2gq2: Difference between revisions

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{{Seed}}
[[Image:2gq2.png|left|200px]]


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==Mycobacterium tuberculosis ThyX-NADP complex==
The line below this paragraph, containing "STRUCTURE_2gq2", creates the "Structure Box" on the page.
<StructureSection load='2gq2' size='340' side='right'caption='[[2gq2]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2gq2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GQ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GQ2 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
{{STRUCTURE_2gq2|  PDB=2gq2  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gq2 OCA], [https://pdbe.org/2gq2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gq2 RCSB], [https://www.ebi.ac.uk/pdbsum/2gq2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gq2 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/THYX_MYCTU THYX_MYCTU] Catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate (By similarity).
== 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/gq/2gq2_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=2gq2 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The novel flavin-dependent thymidylate synthase, ThyX, is absent in humans but several pathogenic bacteria depend exclusively on ThyX activity to synthesize thymidylate. Reduction of the enzyme-bound FAD by NADPH is suggested to be the critical first step in ThyX catalysis. We soaked Mycobacterium tuberculosis ThyX-FAD-BrdUMP ternary complex crystals in a solution containing NADP+ to gain structural insights into the reductive step of the catalytic cycle. Surprisingly, the NADP+ displaced both FAD and BrdUMP from the active site. In the resultant ThyX-NADP+ binary complex, the AMP moiety is bound in a deep pocket similar to that of the same moiety of FAD in the ternary complex, while the nicotinamide part of NADP+ is engaged in a limited number of contacts with ThyX. The additional 2'-phosphate group attached to the AMP ribose of NADP+ could be accommodated with minor rearrangement of water molecules. The newly introduced 2'-phosphate groups are engaged in water-mediated interactions across the non-crystallographic 2-fold axis of the ThyX tetramer, suggesting possibilities for design of high-affinity bivalent inhibitors of this intriguing enzyme.


===Mycobacterium tuberculosis ThyX-NADP complex===
NADP+ expels both the co-factor and a substrate analog from the Mycobacterium tuberculosis ThyX active site: opportunities for anti-bacterial drug design.,Sampathkumar P, Turley S, Sibley CH, Hol WG J Mol Biol. 2006 Jun 30;360(1):1-6. Epub 2006 May 12. PMID:16730023<ref>PMID:16730023</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2gq2" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_16730023}}, adds the Publication Abstract to the page
*[[Thymidylate synthase 3D structures|Thymidylate synthase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 16730023 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_16730023}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2GQ2 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GQ2 OCA].
[[Category: Mycobacterium tuberculosis H37Rv]]
 
[[Category: Hol WG]]
==Reference==
[[Category: Sampathkumar P]]
<ref group="xtra">PMID:16730023</ref><ref group="xtra">PMID:16139296</ref><references group="xtra"/>
[[Category: Sibley CH]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Turley S]]
[[Category: Hol, W G.]]
[[Category: Sampathkumar, P.]]
[[Category: Sibley, C H.]]
[[Category: Turley, S.]]
[[Category: Bivalent drug]]
[[Category: Fdt]]
[[Category: Flavin dependent thymidylate synthase]]
[[Category: Inhibitor design]]
[[Category: M tuberculosis]]
[[Category: Thyx]]
[[Category: Tscp]]
 
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Retrieved from "https://proteopedia.org/2gq2"