1zn9: Difference between revisions

Latest revision as of 09:06, 14 February 2024

Human Adenine Phosphoribosyltransferase in Apo and AMP Complexed Forms

Structural highlights

1zn9 is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.05Å
Ligands:	AMP
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.

Evolutionary Conservation

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

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

Proteopedia Page Contributors and Editors (what is this?)

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

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@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1zn9.png|left|200px]]
-<!--
+==Human Adenine Phosphoribosyltransferase in Apo and AMP Complexed Forms==
-The line below this paragraph, containing "STRUCTURE_1zn9", creates the "Structure Box" on the page.
+<StructureSection load='1zn9' size='340' side='right'caption='[[1zn9]], [[Resolution|resolution]] 2.05&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'>[[1zn9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZN9 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]] 2.05&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene></td></tr>
-{{STRUCTURE_1zn9|  PDB=1zn9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1zn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zn9 OCA], [https://pdbe.org/1zn9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zn9 RCSB], [https://www.ebi.ac.uk/pdbsum/1zn9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zn9 ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/APT_HUMAN APT_HUMAN] Defects in APRT are the cause of adenine phosphoribosyltransferase deficiency (APRTD) [MIM:[https://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 ==
+[https://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.
+== 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/zn/1zn9_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=1zn9 ConSurf].
+<div style="clear:both"></div>
-===Human Adenine Phosphoribosyltransferase in Apo and AMP Complexed Forms===
+==See Also==
+*[[Phosphoribosyltransferase 3D structures|Phosphoribosyltransferase 3D structures]]
+== References ==
-<!--
+<references/>
-The line below this paragraph, {{ABSTRACT_PUBMED_18399692}}, adds the Publication Abstract to the page
+__TOC__
-(as it appears on PubMed at http://www.pubmed.gov), where 18399692 is the PubMed ID number.
+</StructureSection>
--->
-{{ABSTRACT_PUBMED_18399692}}
-==Disease==
-Known disease associated with this structure: Urolithiasis, 2,8-dihydroxyadenine OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=102600 102600]]
-==About this Structure==
-ZN9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZN9 OCA].
-==Reference==
-Structural Complexes of Human Adenine Phosphoribosyltransferase Reveal Novel Features of the APRT Catalytic Mechanism., Silva CH, Silva M, Iulek J, Thiemann OH, J Biomol Struct Dyn. 2008 Jun;25(6):589-98. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18399692 18399692]
-[[Category: Adenine phosphoribosyltransferase]]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Iulek, J.]]
+[[Category: Iulek J]]
-[[Category: Silva, M.]]
+[[Category: Silva M]]
-[[Category: Thiemann, O H.]]
+[[Category: Thiemann OH]]
-[[Category: Tomich, C H.T P.]]
+[[Category: Tomich CHTP]]
-[[Category: Glycosyltransferase]]
-[[Category: Polymorphism]]
-[[Category: Purine salvage]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 07:07:00 2008''

1zn9: Difference between revisions

Latest revision as of 09:06, 14 February 2024

Human Adenine Phosphoribosyltransferase in Apo and AMP Complexed Forms

Structural highlights

Disease

Function

Evolutionary Conservation

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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