1ey2: Difference between revisions

Revision as of 07:16, 17 March 2021

HUMAN HOMOGENTISATE DIOXYGENASE WITH FE(II)

Structural highlights

1ey2 is a 1 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	FE2
NonStd Res:	MSE
Related:	1eyb
Activity:	Homogentisate 1,2-dioxygenase, with EC number 1.13.11.5
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

[HGD_HUMAN] Defects in HGD are the cause of alkaptonuria (AKU) [MIM:203500]. AKU is an autosomal recessive error of metabolism characterized by an increase in the level of homogentisic acid. The clinical manifestations of AKU are urine that turns dark on standing and alkalinization, black ochronotic pigmentation of cartilage and collagenous tissues, and spine arthritis.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8]

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

Homogentisate dioxygenase (HGO) cleaves the aromatic ring during the metabolic degradation of Phe and Tyr. HGO deficiency causes alkaptonuria (AKU), the first human disease shown to be inherited as a recessive Mendelian trait. Crystal structures of apo-HGO and HGO containing an iron ion have been determined at 1.9 and 2.3 A resolution, respectively. The HGO protomer, which contains a 280-residue N-terminal domain and a 140-residue C-terminal domain, associates as a hexamer arranged as a dimer of trimers. The active site iron ion is coordinated near the interface between subunits in the HGO trimer by a Glu and two His side chains. HGO represents a new structural class of dioxygenases. The largest group of AKU associated missense mutations affect residues located in regions of contact between subunits.

Crystal structure of human homogentisate dioxygenase.,Titus GP, Mueller HA, Burgner J, Rodriguez De Cordoba S, Penalva MA, Timm DE Nat Struct Biol. 2000 Jul;7(7):542-6. PMID:10876237^[9]

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

References

↑ Fernandez-Canon JM, Granadino B, Beltran-Valero de Bernabe D, Renedo M, Fernandez-Ruiz E, Penalva MA, Rodriguez de Cordoba S. The molecular basis of alkaptonuria. Nat Genet. 1996 Sep;14(1):19-24. PMID:8782815 doi:10.1038/ng0996-19
↑ Gehrig A, Schmidt SR, Muller CR, Srsen S, Srsnova K, Kress W. Molecular defects in alkaptonuria. Cytogenet Cell Genet. 1997;76(1-2):14-6. PMID:9154114
↑ Beltran-Valero de Bernabe D, Granadino B, Chiarelli I, Porfirio B, Mayatepek E, Aquaron R, Moore MM, Festen JJ, Sanmarti R, Penalva MA, de Cordoba SR. Mutation and polymorphism analysis of the human homogentisate 1, 2-dioxygenase gene in alkaptonuria patients. Am J Hum Genet. 1998 Apr;62(4):776-84. PMID:9529363
↑ Higashino K, Liu W, Ohkawa T, Yamamoto T, Fukui K, Ohno M, Imanishi H, Iwasaki A, Amuro Y, Hada T. A novel point mutation associated with alkaptonuria. Clin Genet. 1998 Mar;53(3):228-9. PMID:9630082
↑ Beltran-Valero de Bernabe D, Jimenez FJ, Aquaron R, Rodriguez de Cordoba S. Analysis of alkaptonuria (AKU) mutations and polymorphisms reveals that the CCC sequence motif is a mutational hot spot in the homogentisate 1,2 dioxygenase gene (HGO). Am J Hum Genet. 1999 May;64(5):1316-22. PMID:10205262 doi:S0002-9297(07)62276-9
↑ Felbor U, Mutsch Y, Grehn F, Muller CR, Kress W. Ocular ochronosis in alkaptonuria patients carrying mutations in the homogentisate 1,2-dioxygenase gene. Br J Ophthalmol. 1999 Jun;83(6):680-3. PMID:10340975
↑ Muller CR, Fregin A, Srsen S, Srsnova K, Halliger-Keller B, Felbor U, Seemanova E, Kress W. Allelic heterogeneity of alkaptonuria in Central Europe. Eur J Hum Genet. 1999 Sep;7(6):645-51. PMID:10482952 doi:10.1038/sj.ejhg.5200343
↑ Beltran-Valero de Bernabe D, Peterson P, Luopajarvi K, Matintalo P, Alho A, Konttinen Y, Krohn K, Rodriguez de Cordoba S, Ranki A. Mutational analysis of the HGO gene in Finnish alkaptonuria patients. J Med Genet. 1999 Dec;36(12):922-3. PMID:10594001
↑ Titus GP, Mueller HA, Burgner J, Rodriguez De Cordoba S, Penalva MA, Timm DE. Crystal structure of human homogentisate dioxygenase. Nat Struct Biol. 2000 Jul;7(7):542-6. PMID:10876237 doi:https://dx.doi.org/10.1038/76756

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OCA

[1] Fernandez-Canon JM, Granadino B, Beltran-Valero de Bernabe D, Renedo M, Fernandez-Ruiz E, Penalva MA, Rodriguez de Cordoba S. The molecular basis of alkaptonuria. Nat Genet. 1996 Sep;14(1):19-24. PMID:8782815 doi:10.1038/ng0996-19

