2e1q: Difference between revisions

Revision as of 08:33, 25 October 2023

Crystal Structure of Human Xanthine Oxidoreductase mutant, Glu803Val

Structural highlights

2e1q is a 4 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 2.6Å
Ligands:	BCT, CA, FAD, FES, MOM, MTE, SAL
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

XDH_HUMAN Defects in XDH are the cause of xanthinuria type 1 (XU1) [MIM:278300. Xanthinuria is characterized by excretion of very large amounts of xanthine in the urine and a tendency to form xanthine stones. Uric acid is strikingly diminished in serum and urine. XU1 is due to isolated xanthine dehydrogenase. XU1 patients can metabolize allopurinol.^[1] ^[2] ^[3] ^[4]

Function

XDH_HUMAN Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid. Contributes to the generation of reactive oxygen species. Has also low oxidase activity towards aldehydes (in vitro).^[5]

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

Xanthine oxidase (oxidoreductase; XOR) and aldehyde oxidase (AO) are similar in protein structure and prosthetic group composition, but differ in substrate preference. Here we show that mutation of two amino acid residues in the active site of human XOR for purine substrates results in conversion of the substrate preference to AO type. Human XOR and its Glu803-to-valine (E803V) and Arg881-to-methionine (R881M) mutants were expressed in an Escherichia coli system. The E803V mutation almost completely abrogated the activity towards hypoxanthine as a substrate, but very weak activity towards xanthine remained. On the other hand, the R881M mutant lacked activity towards xanthine, but retained slight activity towards hypoxanthine. Both mutants, however, exhibited significant aldehyde oxidase activity. The crystal structure of E803V mutant of human XOR was determined at 2.6 A resolution. The overall molybdopterin domain structure of this mutant closely resembles that of bovine milk XOR; amino acid residues in the active centre pocket are situated at very similar positions and in similar orientations, except that Glu803 was replaced by valine, indicating that the decrease in activity towards purine substrate is not due to large conformational change in the mutant enzyme. Unlike wild-type XOR, the mutants were not subject to time-dependent inhibition by allopurinol.

Human xanthine oxidase changes its substrate specificity to aldehyde oxidase type upon mutation of amino acid residues in the active site: roles of active site residues in binding and activation of purine substrate.,Yamaguchi Y, Matsumura T, Ichida K, Okamoto K, Nishino T J Biochem. 2007 Apr;141(4):513-24. Epub 2007 Feb 14. PMID:17301077^[6]

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

References

↑ Ichida K, Amaya Y, Kamatani N, Nishino T, Hosoya T, Sakai O. Identification of two mutations in human xanthine dehydrogenase gene responsible for classical type I xanthinuria. J Clin Invest. 1997 May 15;99(10):2391-7. PMID:9153281 doi:10.1172/JCI119421
↑ Levartovsky D, Lagziel A, Sperling O, Liberman U, Yaron M, Hosoya T, Ichida K, Peretz H. XDH gene mutation is the underlying cause of classical xanthinuria: a second report. Kidney Int. 2000 Jun;57(6):2215-20. PMID:10844591 doi:10.1046/j.1523-1755.2000.00082.x
↑ Sakamoto N, Yamamoto T, Moriwaki Y, Teranishi T, Toyoda M, Onishi Y, Kuroda S, Sakaguchi K, Fujisawa T, Maeda M, Hada T. Identification of a new point mutation in the human xanthine dehydrogenase gene responsible for a case of classical type I xanthinuria. Hum Genet. 2001 Apr;108(4):279-83. PMID:11379872
↑ Gok F, Ichida K, Topaloglu R. Mutational analysis of the xanthine dehydrogenase gene in a Turkish family with autosomal recessive classical xanthinuria. Nephrol Dial Transplant. 2003 Nov;18(11):2278-83. PMID:14551354
↑ Yamaguchi Y, Matsumura T, Ichida K, Okamoto K, Nishino T. Human xanthine oxidase changes its substrate specificity to aldehyde oxidase type upon mutation of amino acid residues in the active site: roles of active site residues in binding and activation of purine substrate. J Biochem. 2007 Apr;141(4):513-24. Epub 2007 Feb 14. PMID:17301077 doi:10.1093/jb/mvm053
↑ Yamaguchi Y, Matsumura T, Ichida K, Okamoto K, Nishino T. Human xanthine oxidase changes its substrate specificity to aldehyde oxidase type upon mutation of amino acid residues in the active site: roles of active site residues in binding and activation of purine substrate. J Biochem. 2007 Apr;141(4):513-24. Epub 2007 Feb 14. PMID:17301077 doi:10.1093/jb/mvm053

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OCA

[1] Ichida K, Amaya Y, Kamatani N, Nishino T, Hosoya T, Sakai O. Identification of two mutations in human xanthine dehydrogenase gene responsible for classical type I xanthinuria. J Clin Invest. 1997 May 15;99(10):2391-7. PMID:9153281 doi:10.1172/JCI119421

[2] Levartovsky D, Lagziel A, Sperling O, Liberman U, Yaron M, Hosoya T, Ichida K, Peretz H. XDH gene mutation is the underlying cause of classical xanthinuria: a second report. Kidney Int. 2000 Jun;57(6):2215-20. PMID:10844591 doi:10.1046/j.1523-1755.2000.00082.x

