8PQS

Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 E88A Mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Snapshots of the Reaction Coordinate of a Thermophilic 2'-Deoxyribonucleoside/ribonucleoside Transferase.

Tang, P.Harding, C.J.Dickson, A.L.da Silva, R.G.Harrison, D.J.Czekster, C.M.

(2024) ACS Catal 14: 3090-3102

  • DOI: https://doi.org/10.1021/acscatal.3c06260
  • Primary Citation of Related Structures:  
    8PQP, 8PQQ, 8PQR, 8PQS, 8PQT, 8QC0, 8RH3

  • 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 Chroococcidiopsis thermalis ( Ct 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 K a 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 Ct 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 Ct NDT in biocatalysis.


  • Organizational Affiliation

    School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside 2-deoxyribosyltransferase
A, B, C, D
155Chroococcidiopsis thermalis PCC 7203Mutation(s): 1 
Gene Names: Chro_1188
UniProt
Find proteins for K9TVX3 (Chroococcidiopsis thermalis (strain PCC 7203))
Explore K9TVX3 
Go to UniProtKB:  K9TVX3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9TVX3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.63α = 90
b = 135.63β = 90
c = 87.56γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited KingdomIBioIC 2020-2-1

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Database references, Refinement description