1qk5: Difference between revisions

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-[[Image:1qk5.png|left|200px]]
-<!--
+==TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE WITH XMP, PYROPHOSPHATE AND TWO MG2+ IONS==
-The line below this paragraph, containing "STRUCTURE_1qk5", creates the "Structure Box" on the page.
+<StructureSection load='1qk5' size='340' side='right'caption='[[1qk5]], [[Resolution|resolution]] 1.60&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'>[[1qk5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Toxoplasma_gondii_RH Toxoplasma gondii RH]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QK5 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]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=XMP:XANTHOSINE-5-MONOPHOSPHATE'>XMP</scene></td></tr>
-{{STRUCTURE_1qk5|  PDB=1qk5  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qk5 OCA], [https://pdbe.org/1qk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qk5 RCSB], [https://www.ebi.ac.uk/pdbsum/1qk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qk5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HGXR_TOXGO HGXR_TOXGO] Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to the N(9) of hypoxanthine, guanine or xanthine.<ref>PMID:11188695</ref>
+== 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/qk/1qk5_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=1qk5 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of the Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase (HGPRT)-xanthosine 5'-monophosphate (XMP)-pyrophosphate-Mg(2+) ternary complex has been determined at 1. 60 A resolution. This biproduct, post-transition state structure is of a T. gondii HGPRT mutant (Asp150Ala or D150A). The D150A mutant has reduced activity (k(cat) lower by 11-, 296-, and 8.6-fold for hypoxanthine, guanine, and xanthine, respectively) compared to wild-type T. gondii HGPRT. The Michaelis constants for purine bases are altered only slightly, whereas those for alpha-D-5-phosphoribosyl 1-pyrophosphate (PRPP) are lower by approximately 6.5-fold. The ternary complex crystallizes in space group C222(1) (a = 55.21 A, b = 112.25 A, and c = 144.28 A) with two subunits in the asymmetric unit; the HGPRT tetramer is completed by the application of 2-fold crystallographic symmetry. All active sites contain XMP inverted question markbound in a fashion similar to that of the guanosine 5'-monophosphate (GMP) and inosine 5'-monophosphate (IMP) complexes reported in the preceding article [Heroux, A., et al. (1999) Biochemistry 38, 14485-14494] inverted question mark, pyrophosphate, and two Mg(2+) ions. Each Mg(2+) ion is octahedrally coordinated by two terminal pyrophosphate oxygen atoms and several ordered water molecules. This structure shows how HGPRT uses two Mg(2+) ions to orient and activate the pyrophosphate moiety of PRPP for attack by a purine base, and why mutation in humans of the residue corresponding to Asp206, the only HGPRT amino acid that directly contacts the Mg(2+) ions, causes Lesch-Nyhan syndrome (HGPRT(Kinston), D193N). The Leu78-Lys79 peptide bond in the active site adopts the cis configuration, which it must to bind PRPP or pyrophosphate. The contribution of cis-trans isomerization of this peptide bond to the energetics of substrate binding and product release is discussed. A comprehensive description of the HGPRT reaction mechanism is also proposed.
-===TOXOPLASMA GONDII HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE WITH XMP, PYROPHOSPHATE AND TWO MG2+ IONS===
+Crystal structure of Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase with XMP, pyrophosphate, and two Mg(2+) ions bound: insights into the catalytic mechanism.,Heroux A, White EL, Ross LJ, Davis RL, Borhani DW Biochemistry. 1999 Nov 2;38(44):14495-506. PMID:10545171<ref>PMID:10545171</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1qk5" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10545171}}, adds the Publication Abstract to the page
+*[[Phosphoribosyltransferase 3D structures|Phosphoribosyltransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10545171 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10545171}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[1qk5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Toxoplasma_gondii Toxoplasma gondii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QK5 OCA].
+[[Category: Toxoplasma gondii RH]]
+[[Category: Borhani DW]]
-==Reference==
+[[Category: Davis RL]]
-<ref group="xtra">PMID:10545171</ref><ref group="xtra">PMID:10545170</ref><ref group="xtra">PMID:8088544</ref><references group="xtra"/>
+[[Category: Heroux A]]
-[[Category: Hypoxanthine phosphoribosyltransferase]]
+[[Category: Ross LJ]]
-[[Category: Toxoplasma gondii]]
+[[Category: White EL]]
-[[Category: Borhani, D W.]]
-[[Category: Davis, R L.]]
-[[Category: Heroux, A.]]
-[[Category: Ross, L J.]]
-[[Category: White, E L.]]
-[[Category: Glycosyltransferase]]
-[[Category: Purine salvage]]
-[[Category: Transferase]]