2af6: Difference between revisions

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-{{Seed}}
-[[Image:2af6.png|left|200px]]
-<!--
+==Crystal structure of Mycobacterium tuberculosis Flavin dependent thymidylate synthase (Mtb ThyX) in the presence of co-factor FAD and substrate analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (BrdUMP)==
-The line below this paragraph, containing "STRUCTURE_2af6", creates the "Structure Box" on the page.
+<StructureSection load='2af6' size='340' side='right'caption='[[2af6]], [[Resolution|resolution]] 2.01&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'>[[2af6]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AF6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AF6 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]] 2.01&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_2af6|  PDB=2af6  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2af6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2af6 OCA], [https://pdbe.org/2af6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2af6 RCSB], [https://www.ebi.ac.uk/pdbsum/2af6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2af6 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/af/2af6_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=2af6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A novel flavin-dependent thymidylate synthase was identified recently as an essential gene in many archaebacteria and some pathogenic eubacteria. This enzyme, ThyX, is a potential antibacterial drug target, since humans and most eukaryotes lack the thyX gene and depend upon the conventional thymidylate synthase (TS) for their dTMP requirements. We have cloned and overexpressed the thyX gene (Rv2754c) from Mycobacterium tuberculosis in Escherichia coli. The M.tuberculosis ThyX (MtbThyX) enzyme complements the E.coli chi2913 strain that lacks its conventional TS activity. The crystal structure of the homotetrameric MtbThyX was determined in the presence of the cofactor FAD and the substrate analog, 5-bromo-2'-deoxyuridine-5'-monophosphate (BrdUMP). In the active site, which is formed by three monomers, FAD is bound in an extended conformation with the adenosine ring in a deep pocket and BrdUMP in a closed conformation near the isoalloxazine ring. Structure-based mutational studies have revealed a critical role played by residues Lys165 and Arg168 in ThyX activity, possibly by governing access to the carbon atom to be methylated of a totally buried substrate dUMP.
-===Crystal structure of Mycobacterium tuberculosis Flavin dependent thymidylate synthase (Mtb ThyX) in the presence of co-factor FAD and substrate analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (BrdUMP)===
+Structure of the Mycobacterium tuberculosis flavin dependent thymidylate synthase (MtbThyX) at 2.0A resolution.,Sampathkumar P, Turley S, Ulmer JE, Rhie HG, Sibley CH, Hol WG J Mol Biol. 2005 Oct 7;352(5):1091-104. PMID:16139296<ref>PMID:16139296</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2af6" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16139296}}, adds the Publication Abstract to the page
+*[[Heat Shock Protein structures|Heat Shock Protein structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16139296 is the PubMed ID number.
+*[[Thymidylate synthase 3D structures|Thymidylate synthase 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_16139296}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-AF6 is a [[Single protein]] structure of sequence 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=2AF6 OCA].
+[[Category: Large Structures]]
-==Reference==
-Structure of the Mycobacterium tuberculosis flavin dependent thymidylate synthase (MtbThyX) at 2.0A resolution., Sampathkumar P, Turley S, Ulmer JE, Rhie HG, Sibley CH, Hol WG, J Mol Biol. 2005 Oct 7;352(5):1091-104. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16139296 16139296]
 [[Category: Mycobacterium tuberculosis]]
-[[Category: Single protein]]
+[[Category: Hol WG]]
-[[Category: Hol, W G.]]
+[[Category: Rhie HG]]
-[[Category: Rhie, H G.]]
+[[Category: Sampathkumar P]]
-[[Category: Sampathkumar, P.]]
+[[Category: Sibley CH]]
-[[Category: Sibley, C H.]]
+[[Category: Turley S]]
-[[Category: Turley, S.]]
+[[Category: Ulmer JE]]
-[[Category: Ulmer, J E.]]
-[[Category: Fdt]]
-[[Category: Flavin dependent thymidylate synthase]]
-[[Category: M tuberculosis]]
-[[Category: Thyx]]
-[[Category: Tscp]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 03:24:58 2008''