[2] Gehrig A, Schmidt SR, Muller CR, Srsen S, Srsnova K, Kress W. Molecular defects in alkaptonuria. Cytogenet Cell Genet. 1997;76(1-2):14-6. PMID:9154114

[3] Beltran-Valero de Bernabe D, Granadino B, Chiarelli I, Porfirio B, Mayatepek E, Aquaron R, Moore MM, Festen JJ, Sanmarti R, Penalva MA, de Cordoba SR. Mutation and polymorphism analysis of the human homogentisate 1, 2-dioxygenase gene in alkaptonuria patients. Am J Hum Genet. 1998 Apr;62(4):776-84. PMID:9529363

[4] Higashino K, Liu W, Ohkawa T, Yamamoto T, Fukui K, Ohno M, Imanishi H, Iwasaki A, Amuro Y, Hada T. A novel point mutation associated with alkaptonuria. Clin Genet. 1998 Mar;53(3):228-9. PMID:9630082

[5] Beltran-Valero de Bernabe D, Jimenez FJ, Aquaron R, Rodriguez de Cordoba S. Analysis of alkaptonuria (AKU) mutations and polymorphisms reveals that the CCC sequence motif is a mutational hot spot in the homogentisate 1,2 dioxygenase gene (HGO). Am J Hum Genet. 1999 May;64(5):1316-22. PMID:10205262 doi:S0002-9297(07)62276-9

[6] Felbor U, Mutsch Y, Grehn F, Muller CR, Kress W. Ocular ochronosis in alkaptonuria patients carrying mutations in the homogentisate 1,2-dioxygenase gene. Br J Ophthalmol. 1999 Jun;83(6):680-3. PMID:10340975

[7] Muller CR, Fregin A, Srsen S, Srsnova K, Halliger-Keller B, Felbor U, Seemanova E, Kress W. Allelic heterogeneity of alkaptonuria in Central Europe. Eur J Hum Genet. 1999 Sep;7(6):645-51. PMID:10482952 doi:10.1038/sj.ejhg.5200343

[8] Beltran-Valero de Bernabe D, Peterson P, Luopajarvi K, Matintalo P, Alho A, Konttinen Y, Krohn K, Rodriguez de Cordoba S, Ranki A. Mutational analysis of the HGO gene in Finnish alkaptonuria patients. J Med Genet. 1999 Dec;36(12):922-3. PMID:10594001

[9] Titus GP, Mueller HA, Burgner J, Rodriguez De Cordoba S, Penalva MA, Timm DE. Crystal structure of human homogentisate dioxygenase. Nat Struct Biol. 2000 Jul;7(7):542-6. PMID:10876237 doi:https://dx.doi.org/10.1038/76756

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@@ Line 3: / Line 3: @@
 <StructureSection load='1ey2' size='340' side='right'caption='[[1ey2]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ey2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EY2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EY2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ey2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EY2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EY2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1eyb|1eyb]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1eyb|1eyb]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Homogentisate_1,2-dioxygenase Homogentisate 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.5 1.13.11.5] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Homogentisate_1,2-dioxygenase Homogentisate 1,2-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.5 1.13.11.5] </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=1ey2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ey2 OCA], [http://pdbe.org/1ey2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ey2 RCSB], [http://www.ebi.ac.uk/pdbsum/1ey2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ey2 ProSAT]</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=1ey2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ey2 OCA], [https://pdbe.org/1ey2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ey2 RCSB], [https://www.ebi.ac.uk/pdbsum/1ey2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ey2 ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/HGD_HUMAN HGD_HUMAN]] Defects in HGD are the cause of alkaptonuria (AKU) [MIM:[http://omim.org/entry/203500 203500]]. AKU is an autosomal recessive error of metabolism characterized by an increase in the level of homogentisic acid. The clinical manifestations of AKU are urine that turns dark on standing and alkalinization, black ochronotic pigmentation of cartilage and collagenous tissues, and spine arthritis.<ref>PMID:8782815</ref> <ref>PMID:9154114</ref> <ref>PMID:9529363</ref> <ref>PMID:9630082</ref> <ref>PMID:10205262</ref> <ref>PMID:10340975</ref> <ref>PMID:10482952</ref> <ref>PMID:10594001</ref>
+[[https://www.uniprot.org/uniprot/HGD_HUMAN HGD_HUMAN]] Defects in HGD are the cause of alkaptonuria (AKU) [MIM:[https://omim.org/entry/203500 203500]]. AKU is an autosomal recessive error of metabolism characterized by an increase in the level of homogentisic acid. The clinical manifestations of AKU are urine that turns dark on standing and alkalinization, black ochronotic pigmentation of cartilage and collagenous tissues, and spine arthritis.<ref>PMID:8782815</ref> <ref>PMID:9154114</ref> <ref>PMID:9529363</ref> <ref>PMID:9630082</ref> <ref>PMID:10205262</ref> <ref>PMID:10340975</ref> <ref>PMID:10482952</ref> <ref>PMID:10594001</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

1ey2: Difference between revisions

Revision as of 07:16, 17 March 2021

HUMAN HOMOGENTISATE DIOXYGENASE WITH FE(II)

Structural highlights

Disease

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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