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'''Unreleased structure'''


The entry 6fcl is ON HOLD until Paper Publication
==Crystal Structure of Human APRT wild type in complex with AMP==
<StructureSection load='6fcl' size='340' side='right' caption='[[6fcl]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6fcl]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FCL FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6fch|6fch]], [[6fci|6fci]], [[6fd4|6fd4]], [[6fd5|6fd5]], [[6fd6|6fd6]]</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenine_phosphoribosyltransferase Adenine phosphoribosyltransferase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6fcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fcl OCA], [http://pdbe.org/6fcl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fcl RCSB], [http://www.ebi.ac.uk/pdbsum/6fcl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fcl ProSAT]</span></td></tr>
</table>
== Disease ==
[[http://www.uniprot.org/uniprot/APT_HUMAN APT_HUMAN]] Defects in APRT are the cause of adenine phosphoribosyltransferase deficiency (APRTD) [MIM:[http://omim.org/entry/614723 614723]]; also known as 2,8-dihydroxyadenine urolithiasis. An enzymatic deficiency that can lead to urolithiasis and renal failure. Patients have 2,8-dihydroxyadenine (DHA) urinary stones.<ref>PMID:1746557</ref> <ref>PMID:7915931</ref> <ref>PMID:3680503</ref> <ref>PMID:3343350</ref> <ref>PMID:1353080</ref> <ref>PMID:11243733</ref> <ref>PMID:15571218</ref> <ref>PMID:21635362</ref>  
== Function ==
[[http://www.uniprot.org/uniprot/APT_HUMAN APT_HUMAN]] Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Phosphoribosyltransferases catalyze the displacement of a PRPP alpha-1'-pyrophosphate to a nitrogen-containing nucleobase. How they control the balance of substrates/products binding and activities is poorly understood. Here, we investigated the human adenine phosphoribosyltransferase (hAPRT) that produces AMP in the purine salvage pathway. We show that a single oxygen atom from the Tyr105 side chain is responsible for selecting the active conformation of the 12 amino acid long catalytic loop. Using in vitro, cellular, and in crystallo approaches, we demonstrated that Tyr105 is key for the fine-tuning of the kinetic activity efficiencies of the forward and reverse reactions. Together, our results reveal an evolutionary pressure on the strictly conserved Tyr105 and on the dynamic motion of the flexible loop in phosphoribosyltransferases that is essential for purine biosynthesis in cells. These data also provide the framework for designing novel adenine derivatives that could modulate, through hAPRT, diseases-involved cellular pathways.


Authors: Nioche, P., Huyet, J., Ozeir, M.
Structural Insights into the Forward and Reverse Enzymatic Reactions in Human Adenine Phosphoribosyltransferase.,Huyet J, Ozeir M, Burgevin MC, Pinson B, Chesney F, Remy JM, Siddiqi AR, Lupoli R, Pinon G, Saint-Marc C, Gibert JF, Morales R, Ceballos-Picot I, Barouki R, Daignan-Fornier B, Olivier-Bandini A, Auge F, Nioche P Cell Chem Biol. 2018 Jun 21;25(6):666-676.e4. doi:, 10.1016/j.chembiol.2018.02.011. Epub 2018 Mar 22. PMID:29576532<ref>PMID:29576532</ref>


Description: Crystal structure of wild type human adenine phosphoribosyltransferase (APRT) in complex with AMP, Mg2+ and PRPP
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Ozeir, M]]
<div class="pdbe-citations 6fcl" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Adenine phosphoribosyltransferase]]
[[Category: Huyet, J]]
[[Category: Huyet, J]]
[[Category: Nioche, P]]
[[Category: Nioche, P]]
[[Category: Ozeir, M]]
[[Category: Rossmann fold]]
[[Category: Transferase]]

Latest revision as of 19:21, 15 August 2018

Crystal Structure of Human APRT wild type in complex with AMPCrystal Structure of Human APRT wild type in complex with AMP

Structural highlights

6fcl is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Activity:Adenine phosphoribosyltransferase, with EC number 2.4.2.7
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

[APT_HUMAN] Defects in APRT are the cause of adenine phosphoribosyltransferase deficiency (APRTD) [MIM:614723]; also known as 2,8-dihydroxyadenine urolithiasis. An enzymatic deficiency that can lead to urolithiasis and renal failure. Patients have 2,8-dihydroxyadenine (DHA) urinary stones.[1] [2] [3] [4] [5] [6] [7] [8]

Function

[APT_HUMAN] Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis.

Publication Abstract from PubMed

Phosphoribosyltransferases catalyze the displacement of a PRPP alpha-1'-pyrophosphate to a nitrogen-containing nucleobase. How they control the balance of substrates/products binding and activities is poorly understood. Here, we investigated the human adenine phosphoribosyltransferase (hAPRT) that produces AMP in the purine salvage pathway. We show that a single oxygen atom from the Tyr105 side chain is responsible for selecting the active conformation of the 12 amino acid long catalytic loop. Using in vitro, cellular, and in crystallo approaches, we demonstrated that Tyr105 is key for the fine-tuning of the kinetic activity efficiencies of the forward and reverse reactions. Together, our results reveal an evolutionary pressure on the strictly conserved Tyr105 and on the dynamic motion of the flexible loop in phosphoribosyltransferases that is essential for purine biosynthesis in cells. These data also provide the framework for designing novel adenine derivatives that could modulate, through hAPRT, diseases-involved cellular pathways.

