6YMH

X-ray structure of the K72I, Y129F, R133L, H199A quadruple mutant of PNP-oxidase from E. coli in complex with PLP


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
B [auth BBB]SCOP2B SuperfamilyFMN-binding split barrel 8042082 3000856 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth AAA]Putative_PNPOxe6ymhAAA1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: Putative_PNPOxECOD (1.6)
B [auth BBB]Putative_PNPOxe6ymhBBB1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: Putative_PNPOxECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth AAA],
B [auth BBB]
PF10590Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region (PNP_phzG_C)Pyridoxine 5'-phosphate oxidase C-terminal dimerisation regionThis domain represents one of the two dimerisation regions of the protein, located at the edge of the dimer interface, at the C-terminus, being the last three beta strands, S6, S7, and S8 along with the last three residues to the end. In Swiss:P21159 ...This domain represents one of the two dimerisation regions of the protein, located at the edge of the dimer interface, at the C-terminus, being the last three beta strands, S6, S7, and S8 along with the last three residues to the end. In Swiss:P21159, S6 runs from residues 178-192, S7 from 200-206 and S8 from 211-215. the extended loop, of residues 167-177 may well be involved in the pocket formed between the two dimers that positions the FMN molecule [1].To date, the only time functional oxidase or phenazine biosynthesis activities have been experimentally demonstrated is when the sequences contain both Pfam:PF01243 and Pfam:PF10590. It is unknown the role performed by each domain in bringing about molecular functions of either oxidase or phenazine activity [2].
Domain
A [auth AAA],
B [auth BBB]
PF01243Pyridoxamine 5'-phosphate oxidase (Putative_PNPOx)Pyridoxamine 5'-phosphate oxidaseFamily of domains with putative PNPOx function. Family members were predicted to encode pyridoxamine 5'-phosphate oxidase, based on sequence similarity. However, there is no experimental data to validate the predicted activity and purified proteins, ...Family of domains with putative PNPOx function. Family members were predicted to encode pyridoxamine 5'-phosphate oxidase, based on sequence similarity. However, there is no experimental data to validate the predicted activity and purified proteins, such as Swiss:Q06199 and its paralogs, do not possess this activity, nor do they bind to flavin mononucleotide (FMN). To date, the only time functional oxidase activity has been experimentally demonstrated is when the sequences contain both Pfam:PF01243 and Pfam:PF10590. Moreover, some of the family members that contain both domains have been shown to be involved in phenazine biosynthesis. While some molecular function has been experimentally validated for the proteins containing both domains, the role performed by each domain on its own is unknown [1].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth AAA],
B [auth BBB]
Pyridoxine/pyridoxamine 5'-phosphate oxidase