8qc0: Difference between revisions
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New page: '''Unreleased structure''' The entry 8qc0 is ON HOLD Authors: Tang, P., Harding, C.J., Czekster, C.M. Description: Nucleoside 2''deoxyribosyltransferase from Chroococcidiopsis thermali... |
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==Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 WT ribosylated== | |||
<StructureSection load='8qc0' size='340' side='right'caption='[[8qc0]], [[Resolution|resolution]] 2.02Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8qc0]] is a 4 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=8QC0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8QC0 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]] 2.02Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RIB:RIBOSE'>RIB</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=8qc0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8qc0 OCA], [https://pdbe.org/8qc0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8qc0 RCSB], [https://www.ebi.ac.uk/pdbsum/8qc0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8qc0 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 8qc0" style="background-color:#fffaf0;"></div> | ||
[[Category: Harding | == References == | ||
[[Category: | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Chroococcidiopsis thermalis PCC 7203]] | |||
[[Category: Large Structures]] | |||
[[Category: Czekster CM]] | |||
[[Category: Harding CJ]] | |||
[[Category: Tang P]] | |||
