1vk8: Difference between revisions
New page: left|200px<br /><applet load="1vk8" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vk8, resolution 1.80Å" /> '''Crystal structure of... |
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== | ==CRYSTAL STRUCTURE OF A PUTATIVE THIAMINE BIOSYNTHESIS/SALVAGE PROTEIN (TM0486) FROM THERMOTOGA MARITIMA AT 1.80 A RESOLUTION== | ||
<StructureSection load='1vk8' size='340' side='right'caption='[[1vk8]], [[Resolution|resolution]] 1.80Å' scene=''> | |||
[[Category: | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1vk8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VK8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VK8 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]] 1.8Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1vk8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vk8 OCA], [https://pdbe.org/1vk8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vk8 RCSB], [https://www.ebi.ac.uk/pdbsum/1vk8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vk8 ProSAT], [https://www.topsan.org/Proteins/JCSG/1vk8 TOPSAN]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q9WYV6_THEMA Q9WYV6_THEMA] | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vk/1vk8_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1vk8 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The COG database was used for a comparative genome analysis with genomes from anaerobic and aerobic microorganisms with the aim of identifying proteins specific to the anaerobic way of life. A total of 33 COGs were identified, five of which correspond to proteins of unknown function. We focused our study on TM0486 from Thermotoga maritima, which belongs to one of these COGs of unknown function, namely COG0011. The crystal structure of the protein was determined at 2 A resolution. The structure adopts a beta alpha beta beta alpha beta ferredoxin-like fold and assembles as a homotetramer. The structure also revealed the presence of a pocket in each monomer that bound an unidentified ligand. NMR and calorimetry revealed that TM0486 specifically bound thiamin with a K(d) of 1.58 microM, but not hydroxymethyl pyrimidine (HMP), which has been implicated as a potential ligand. We demonstrated that the TM0486 gene belongs to the same multicistronic unit as TM0483, TM0484 and TM0485. Although these three genes have been assigned to the transport of HMP, with TM0484 being the periplasmic thiamin/HMP-binding protein and TM0485 and TM0483 the transmembrane and the ATPase components, respectively, our results led us to conclude that this operon encodes an ABC transporter dedicated to thiamin, with TM0486 transporting charged thiamin in the cytoplasm. Given that this transcriptional unit was up-regulated when T. maritima was exposed to oxidative conditions, we propose that, by chelating cytoplasmic thiamin, TM0486 and, by extension, proteins belonging to COG0011 are involved in the response mechanism to stress that could arise during aerobic conditions. | |||
TM0486 from the hyperthermophilic anaerobe Thermotoga maritima is a thiamin-binding protein involved in response of the cell to oxidative conditions.,Dermoun Z, Foulon A, Miller MD, Harrington DJ, Deacon AM, Sebban-Kreuzer C, Roche P, Lafitte D, Bornet O, Wilson IA, Dolla A J Mol Biol. 2010 Jul 16;400(3):463-76. Epub 2010 May 13. PMID:20471400<ref>PMID:20471400</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1vk8" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Thermotoga maritima]] | [[Category: Thermotoga maritima]] | ||
Latest revision as of 03:36, 21 November 2024
CRYSTAL STRUCTURE OF A PUTATIVE THIAMINE BIOSYNTHESIS/SALVAGE PROTEIN (TM0486) FROM THERMOTOGA MARITIMA AT 1.80 A RESOLUTIONCRYSTAL STRUCTURE OF A PUTATIVE THIAMINE BIOSYNTHESIS/SALVAGE PROTEIN (TM0486) FROM THERMOTOGA MARITIMA AT 1.80 A RESOLUTION
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe COG database was used for a comparative genome analysis with genomes from anaerobic and aerobic microorganisms with the aim of identifying proteins specific to the anaerobic way of life. A total of 33 COGs were identified, five of which correspond to proteins of unknown function. We focused our study on TM0486 from Thermotoga maritima, which belongs to one of these COGs of unknown function, namely COG0011. The crystal structure of the protein was determined at 2 A resolution. The structure adopts a beta alpha beta beta alpha beta ferredoxin-like fold and assembles as a homotetramer. The structure also revealed the presence of a pocket in each monomer that bound an unidentified ligand. NMR and calorimetry revealed that TM0486 specifically bound thiamin with a K(d) of 1.58 microM, but not hydroxymethyl pyrimidine (HMP), which has been implicated as a potential ligand. We demonstrated that the TM0486 gene belongs to the same multicistronic unit as TM0483, TM0484 and TM0485. Although these three genes have been assigned to the transport of HMP, with TM0484 being the periplasmic thiamin/HMP-binding protein and TM0485 and TM0483 the transmembrane and the ATPase components, respectively, our results led us to conclude that this operon encodes an ABC transporter dedicated to thiamin, with TM0486 transporting charged thiamin in the cytoplasm. Given that this transcriptional unit was up-regulated when T. maritima was exposed to oxidative conditions, we propose that, by chelating cytoplasmic thiamin, TM0486 and, by extension, proteins belonging to COG0011 are involved in the response mechanism to stress that could arise during aerobic conditions. TM0486 from the hyperthermophilic anaerobe Thermotoga maritima is a thiamin-binding protein involved in response of the cell to oxidative conditions.,Dermoun Z, Foulon A, Miller MD, Harrington DJ, Deacon AM, Sebban-Kreuzer C, Roche P, Lafitte D, Bornet O, Wilson IA, Dolla A J Mol Biol. 2010 Jul 16;400(3):463-76. Epub 2010 May 13. PMID:20471400[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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