1l1q: Difference between revisions

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-{{Seed}}
-[[Image:1l1q.png|left|200px]]
-<!--
+==Crystal Structure of APRTase from Giardia lamblia Complexed with 9-deazaadenine==
-The line below this paragraph, containing "STRUCTURE_1l1q", creates the "Structure Box" on the page.
+<StructureSection load='1l1q' size='340' side='right'caption='[[1l1q]], [[Resolution|resolution]] 1.85&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'>[[1l1q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Giardia_intestinalis Giardia intestinalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L1Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L1Q 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]] 1.85&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9DA:9-DEAZAADENINE'>9DA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1l1q|  PDB=1l1q  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1l1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l1q OCA], [https://pdbe.org/1l1q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l1q RCSB], [https://www.ebi.ac.uk/pdbsum/1l1q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l1q ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q967M2_GIAIN Q967M2_GIAIN]
+== 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/l1/1l1q_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=1l1q ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The adenine phosphoribosyltransferase (APRTase) from Giardia lamblia was co-crystallized with 9-deazaadenine and sulfate or with 9-deazaadenine and Mg-phosphoribosylpyrophosphate. The complexes were solved and refined to 1.85 and 1.95 A resolution. Giardia APRTase is a symmetric homodimer with the monomers built around Rossman fold cores, an element common to all known purine phosphoribosyltransferases. The catalytic sites are capped with a small hood domain that is unique to the APRTases. These structures reveal several features relevant to the catalytic function of APRTase: 1) a non-proline cis peptide bond (Glu(61)-Ser(62)) is required to form the pyrophosphate binding site in the APRTase.9dA.MgPRPP complex but is a trans peptide bond in the absence of pyrophosphate group, as observed in the APRTase.9dA.SO4 complex; 2) a catalytic site loop is closed and fully ordered in both complexes, with Glu(100) from the catalytic loop acting as the acid/base for protonation/deprotonation of N-7 of the adenine ring; 3) the pyrophosphoryl charge is neutralized by a single Mg2+ ion and Arg(63), in contrast to the hypoxanthine-guanine phosphoribosyltransferases, which use two Mg2+ ions; and 4) the nearest structural neighbors to APRTases are the orotate phosphoribosyltransferases, suggesting different paths of evolution for adenine relative to other purine PRTases. An overlap comparison of AMP and 9-deazaadenine plus Mg-PRPP at the catalytic sites of APRTases indicated that reaction coordinate motion involves a 2.1-A excursion of the ribosyl anomeric carbon, whereas the adenine ring and the 5-phosphoryl group remained fixed. G. lamblia APRTase therefore provides another example of nucleophilic displacement by electrophile migration.
-===Crystal Structure of APRTase from Giardia lamblia Complexed with 9-deazaadenine===
+Closed site complexes of adenine phosphoribosyltransferase from Giardia lamblia reveal a mechanism of ribosyl migration.,Shi W, Sarver AE, Wang CC, Tanaka KS, Almo SC, Schramm VL J Biol Chem. 2002 Oct 18;277(42):39981-8. Epub 2002 Aug 8. PMID:12171925<ref>PMID:12171925</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1l1q" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12171925}}, adds the Publication Abstract to the page
+*[[Phosphoribosyltransferase 3D structures|Phosphoribosyltransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12171925 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12171925}}
+__TOC__
+</StructureSection>
-==About this Structure==
-L1Q is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Giardia_intestinalis Giardia intestinalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L1Q OCA].
-==Reference==
-<ref group="xtra">PMID:12171925</ref><references group="xtra"/>
-[[Category: Adenine phosphoribosyltransferase]]
 [[Category: Giardia intestinalis]]
-[[Category: Almo, S C.]]
+[[Category: Large Structures]]
-[[Category: Sarver, A E.]]
+[[Category: Almo SC]]
-[[Category: Schramm, V L.]]
+[[Category: Sarver AE]]
-[[Category: Shi, W.]]
+[[Category: Schramm VL]]
-[[Category: Tanaka, K S.]]
+[[Category: Shi W]]
-[[Category: Wang, C C.]]
+[[Category: Tanaka KS]]
-[[Category: Adenine]]
+[[Category: Wang CC]]
-[[Category: Aprtase]]
-[[Category: Catalytic loop]]
-[[Category: Giardia lamblia]]
-[[Category: Purine metabolism]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:03:08 2009''