8PQR

Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 WT bound to DAD_Immucillin-H

Summary for 8PQR

• Entry DOI: 10.2210/pdb8pqr/pdb
• Descriptor: Nucleoside 2-deoxyribosyltransferase, 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one (3 entities in total)
• Functional Keywords: dad_immucillin-h, transferase, protein binding
• Biological source: Chroococcidiopsis thermalis PCC 7203
• Total number of polymer chains: 4
• Total formula weight: 71817.74

Authors

Tang, P.,Harding, C.J.,Czekster, C.M. (deposition date: 2023-07-11, release date: 2024-02-21, Last modification date: 2024-03-20)

Primary citation

Tang, P.,Harding, C.J.,Dickson, A.L.,da Silva, R.G.,Harrison, D.J.,Czekster, C.M.
Snapshots of the Reaction Coordinate of a Thermophilic 2'-Deoxyribonucleoside/ribonucleoside Transferase.
Acs Catalysis, 14:3090-3102, 2024

PubMed Abstract: Nucleosides are ubiquitous to life and are required for the synthesis of DNA, RNA, and other molecules crucial for cell survival. Despite the notoriously difficult organic synthesis of nucleosides, 2'-deoxynucleoside analogues can interfere with natural DNA replication and repair and are successfully employed as anticancer, antiviral, and antimicrobial compounds. Nucleoside 2'-deoxyribosyltransferase (dNDT) enzymes catalyze transglycosylation via a covalent 2'-deoxyribosylated enzyme intermediate with retention of configuration, having applications in the biocatalytic synthesis of 2'-deoxynucleoside analogues in a single step. Here, we characterize the structure and function of a thermophilic dNDT, the protein from (NDT). We combined enzyme kinetics with structural and biophysical studies to dissect mechanistic features in the reaction coordinate, leading to product formation. Bell-shaped pH-rate profiles demonstrate activity in a broad pH range of 5.5-9.5, with two very distinct p values. A pronounced viscosity effect on the turnover rate indicates a diffusional step, likely product (nucleobase1) release, to be rate-limiting. Temperature studies revealed an extremely curved profile, suggesting a large negative activation heat capacity. We trapped a 2'-fluoro-2'-deoxyarabinosyl-enzyme intermediate by mass spectrometry and determined high-resolution structures of the protein in its unliganded, substrate-bound, ribosylated, 2'-difluoro-2'-deoxyribosylated, and in complex with probable transition-state analogues. We reveal key features underlying (2'-deoxy)ribonucleoside selection, as NDT can also use ribonucleosides as substrates, albeit with a lower efficiency. Ribonucleosides are the building blocks of RNA and other key intracellular metabolites participating in energy and metabolism, expanding the scope of use of NDT in biocatalysis.

PubMed: 38449528
DOI: 10.1021/acscatal.3c06260

Experimental method

X-RAY DIFFRACTION (1.586 Å)