1slh: Difference between revisions

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-{{Seed}}
-[[Image:1slh.png|left|200px]]
-<!--
+==Mycobacterium tuberculosis dUTPase complexed with magnesium and dUDP==
-The line below this paragraph, containing "STRUCTURE_1slh", creates the "Structure Box" on the page.
+<StructureSection load='1slh' size='340' side='right'caption='[[1slh]], [[Resolution|resolution]] 3.00&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'>[[1slh]] is a 3 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=1SLH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SLH 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]] 3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DUD:DEOXYURIDINE-5-DIPHOSPHATE'>DUD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-{{STRUCTURE_1slh|  PDB=1slh  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1slh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1slh OCA], [https://pdbe.org/1slh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1slh RCSB], [https://www.ebi.ac.uk/pdbsum/1slh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1slh ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DUT_MYCTU DUT_MYCTU] This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA.[HAMAP-Rule:MF_00116]
+== 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/sl/1slh_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1slh ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of Mycobacterium tuberculosis dUTP nucleotidohydrolase (dUTPase) has been determined at 1.3 Angstrom resolution in complex with magnesium ion and the non-hydrolyzable substrate analog, alpha,beta-imido dUTP. dUTPase is an enzyme essential for depleting potentially toxic concentrations of dUTP in the cell. Given the importance of its biological role, it has been proposed that inhibiting M.tuberculosis dUTPase might be an effective means to treat tuberculosis infection in humans. The crystal structure presented here offers some insight into the potential for designing a specific inhibitor of the M.tuberculosis dUTPase enzyme. The structure also offers new insights into the mechanism of dUTP hydrolysis by providing an accurate representation of the enzyme-substrate complex in which both the metal ion and dUTP analog are included. The structure suggests that inclusion of a magnesium ion is important for stabilizing the position of the alpha-phosphorus for an in-line nucleophilic attack. In the absence of magnesium, the alpha-phosphate of dUTP can have either of the two positions which differ by 4.5 Angstrom. A transiently ordered C-terminal loop further assists catalysis by shielding the general base, Asp83, from solvent thus elevating its pK(a) so that it might in turn activate a tightly bound water molecule for nucleophilic attack. The metal ion coordinates alpha, beta, and gamma phosphate groups with tridentate geometry identical with that observed in the crystal structure of DNA polymerase beta complexed with magnesium and dNTP analog, revealing some common features in catalytic mechanism.
-===Mycobacterium tuberculosis dUTPase complexed with magnesium and dUDP===
+Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism.,Chan S, Segelke B, Lekin T, Krupka H, Cho US, Kim MY, So M, Kim CY, Naranjo CM, Rogers YC, Park MS, Waldo GS, Pashkov I, Cascio D, Perry JL, Sawaya MR J Mol Biol. 2004 Aug 6;341(2):503-17. PMID:15276840<ref>PMID:15276840</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1slh" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15276840}}, adds the Publication Abstract to the page
+*[[DUTPase 3D structures|DUTPase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15276840 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15276840}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-SLH is a 3 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=1SLH OCA].
-==Reference==
-<ref group="xtra">PMID:15276840</ref><references group="xtra"/>
 [[Category: Mycobacterium tuberculosis]]
-[[Category: DUTP diphosphatase]]
+[[Category: Cascio D]]
-[[Category: Cascio, D.]]
+[[Category: Chan S]]
-[[Category: Chan, S.]]
+[[Category: Cho US]]
-[[Category: Cho, U S.]]
+[[Category: Eisenberg D]]
-[[Category: Eisenberg, D.]]
+[[Category: Kim C-Y]]
-[[Category: Kim, C Y.]]
+[[Category: Kim M-Y]]
-[[Category: Kim, M Y.]]
+[[Category: Krupka H]]
-[[Category: Krupka, H.]]
+[[Category: Lekin T]]
-[[Category: Lekin, T.]]
+[[Category: Naranjo CM]]
-[[Category: Naranjo, C M.]]
+[[Category: Park MS]]
-[[Category: Park, M S.]]
+[[Category: Pashkov I]]
-[[Category: Pashkov, I.]]
+[[Category: Perry JL]]
-[[Category: Perry, J L.]]
+[[Category: Rogers YC]]
-[[Category: Rogers, Y C.]]
+[[Category: Sawaya MR]]
-[[Category: Sawaya, M R.]]
+[[Category: Segelke B]]
-[[Category: Segelke, B.]]
+[[Category: So M]]
-[[Category: So, M.]]
+[[Category: Terwilliger TC]]
-[[Category: TBSGC, TB Structural Genomics Consortium.]]
+[[Category: Waldo GS]]
-[[Category: Terwilliger, T C.]]
+[[Category: Yeates TO]]
-[[Category: Waldo, G S.]]
-[[Category: Yeates, T O.]]
-[[Category: Jelly-roll]]
-[[Category: Protein structure initiative]]
-[[Category: Psi]]
-[[Category: Structural genomic]]
-[[Category: Tb structural genomics consortium]]
-[[Category: Tbsgc]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:14:01 2009''