Summary: Pyridoxamine 5'-phosphate oxidase
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Internal database links
|Similarity to PfamA using HHSearch:||DUF385 DUF447 FMN_bind_2 Pyridox_oxase_2 Pyridox_ox_2 Pyrid_oxidase_2|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR011576
Pyridoxamine 5'-phosphate oxidase (PNPOx; EC) is a FMN flavoprotein that catalyses the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). This reaction serves as the terminal step in the de novo biosynthesis of PLP in Escherichia coli and as a part of the salvage pathway of this coenzyme in both E. coli and mammalian cells [PUBMED:12686112, PUBMED:12824491]. The binding sites for FMN and for substrate have been highly conserved throughout evolution.
This entry represents the FMN-binding domain present in pyridoxamine 5'-phosphate oxidases, as well as in a number of proteins that have not been demonstrated to have enzymatic activity. The FMN-binding domain has a structure consisting of a beta-barrel with Greek key topology, and is related to the ferredoxin reductase-like FAD-binding domain. PNPOx has a different dimerisation mode than that found in flavin reductases, which also carry an FMN-binding domain with a similar topology.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||pyridoxamine-phosphate oxidase activity (GO:0004733)|
|FMN binding (GO:0010181)|
|Biological process||oxidation-reduction process (GO:0055114)|
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This includes those related to the ferredoxin reductase-like FAD-binding domain and those that are Pyridoxine 5'-phosphate oxidase (PNP)-like.
The clan contains the following 8 members:DUF385 DUF447 Flavin_Reduct FMN_bind_2 Pyrid_oxidase_2 Pyridox_ox_2 Pyridox_oxase_2 Pyridox_oxidase
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Curation and family details
|Number in seed:||141|
|Number in full:||8674|
|Average length of the domain:||89.20 aa|
|Average identity of full alignment:||19 %|
|Average coverage of the sequence by the domain:||47.13 %|
|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:||15|
|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 Pyridox_oxidase domain has been found. There are 83 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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