Structure of PDB 3hy8 Chain A

Receptor sequence

>3hy8A (length=211) Species: 9606 (Homo sapiens)

FEETHLTSLDPVKQFAAWFEEAVQCPDIGEANAMCLATCTRDGKPSARML
LLKGFGKDGFRFFTNFESRKGKELDSNPFASLVFYWEPLNRQVRVEGPVK
KLPEEEAECYFHSRPKSSQIGAVVSHQSSVIPDREYLRKKNEELEQLYQD
QEVPKPKSWGGYVLYPQVMEFWQGQTNRLHDWIVFRRGLPTPLGPMTHRG
EEDWLYERLAP

3D structure

• PDB: 3hy8 Molecular basis of reduced pyridoxine 5'-phosphate oxidase catalytic activity in neonatal epileptic encephalopathy disorder
• Chain: A
• Resolution: 2.5 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): R225
• Catalytic site (residue number reindexed from 1): R178
• Enzyme Commision number: 1.4.3.5: pyridoxal 5'-phosphate synthase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	FMN	A	R95 M96 L97 L98 T111 R116 K117 Q174	R48 M49 L50 L51 T64 R69 K70 Q127	MOAD: Kd=672nM
BS02	PLP	A	E77 R161	E30 R114
BS03	PO4	A	K100 R108 Y157	K53 R61 Y110
BS04	PO4	A	S55 K60 E251	S8 K13 E201

Gene Ontology

Molecular Function

• GO:0004733 pyridoxamine phosphate oxidase activity
• GO:0005515 protein binding
• GO:0010181 FMN binding
• GO:0016491 oxidoreductase activity
• GO:0030170 pyridoxal phosphate binding
• GO:0042803 protein homodimerization activity

Biological Process

• GO:0008615 pyridoxine biosynthetic process
• GO:0042816 vitamin B6 metabolic process
• GO:0042818 pyridoxamine metabolic process
• GO:0042822 pyridoxal phosphate metabolic process
• GO:0042823 pyridoxal phosphate biosynthetic process
• GO:1901615 organic hydroxy compound metabolic process

Cellular Component

• GO:0005739 mitochondrion
• GO:0005829 cytosol

External links

• PDB: RCSB:3hy8, PDBe:3hy8, PDBj:3hy8
• PDBsum: 3hy8
• PubMed: 19759001
• UniProt: Q9NVS9|PNPO_HUMAN Pyridoxine-5'-phosphate oxidase (Gene Name=PNPO)