7mdi: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==== | ==Structure of the Neisseria gonorrhoeae ribonucleotide reductase in the inactive state== | ||
<StructureSection load='7mdi' size='340' side='right'caption='[[7mdi]]' scene=''> | <StructureSection load='7mdi' size='340' side='right'caption='[[7mdi]], [[Resolution|resolution]] 4.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br> | <table><tr><td colspan='2'>[[7mdi]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_gonorrhoeae_FA_1090 Neisseria gonorrhoeae FA 1090]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MDI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MDI FirstGlance]. <br> | ||
</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=7mdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mdi OCA], [https://pdbe.org/7mdi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mdi RCSB], [https://www.ebi.ac.uk/pdbsum/7mdi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mdi ProSAT]</span></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 4.3Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CDP:CYTIDINE-5-DIPHOSPHATE'>CDP</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7mdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mdi OCA], [https://pdbe.org/7mdi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mdi RCSB], [https://www.ebi.ac.uk/pdbsum/7mdi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mdi ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q5F8Z6_NEIG1 Q5F8Z6_NEIG1] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[RuleBase:RU003410] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Ribonucleotide reductase (RNR) is an essential enzyme that converts ribonucleotides to deoxyribonucleotides and is a promising antibiotic target, but few RNRs have been structurally characterized. We present the use of the chameleon, a commercially-available piezoelectric cryogenic electron microscopy plunger, to address complex denaturation in the Neisseria gonorrhoeae class Ia RNR. Here, we characterize the extent of denaturation of the ring-shaped complex following grid preparation using a traditional plunger and using a chameleon with varying dispense-to-plunge times. We also characterize how dispense-to-plunge time influences the amount of protein sample required for grid preparation and preferred orientation of the sample. We demonstrate that the fastest dispense-to-plunge time of 54 ms is sufficient for generation of a data set that produces a high quality structure, and that a traditional plunging technique or slow chameleon dispense-to-plunge times generate data sets limited in resolution by complex denaturation. The 4.3 A resolution structure of Neisseria gonorrhoeae class Ia RNR in the inactive alpha4beta4 oligomeric state solved using the chameleon with a fast dispense-to-plunge time yields molecular information regarding similarities and differences to the well studied Escherichia coli class Ia RNR alpha4beta4 ring. | |||
Effects of chameleon dispense-to-plunge speed on particle concentration, complex formation, and final resolution: A case study using the Neisseria gonorrhoeae ribonucleotide reductase inactive complex.,Levitz TS, Brignole EJ, Fong I, Darrow MC, Drennan CL J Struct Biol. 2022 Mar;214(1):107825. doi: 10.1016/j.jsb.2021.107825. Epub 2021 , Dec 11. PMID:34906669<ref>PMID:34906669</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7mdi" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Neisseria gonorrhoeae FA 1090]] | ||
[[Category: Brignole EJ]] | |||
[[Category: Drennan CL]] | |||
[[Category: Levitz TS]] | |||
Latest revision as of 22:39, 29 May 2024
Structure of the Neisseria gonorrhoeae ribonucleotide reductase in the inactive stateStructure of the Neisseria gonorrhoeae ribonucleotide reductase in the inactive state
Structural highlights
FunctionQ5F8Z6_NEIG1 Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.[RuleBase:RU003410] Publication Abstract from PubMedRibonucleotide reductase (RNR) is an essential enzyme that converts ribonucleotides to deoxyribonucleotides and is a promising antibiotic target, but few RNRs have been structurally characterized. We present the use of the chameleon, a commercially-available piezoelectric cryogenic electron microscopy plunger, to address complex denaturation in the Neisseria gonorrhoeae class Ia RNR. Here, we characterize the extent of denaturation of the ring-shaped complex following grid preparation using a traditional plunger and using a chameleon with varying dispense-to-plunge times. We also characterize how dispense-to-plunge time influences the amount of protein sample required for grid preparation and preferred orientation of the sample. We demonstrate that the fastest dispense-to-plunge time of 54 ms is sufficient for generation of a data set that produces a high quality structure, and that a traditional plunging technique or slow chameleon dispense-to-plunge times generate data sets limited in resolution by complex denaturation. The 4.3 A resolution structure of Neisseria gonorrhoeae class Ia RNR in the inactive alpha4beta4 oligomeric state solved using the chameleon with a fast dispense-to-plunge time yields molecular information regarding similarities and differences to the well studied Escherichia coli class Ia RNR alpha4beta4 ring. Effects of chameleon dispense-to-plunge speed on particle concentration, complex formation, and final resolution: A case study using the Neisseria gonorrhoeae ribonucleotide reductase inactive complex.,Levitz TS, Brignole EJ, Fong I, Darrow MC, Drennan CL J Struct Biol. 2022 Mar;214(1):107825. doi: 10.1016/j.jsb.2021.107825. Epub 2021 , Dec 11. PMID:34906669[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||