Q89RY8 (PDXH_BRAJA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Pyridoxine/pyridoxamine 5'-phosphate oxidase
EC=1.4.3.5

Alternative name(s):
PNP/PMP oxidase
Short name=PNPOx
Pyridoxal 5'-phosphate synthase

Gene names

Name:	pdxH
Ordered Locus Names:	bll2624

Organism

Bradyrhizobium japonicum (strain USDA 110) [Reference proteome] [HAMAP]

Taxonomic identifier

224911 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Alphaproteobacteria › Rhizobiales › Bradyrhizobiaceae › Bradyrhizobium › Bradyrhizobium japonicum

Protein attributes

Sequence length	213 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP) By similarity. HAMAP-Rule MF_01629
Catalytic activity	Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2. HAMAP-Rule MF_01629 Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2. HAMAP-Rule MF_01629
Cofactor	Binds 1 FMN per subunit By similarity.
Pathway	Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1. HAMAP-Rule MF_01629 Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxine 5'-phosphate: step 1/1.
Subunit structure	Homodimer By similarity.
Sequence similarities	Belongs to the pyridoxamine 5'-phosphate oxidase family.

Ontologies

Keywords
Biological process	Pyridoxine biosynthesis
Ligand	FMN Flavoprotein
Molecular function	Oxidoreductase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	pyridoxal phosphate biosynthetic process Inferred from electronic annotation. Source: GOC pyridoxine biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	FMN binding Inferred from electronic annotation. Source: HAMAP pyridoxamine-phosphate oxidase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 213	213	Pyridoxine/pyridoxamine 5'-phosphate oxidase HAMAP-Rule MF_01629		PRO_0000167692
Regions
	Nucleotide binding	75 – 76	2	FMN By similarity
	Nucleotide binding	139 – 140	2	FMN By similarity
	Region	190 – 192	3	Substrate binding By similarity
Sites
	Binding site	60	1	FMN By similarity
	Binding site	63	1	FMN; via amide nitrogen By similarity
	Binding site	65	1	Substrate By similarity
	Binding site	82	1	FMN By similarity
	Binding site	122	1	Substrate By similarity
	Binding site	126	1	Substrate By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q89RY8 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: D12CF55C86CFBFB6	FASTA	213	24,181
	10 20 30 40 50 60 MTDTTSMKHQ TPLTSGDFTA ADEPFALFET WLNEAIKSEP NDPNAMALAT VDPDGLPDVR 70 80 90 100 110 120 MVLMKGFDTE GFVFYSHIAS QKGRELAANP KAALLFHWKS LRRQVRIRGN VTPVTDAEAD 130 140 150 160 170 180 AYFATRPKQA QIGAWASKQS EALESRFAFE QAIAKVAAKY IIGEVPRPPG WSGWRITPVR 190 200 210 IEFWHDRPFR LHDRIEFRRD AAGQKWSKTR MYP

References

[1]

"Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110." Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S., Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M., Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S. DNA Res. 9:189-197(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: USDA 110.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BA000040 Genomic DNA. Translation: BAC47889.1.
RefSeq	NP_769264.1. NC_004463.1.
3D structure databases
ProteinModelPortal	Q89RY8.
ModBase	Search...
Protein-protein interaction databases
STRING	224911.bll2624.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	BAC47889; BAC47889; BAC47889.
GeneID	1051429.
KEGG	bja:bll2624.
PATRIC	21188678. VBIBraJap65052_2598.
Phylogenomic databases
eggNOG	COG0259.
HOGENOM	HOG000242755.
KO	K00275.
OMA	HWSGFRI.
ProtClustDB	PRK05679.
Enzyme and pathway databases
BioCyc	BJAP224911:GJEJ-2647-MONOMER.
UniPathway	UPA00190; UER00304. UPA00190; UER00305.
Family and domain databases
Gene3D	2.30.110.10. 1 hit.
HAMAP	MF_01629. PdxH.
InterPro	IPR000659. Pyridox_Oxase. IPR019740. Pyridox_Oxase_CS. IPR011576. Pyridox_Oxase_FMN-bd. IPR019576. Pyridoxamine_oxidase_dimer_C. IPR012349. Split_barrel_FMN-bd. [Graphical view]
PANTHER	PTHR10851. PTHR10851. 1 hit.
Pfam	PF10590. PNPOx_C. 1 hit. PF01243. Pyridox_oxidase. 1 hit. [Graphical view]
PIRSF	PIRSF000190. Pyd_amn-ph_oxd. 1 hit.
SUPFAM	SSF50475. FMN_binding. 1 hit.
TIGRFAMs	TIGR00558. pdxH. 1 hit.
PROSITE	PS01064. PYRIDOX_OXIDASE. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PDXH_BRAJA

Accession

Primary (citable) accession number: Q89RY8

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 24, 2006
Last sequence update:	June 1, 2003
Last modified:	May 1, 2013
This is version 69 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program