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1l1r

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

Structural highlights

1l1r is a 1 chain structure with sequence from Giardia intestinalis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.95Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q967M2_GIAIN

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Shi W, Sarver AE, Wang CC, Tanaka KS, Almo SC, Schramm VL. Closed site complexes of adenine phosphoribosyltransferase from Giardia lamblia reveal a mechanism of ribosyl migration. J Biol Chem. 2002 Oct 18;277(42):39981-8. Epub 2002 Aug 8. PMID:12171925 doi:10.1074/jbc.M205596200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1l1r"

@@ Line 3: / Line 3: @@
 <StructureSection load='1l1r' size='340' side='right'caption='[[1l1r]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1l1r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Giain Giain]. 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>
+<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>
-</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PRP:ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC+ACID'>PRP</scene></td></tr>
+</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>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1l1q|1l1q]]</div></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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PRP:ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC+ACID'>PRP</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Adenine_phosphoribosyltransferase Adenine phosphoribosyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.7 2.4.2.7] </span></td></tr>
 <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>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q967M2_GIAIN Q967M2_GIAIN]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 35: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Adenine phosphoribosyltransferase]]
+[[Category: Giardia intestinalis]]
-[[Category: Giain]]
 [[Category: Large Structures]]
-[[Category: Almo, S C]]
+[[Category: Almo SC]]
-[[Category: Sarver, A E]]
+[[Category: Sarver AE]]
-[[Category: Schramm, V L]]
+[[Category: Schramm VL]]
-[[Category: Shi, W]]
+[[Category: Shi W]]
-[[Category: Tanaka, K S]]
+[[Category: Tanaka KS]]
-[[Category: Wang, C C]]
+[[Category: Wang CC]]
-[[Category: Adenine]]
-[[Category: Aprtase]]
-[[Category: Catalytic loop]]
-[[Category: Giardia lamblia]]
-[[Category: Purine metabolism]]
-[[Category: Transferase]]

1l1r

From Proteopedia

Current revision

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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