6hgr: Difference between revisions

Latest revision as of 06:31, 21 August 2019

Crystal Structure of Human APRT wild type in complex with IMP

Structural highlights

6hgr is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	IMP
Related:	6hgp, 6hgq, 6fch, 6fci, 6fcl, 6fd4, 6fd5, 6fd6
Gene:	APRT (HUMAN)
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

The reversible adenine phosphoribosyltransferase enzyme (APRT) is essential for purine homeostasis in prokaryotes and eukaryotes. In humans, APRT (hAPRT) is the only enzyme known to produce AMP in cells from dietary adenine. APRT can also process adenine analogs, which are involved in plant development or neuronal homeostasis. However, the molecular mechanism underlying substrate specificity of APRT and catalysis in both directions of the reaction remains poorly understood. Here we present the crystal structures of hAPRT complexed to three cellular nucleotide analogs (Hypoxanthine, IMP and GMP) that we compare to the phosphate-bound enzyme. We established that binding to hAPRT is substrate-shape-specific in the forward reaction, while it is base-specific in the reverse reaction. Furthermore, a quantum mechanics/molecular mechanics (QM/MM) analysis suggests that the forward reaction is mainly a nucleophilic substitution of type 2 (SN2) with a mix of SN1-type molecular mechanism. Based on our structural analysis, a magnesium-assisted SN2-type mechanism would be involved in the reverse reaction. These results provide a framework for understanding the molecular mechanism and substrate discrimination in both directions by APRTs. This knowledge can play an instrumental role in the design of inhibitors, such as antiparasitic agents, or adenine-based substrates.

Structural basis for substrate selectivity and nucleophilic substitution mechanisms in human adenine phosphoribosyltransferase catalyzed reaction.,Ozeir M, Huyet J, 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 J Biol Chem. 2019 Jun 3. pii: RA119.009087. doi: 10.1074/jbc.RA119.009087. PMID:31160323^[9]

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

References

↑ 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
↑ 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
↑ 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:https://dx.doi.org/10.1172/JCI113219
↑ 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:https://dx.doi.org/10.1172/JCI113408
↑ 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:https://dx.doi.org/10.1172/JCI115825
↑ 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
↑ 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
↑ 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
↑ Ozeir M, Huyet J, 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 basis for substrate selectivity and nucleophilic substitution mechanisms in human adenine phosphoribosyltransferase catalyzed reaction. J Biol Chem. 2019 Jun 3. pii: RA119.009087. doi: 10.1074/jbc.RA119.009087. PMID:31160323 doi:https://dx.doi.org/10.1074/jbc.RA119.009087

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OCA

[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:https://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:https://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:https://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] Ozeir M, Huyet J, 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 basis for substrate selectivity and nucleophilic substitution mechanisms in human adenine phosphoribosyltransferase catalyzed reaction. J Biol Chem. 2019 Jun 3. pii: RA119.009087. doi: 10.1074/jbc.RA119.009087. PMID:31160323 doi:https://dx.doi.org/10.1074/jbc.RA119.009087

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@@ Line 3: / Line 3: @@
 <StructureSection load='6hgr' size='340' side='right'caption='[[6hgr]], [[Resolution|resolution]] 1.52&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6hgr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HGR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6hgr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HGR FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6hgp|6hgp]], [[6hgq|6hgq]], [[6fch|6fch]], [[6fci|6fci]], [[6fcl|6fcl]], [[6fd4|6fd4]], [[6fd5|6fd5]], [[6fd6|6fd6]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APRT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6hgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hgr OCA], [http://pdbe.org/6hgr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hgr RCSB], [http://www.ebi.ac.uk/pdbsum/6hgr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hgr ProSAT]</span></td></tr>
@@ Line 27: / Line 28: @@
 </StructureSection>
 [[Category: Adenine phosphoribosyltransferase]]
+[[Category: Human]]
 [[Category: Large Structures]]
 [[Category: Huyet, J]]

6hgr: Difference between revisions

Latest revision as of 06:31, 21 August 2019

Crystal Structure of Human APRT wild type in complex with IMP

Structural highlights

Disease

Function

Publication Abstract from PubMed

References

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