1r3r: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1r3r]] is a 1 chain structure with 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=1R3R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R3R FirstGlance]. <br>
<table><tr><td colspan='2'>[[1r3r]] is a 1 chain structure with 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=1R3R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R3R FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1uro|1uro]], [[1r3q|1r3q]], [[1r3s|1r3s]], [[1r3t|1r3t]], [[1r3v|1r3v]], [[1r3w|1r3w]], [[1r3y|1r3y]]</td></tr>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1uro|1uro]], [[1r3q|1r3q]], [[1r3s|1r3s]], [[1r3t|1r3t]], [[1r3v|1r3v]], [[1r3w|1r3w]], [[1r3y|1r3y]]</td></tr>
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uroporphyrinogen_decarboxylase Uroporphyrinogen decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.37 4.1.1.37] </span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uroporphyrinogen_decarboxylase Uroporphyrinogen decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.37 4.1.1.37] </span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r3r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1r3r RCSB], [http://www.ebi.ac.uk/pdbsum/1r3r PDBsum]</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=1r3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r3r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1r3r RCSB], [http://www.ebi.ac.uk/pdbsum/1r3r PDBsum]</span></td></tr>
<table>
</table>
== Disease ==
== Disease ==
[[http://www.uniprot.org/uniprot/DCUP_HUMAN DCUP_HUMAN]] Defects in UROD are the cause of familial porphyria cutanea tarda (FPCT) [MIM:[http://omim.org/entry/176100 176100]]; also known as porphyria cutanea tarda type II. FPCT is an autosomal dominant disorder characterized by light-sensitive dermatitis, with onset in later life. It is associated with the excretion of large amounts of uroporphyrin in the urine. Iron overload is often present in association with varying degrees of liver damage. Besides the familial form of PCT, a relatively common idiosyncratic form is known in which only the liver enzyme is reduced. This form is referred to as porphyria cutanea tarda "sporadic" type or type I [MIM:[http://omim.org/entry/176090 176090]]. PCT type I occurs sporadically as an unusual accompaniment of common hepatic disorders such as alcohol-associated liver disease.<ref>PMID:2243121</ref> <ref>PMID:11719352</ref> <ref>PMID:2920211</ref> <ref>PMID:7706766</ref> <ref>PMID:8896428</ref> <ref>PMID:9792863</ref> <ref>PMID:10338097</ref> <ref>PMID:10477430</ref> <ref>PMID:11069625</ref> <ref>PMID:11295834</ref>  Defects in UROD are the cause of hepatoerythropoietic porphyria (HEP) [MIM:[http://omim.org/entry/176100 176100]]. HEP is a rare autosomal recessive disorder. It is the severe form of cutaneous porphyria, and presents in infancy. The level of UROD is very low in erythrocytes and cultured skin fibroblasts, suggesting that HEP is the homozygous state for porphyria cutanea tarda.<ref>PMID:8896428</ref> <ref>PMID:8644733</ref> <ref>PMID:3775362</ref> <ref>PMID:1905636</ref> <ref>PMID:1634232</ref> <ref>PMID:8176248</ref> <ref>PMID:12071824</ref> <ref>PMID:15491440</ref> <ref>PMID:17240319</ref> <ref>PMID:21668429</ref>   
[[http://www.uniprot.org/uniprot/DCUP_HUMAN DCUP_HUMAN]] Defects in UROD are the cause of familial porphyria cutanea tarda (FPCT) [MIM:[http://omim.org/entry/176100 176100]]; also known as porphyria cutanea tarda type II. FPCT is an autosomal dominant disorder characterized by light-sensitive dermatitis, with onset in later life. It is associated with the excretion of large amounts of uroporphyrin in the urine. Iron overload is often present in association with varying degrees of liver damage. Besides the familial form of PCT, a relatively common idiosyncratic form is known in which only the liver enzyme is reduced. This form is referred to as porphyria cutanea tarda "sporadic" type or type I [MIM:[http://omim.org/entry/176090 176090]]. PCT type I occurs sporadically as an unusual accompaniment of common hepatic disorders such as alcohol-associated liver disease.<ref>PMID:2243121</ref> <ref>PMID:11719352</ref> <ref>PMID:2920211</ref> <ref>PMID:7706766</ref> <ref>PMID:8896428</ref> <ref>PMID:9792863</ref> <ref>PMID:10338097</ref> <ref>PMID:10477430</ref> <ref>PMID:11069625</ref> <ref>PMID:11295834</ref>  Defects in UROD are the cause of hepatoerythropoietic porphyria (HEP) [MIM:[http://omim.org/entry/176100 176100]]. HEP is a rare autosomal recessive disorder. It is the severe form of cutaneous porphyria, and presents in infancy. The level of UROD is very low in erythrocytes and cultured skin fibroblasts, suggesting that HEP is the homozygous state for porphyria cutanea tarda.<ref>PMID:8896428</ref> <ref>PMID:8644733</ref> <ref>PMID:3775362</ref> <ref>PMID:1905636</ref> <ref>PMID:1634232</ref> <ref>PMID:8176248</ref> <ref>PMID:12071824</ref> <ref>PMID:15491440</ref> <ref>PMID:17240319</ref> <ref>PMID:21668429</ref>   
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Uroporphyrinogen decarboxylase]]
[[Category: Uroporphyrinogen decarboxylase]]
[[Category: Hill, C P.]]
[[Category: Hill, C P]]
[[Category: Kushner, J P.]]
[[Category: Kushner, J P]]
[[Category: Phillips, J D.]]
[[Category: Phillips, J D]]
[[Category: Whitby, F G.]]
[[Category: Whitby, F G]]
[[Category: Lyase]]
[[Category: Lyase]]
[[Category: Uroporphyrinogen decarboxylase coproporphyrinogen]]
[[Category: Uroporphyrinogen decarboxylase coproporphyrinogen]]
[[Category: X-ray crystallography]]
[[Category: X-ray crystallography]]

