1l1r

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[[Image:1l1r.jpg|left|200px]]
 
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==Crystal Structure of APRTase from Giardia lamblia Complexed with 9-deazaadenine, Mg2+ and PRPP==
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The line below this paragraph, containing "STRUCTURE_1l1r", creates the "Structure Box" on the page.
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<StructureSection load='1l1r' size='340' side='right'caption='[[1l1r]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1l1r]] 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=1L1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L1R FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#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=9DA:9-DEAZAADENINE'>9DA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PRP:ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC+ACID'>PRP</scene></td></tr>
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{{STRUCTURE_1l1r| PDB=1l1r | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1l1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l1r OCA], [https://pdbe.org/1l1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l1r RCSB], [https://www.ebi.ac.uk/pdbsum/1l1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l1r ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q967M2_GIAIN Q967M2_GIAIN]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l1/1l1r_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1l1r ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''Crystal Structure of APRTase from Giardia lamblia Complexed with 9-deazaadenine, Mg2+ and PRPP'''
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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>
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==Overview==
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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.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1L1R is a [[Single protein]] 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=1L1R OCA].
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</div>
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<div class="pdbe-citations 1l1r" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/12171925 12171925]
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*[[Phosphoribosyltransferase 3D structures|Phosphoribosyltransferase 3D structures]]
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[[Category: Adenine phosphoribosyltransferase]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Giardia intestinalis]]
[[Category: Giardia intestinalis]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Almo, S C.]]
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[[Category: Almo SC]]
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[[Category: Sarver, A E.]]
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[[Category: Sarver AE]]
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[[Category: Schramm, V L.]]
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[[Category: Schramm VL]]
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[[Category: Shi, W.]]
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[[Category: Shi W]]
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[[Category: Tanaka, K S.]]
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[[Category: Tanaka KS]]
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[[Category: Wang, C C.]]
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[[Category: Wang CC]]
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[[Category: Adenine]]
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[[Category: Aprtase]]
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[[Category: Catalytic loop]]
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[[Category: Giardia lamblia]]
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[[Category: Purine metabolism]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 23:26:36 2008''
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Current revision

Crystal Structure of APRTase from Giardia lamblia Complexed with 9-deazaadenine, Mg2+ and PRPP

PDB ID 1l1r

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