Pyridoxal 5′‐phosphate (
PLP
) is a cofactor for many vitamin B6‐requiring enzymes that are important for the synthesis of neurotransmitters. Pyridoxine 5′‐phosphate oxidase (
PNPO
) is one of two enzymes that produce
PLP
. Some 16 known mutations in human
PNPO
(
hPNPO
), including R95C and R229W, lead to deficiency of
PLP
in the cell and have been shown to cause neonatal epileptic encephalopathy (
NEE
). This disorder has no effective treatment, and is often fatal unless treated with
PLP
. In this study, we show that R95C
hPNPO
exhibits a 15‐fold reduction in affinity for the
FMN
cofactor, a 71‐fold decrease in affinity for the substrate
PNP
, a 4.9‐fold decrease in specific activity, and a 343‐fold reduction in catalytic activity, compared to the wild‐type enzyme. We have reported similar findings for R229W
hPNPO
. This report also shows that wild‐type, R95C and R229W
hPNPO
bind
PLP
tightly at a noncatalytic site and transfer it to activate an apo‐B6 enzyme into the catalytically active holo‐form. We also show for the first time that
hPNPO
forms specific interactions with several B6 enzymes with dissociation constants ranging from 0.3 to 12.3 μ
m
. Our results suggest a possible
in vivo
role for the tight binding of
PLP
in
hPNPO
, whether wild‐type or variant, by protecting the very reactive
PLP
, and transferring this
PLP
directly to activate apo‐B6 enzymes.