Structural Insights into the Forward and Reverse Enzymatic Reactions in Human Adenine Phosphoribosyltransferase.,Huyet J, Ozeir M, Burgevin MC, Pinson B, Chesney F, Remy JM, Siddiqi AR, Lupoli R, Pinon G, Saint-Marc C, Gibert JF, Morales R, Ceballos-Picot I, Barouki R, Daignan-Fornier B, Olivier-Bandini A, Auge F, Nioche P Cell Chem Biol. 2018 Jun 21;25(6):666-676.e4. doi:, 10.1016/j.chembiol.2018.02.011. Epub 2018 Mar 22. PMID:29576532[9]

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

References

  1. ↑ Chen J, Sahota A, Laxdal T, Scrine M, Bowman S, Cui C, Stambrook PJ, Tischfield JA. Identification of a single missense mutation in the adenine phosphoribosyltransferase (APRT) gene from five Icelandic patients and a British patient. Am J Hum Genet. 1991 Dec;49(6):1306-11. PMID:1746557
  2. ↑ Sahota A, Chen J, Boyadjiev SA, Gault MH, Tischfield JA. Missense mutation in the adenine phosphoribosyltransferase gene causing 2,8-dihydroxyadenine urolithiasis. Hum Mol Genet. 1994 May;3(5):817-8. PMID:7915931
  3. ↑ Hidaka Y, Palella TD, O'Toole TE, Tarle SA, Kelley WN. Human adenine phosphoribosyltransferase. Identification of allelic mutations at the nucleotide level as a cause of complete deficiency of the enzyme. J Clin Invest. 1987 Nov;80(5):1409-15. PMID:3680503 doi:http://dx.doi.org/10.1172/JCI113219
  4. ↑ Hidaka Y, Tarle SA, Fujimori S, Kamatani N, Kelley WN, Palella TD. Human adenine phosphoribosyltransferase deficiency. Demonstration of a single mutant allele common to the Japanese. J Clin Invest. 1988 Mar;81(3):945-50. PMID:3343350 doi:http://dx.doi.org/10.1172/JCI113408
  5. ↑ Kamatani N, Hakoda M, Otsuka S, Yoshikawa H, Kashiwazaki S. Only three mutations account for almost all defective alleles causing adenine phosphoribosyltransferase deficiency in Japanese patients. J Clin Invest. 1992 Jul;90(1):130-5. PMID:1353080 doi:http://dx.doi.org/10.1172/JCI115825
  6. ↑ Deng L, Yang M, Frund S, Wessel T, De Abreu RA, Tischfield JA, Sahota A. 2,8-Dihydroxyadenine urolithiasis in a patient with considerable residual adenine phosphoribosyltransferase activity in cell extracts but with mutations in both copies of APRT. Mol Genet Metab. 2001 Mar;72(3):260-4. PMID:11243733 doi:10.1006/mgme.2000.3142
  7. ↑ Taniguchi A, Tsuchida S, Kuno S, Mita M, Machida T, Ioritani N, Terai C, Yamanaka H, Kamatani N. Identification of two novel mutations in adenine phosphoribosyltransferase gene in patients with 2,8-dihydroxyadenine urolithiasis. Nucleosides Nucleotides Nucleic Acids. 2004 Oct;23(8-9):1141-5. PMID:15571218 doi:10.1081/NCN-200027393
  8. ↑ Nozue H, Kamoda T, Saitoh H, Ichikawa K, Taniguchi A. A Japanese boy with adenine phosphoribosyltransferase (APRT) deficiency caused by compound heterozygosity including a novel missense mutation in APRT gene. Acta Paediatr. 2011 Dec;100(12):e285-8. doi: 10.1111/j.1651-2227.2011.02371.x., Epub 2011 Jun 17. PMID:21635362 doi:10.1111/j.1651-2227.2011.02371.x
  9. ↑ Huyet J, Ozeir M, Burgevin MC, Pinson B, Chesney F, Remy JM, Siddiqi AR, Lupoli R, Pinon G, Saint-Marc C, Gibert JF, Morales R, Ceballos-Picot I, Barouki R, Daignan-Fornier B, Olivier-Bandini A, Auge F, Nioche P. Structural Insights into the Forward and Reverse Enzymatic Reactions in Human Adenine Phosphoribosyltransferase. Cell Chem Biol. 2018 Jun 21;25(6):666-676.e4. doi:, 10.1016/j.chembiol.2018.02.011. Epub 2018 Mar 22. PMID:29576532 doi:http://dx.doi.org/10.1016/j.chembiol.2018.02.011

6fcl, resolution 1.50Å

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