Crystal structure of product-bound complex of UDP-N-acetyl-d-mannosamine dehydrogenase from Pyrococcus horikoshii OT3

Analysis of nucleotide diphosphate sugar dehydrogenases reveals family and group‐specific relationships

“…Another valine identified by GEnt in SaUDPNAMDH is Val254{407} which is found in 35 out of 38 UDPNAMDH sequences, with the other three UDPNAMDH sequences having leucine. In the P. horikoshii UDPNAMDH Val254{407} lines the pocket where the uridine group of UDP‐ManNAcA is located . Similarly, the α‐carbons of Tyr256{407} in SpUDPGDH and Phe264{407} in PaGDPMDH are within 5 Å of C1D of the ribose ring of UDP‐xylopyranose and GDP‐mannopyranosyl ester, respectively.…”

“…The side chain of His257{410} is about 4 Å from the nicotinamide ring of NAD + and approximately 5.5 Å from the 2′ and 3′ hydroxyls of the nicotinamide ribose in SaUDPNAMDH. In the P. horikoshii UDPNAMDH His257{410} side chain hydrogen bonds to a water molecule that in turn is bonded to the O2B atom of UDP‐ManNAcA . Tyr259{410} at the corresponding position in SpUDPGDH is approximately 4.5 Å from the 2′ and 3′ hydroxyl groups of the nicotinamide ribose of NAD + .…”

“…Next, His242{391} is found in 35 out of 38 UDPNAMDH sequences (92% conserved) and is replaced in other NDP‐SDH groups by aspartate, which is 78% conserved in the entire alignment. The side chain of His242{391} forms an ion pair with Glu207{355} from the neighbouring subunit and also lies 3.8 Å from the [Eu(DPA) 3 ] 3− complex bound in the substrate site of that neighbouring subunit in SaUDPNAMDH. It is possible that His242{391} in UDPNAMDH makes a similar intersubunit contact as the conserved Arg244{393} in SpUDPGDH (note that the residues are only two index positions away).…”

“…It is possible that His242{391} in UDPNAMDH makes a similar intersubunit contact as the conserved Arg244{393} in SpUDPGDH (note that the residues are only two index positions away). In fact, UDPNAMDHs would have two intersubunit contacts with their substrate, His242{391} and Arg244{393}, which lies 3.2 Å from the [Eu(DPA) 3 ] 3− complex in SaUDPNAMDH and 2.8 Å from O7″ and 2.9 Å from O3″ of UDP‐ManNAcA in P. horikoshii UDPNAMDH . Interestingly, Arg244{393} in SpUDPGDH interacts with the 2″ hydroxyl of glucose in UDP‐Glc.…”

“…A from the 2 0 and 3 0 hydroxyls of the nicotinamide ribose in SaUDP-NAMDH. In the P. horikoshii UDPNAMDH His257 {410} side chain hydrogen bonds to a water molecule that in turn is bonded to the O2B atom of UDP-Man-NAcA [48]. Tyr259{410} at the corresponding position in SpUDPGDH is approximately 4.5…”