine biosynthetic process (GO:0008615)|
|oxidation-reduction process (GO:0055114)|
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|Seed source:||TIGRFAMs (release 2.0);|
|Author:||TIGRFAMs, Finn RD|
|Number in seed:||16|
|Number in full:||2867|
|Average length of the domain:||293.60 aa|
|Average identity of full alignment:||39 %|
|Average coverage of the sequence by the domain:||88.25 %|
|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:||7|
|Download:||download the raw HMM for this family|
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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 PdxA domain has been found. There are 19 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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