NDLI: Structural and Biochemical Studies on the Reaction Mechanism of Uridine

Content Provider	Springer Nature Link
Author	Tomoike, Fumiaki Nakagawa, riko Kuramitsu, Seiki Masui, Ryoji
Copyright Year	2015
Abstract	Uridine–cytidine kinase catalyzes phosphorylation of the pyrimidine nucleosides uridine and cytidine and plays an important role in nucleotide metabolism. However, the detailed molecular mechanism of these reactions remains to be elucidated. Here, we determined the structure of the ternary complex of Uridine–cytidine kinase from Thermus thermophilus HB8 with both cytidine and β,γ-methyleneadenosine 5′-triphosphate, a non-hydrolysable ATP analogue. Substrate binding is accompanied by substantial domain movement that allows the substrate-binding cleft to close. The terminal phosphodiester bond of the ATP analogue is in an ideal location for an inline attack of the 5′-hydroxyl group of cytidine. Asp40 is located near the 5′-hydroxyl group of cytidine. Mutation of this conserved residue to Asn or Ala resulted in a complete loss of enzyme activity, which is consistent with the notion that Asp40 acts as a general base that activates the 5′-hydroxyl group of cytidine. The pH profile of the activity showed an apparent pK $_{a}$ value of 7.4. Based on this structure, a likely mechanism of the catalytic step is discussed.
Starting Page	411
Ending Page	420
Page Count	10
File Format	PDF
ISSN	15723887
Journal	The Protein Journal
Volume Number	34
Issue Number	6
e-ISSN	15734943
Language	English
Publisher	Springer US
Publisher Date	2015-10-28
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Uridine–cytidine kinase Phosphate transfer Crystal structure Mutational study Pyrimidine nucleoside pH dependence Bioorganic Chemistry Biochemistry Organic Chemistry Animal Anatomy / Morphology / Histology
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Analytical Chemistry Biochemistry Bioengineering

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