[3] Sakamoto N, Yamamoto T, Moriwaki Y, Teranishi T, Toyoda M, Onishi Y, Kuroda S, Sakaguchi K, Fujisawa T, Maeda M, Hada T. Identification of a new point mutation in the human xanthine dehydrogenase gene responsible for a case of classical type I xanthinuria. Hum Genet. 2001 Apr;108(4):279-83. PMID:11379872

[4] Gok F, Ichida K, Topaloglu R. Mutational analysis of the xanthine dehydrogenase gene in a Turkish family with autosomal recessive classical xanthinuria. Nephrol Dial Transplant. 2003 Nov;18(11):2278-83. PMID:14551354

[5] Yamaguchi Y, Matsumura T, Ichida K, Okamoto K, Nishino T. Human xanthine oxidase changes its substrate specificity to aldehyde oxidase type upon mutation of amino acid residues in the active site: roles of active site residues in binding and activation of purine substrate. J Biochem. 2007 Apr;141(4):513-24. Epub 2007 Feb 14. PMID:17301077 doi:10.1093/jb/mvm053

[6] Yamaguchi Y, Matsumura T, Ichida K, Okamoto K, Nishino T. Human xanthine oxidase changes its substrate specificity to aldehyde oxidase type upon mutation of amino acid residues in the active site: roles of active site residues in binding and activation of purine substrate. J Biochem. 2007 Apr;141(4):513-24. Epub 2007 Feb 14. PMID:17301077 doi:10.1093/jb/mvm053

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[5]

[6]

@@ Line 3: / Line 3: @@
 <StructureSection load='2e1q' size='340' side='right'caption='[[2e1q]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2e1q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E1Q FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2e1q]] is a 4 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=2E1Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E1Q FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MOM:HYDROXY(DIOXO)MOLYBDENUM'>MOM</scene>, <scene name='pdbligand=MTE:PHOSPHONIC+ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER'>MTE</scene>, <scene name='pdbligand=SAL:2-HYDROXYBENZOIC+ACID'>SAL</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]] 2.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MOM:HYDROXY(DIOXO)MOLYBDENUM'>MOM</scene>, <scene name='pdbligand=MTE:PHOSPHONIC+ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER'>MTE</scene>, <scene name='pdbligand=SAL:2-HYDROXYBENZOIC+ACID'>SAL</scene></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=2e1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1q OCA], [https://pdbe.org/2e1q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e1q RCSB], [https://www.ebi.ac.uk/pdbsum/2e1q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e1q ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[https://www.uniprot.org/uniprot/XDH_HUMAN XDH_HUMAN]] Defects in XDH are the cause of xanthinuria type 1 (XU1) [MIM:[https://omim.org/entry/278300 278300]]. Xanthinuria is characterized by excretion of very large amounts of xanthine in the urine and a tendency to form xanthine stones. Uric acid is strikingly diminished in serum and urine. XU1 is due to isolated xanthine dehydrogenase. XU1 patients can metabolize allopurinol.<ref>PMID:9153281</ref> <ref>PMID:10844591</ref> <ref>PMID:11379872</ref> <ref>PMID:14551354</ref>
+[https://www.uniprot.org/uniprot/XDH_HUMAN XDH_HUMAN] Defects in XDH are the cause of xanthinuria type 1 (XU1) [MIM:[https://omim.org/entry/278300 278300]. Xanthinuria is characterized by excretion of very large amounts of xanthine in the urine and a tendency to form xanthine stones. Uric acid is strikingly diminished in serum and urine. XU1 is due to isolated xanthine dehydrogenase. XU1 patients can metabolize allopurinol.<ref>PMID:9153281</ref> <ref>PMID:10844591</ref> <ref>PMID:11379872</ref> <ref>PMID:14551354</ref>
 == Function ==
-[[https://www.uniprot.org/uniprot/XDH_HUMAN XDH_HUMAN]] Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid. Contributes to the generation of reactive oxygen species. Has also low oxidase activity towards aldehydes (in vitro).<ref>PMID:17301077</ref>
+[https://www.uniprot.org/uniprot/XDH_HUMAN XDH_HUMAN] Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid. Contributes to the generation of reactive oxygen species. Has also low oxidase activity towards aldehydes (in vitro).<ref>PMID:17301077</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Ichida, K]]
+[[Category: Ichida K]]
-[[Category: Matsumura, T]]
+[[Category: Matsumura T]]
-[[Category: Nishino, T]]
+[[Category: Nishino T]]
-[[Category: Okamoto, K]]
+[[Category: Okamoto K]]
-[[Category: Yamaguchi, Y]]
+[[Category: Yamaguchi Y]]
-[[Category: Fad]]
-[[Category: Molybdenum cofactor]]
-[[Category: Oxidoreductase]]
-[[Category: Xanthine oxidase]]

2e1q: Difference between revisions

Revision as of 08:33, 25 October 2023

Crystal Structure of Human Xanthine Oxidoreductase mutant, Glu803Val

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

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