Family

Uncharacterised protein family UPF0001 (IPR011078)

Short name: UPF0001

Family relationships

None.

Description

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 [PMID: 8690703, PMID: 7748903, PMID: 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 [PMID: 17109392]. Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy [PMID: 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 [PMID: 15581583].

Proteins in this entry occur in archaea, bacteria and eukaryotes. They are encoded by genes which are often co-transcribed with proline biosysnthesis genes [PMID: 10496079], although their function in vivo has not yet been demonstrated.

The structure of the yeast protein YBL036C (P38197) has been determined to a resolution of 2.0 A [PMID: 12499548]. Similar in structure to the N-terminal domains of alanine racemase and ornithine decarboxylase, it forms a TIM barrel fold which begins with a long N-terminal helix, rather than the classical beta strand found at the beginning of most other TIM barrels. Unlike alanine racemase and ornithine decarboxylase, which are two-domain dimeric proteins, the yeast protein is a single domain monomer. A pyridoxal 5'-phosphate cofactor is covalently bound towards the C-terminal end of the barrel, which is the usual active site in TIM-barrel folds. Some racemase activity was observed for this protein and it was suggested by the authors that it may function as a general racemase [PMID: 12499548].

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
PROSITE patterns
PANTHER
TIGRFAMs
PIRSF