View source for 8pqp


==Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 D62N Mutant bound to ImmH-Forodesine==
<StructureSection load='8pqp' size='340' side='right'caption='[[8pqp]], [[Resolution|resolution]] 1.71&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8pqp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Chroococcidiopsis_thermalis_PCC_7203 Chroococcidiopsis thermalis PCC 7203]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8PQP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PQP FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.709&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IMH:1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL'>IMH</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8pqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pqp OCA], [https://pdbe.org/8pqp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pqp RCSB], [https://www.ebi.ac.uk/pdbsum/8pqp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pqp ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/K9TVX3_CHRTP K9TVX3_CHRTP] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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 (CtNDT). 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 pK(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 CtNDT 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 CtNDT in biocatalysis.

Snapshots of the Reaction Coordinate of a Thermophilic 2'-Deoxyribonucleoside/ribonucleoside Transferase.,Tang P, Harding CJ, Dickson AL, da Silva RG, Harrison DJ, Czekster CM ACS Catal. 2024 Feb 13;14(5):3090-3102. doi: 10.1021/acscatal.3c06260. , eCollection 2024 Mar 1. PMID:38449528<ref>PMID:38449528</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8pqp" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Chroococcidiopsis thermalis PCC 7203]]
[[Category: Large Structures]]
[[Category: Czekster MC]]
[[Category: Harding CJ]]
[[Category: Tang P]]