Revision as of 09:52, 6 January 2015

Uroporphyrinogen Decarboxylase with mutation D86NUroporphyrinogen Decarboxylase with mutation D86N

Structural highlights

1r3r is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Activity:Uroporphyrinogen decarboxylase, with EC number 4.1.1.37
Resources:FirstGlance, OCA, RCSB, PDBsum

Disease

[DCUP_HUMAN] Defects in UROD are the cause of familial porphyria cutanea tarda (FPCT) [MIM:176100]; also known as porphyria cutanea tarda type II. FPCT is an autosomal dominant disorder characterized by light-sensitive dermatitis, with onset in later life. It is associated with the excretion of large amounts of uroporphyrin in the urine. Iron overload is often present in association with varying degrees of liver damage. Besides the familial form of PCT, a relatively common idiosyncratic form is known in which only the liver enzyme is reduced. This form is referred to as porphyria cutanea tarda "sporadic" type or type I [MIM:176090]. PCT type I occurs sporadically as an unusual accompaniment of common hepatic disorders such as alcohol-associated liver disease.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] Defects in UROD are the cause of hepatoerythropoietic porphyria (HEP) [MIM:176100]. HEP is a rare autosomal recessive disorder. It is the severe form of cutaneous porphyria, and presents in infancy. The level of UROD is very low in erythrocytes and cultured skin fibroblasts, suggesting that HEP is the homozygous state for porphyria cutanea tarda.[11] [12] [13] [14] [15] [16] [17] [18] [19] [20]

Function

[DCUP_HUMAN] Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III.

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

Uroporphyrinogen decarboxylase (URO-D), an essential enzyme that functions in the heme biosynthetic pathway, catalyzes decarboxylation of all four acetate groups of uroporphyrinogen to form coproporphyrinogen. Here we report crystal structures of URO-D in complex with the I and III isomer coproporphyrinogen products. Crystallization required use of a novel enzymatic approach to generate the highly oxygen-sensitive porphyrinogen substrate in situ. The tetrapyrrole product adopts a domed conformation that lies against a collar of conserved hydrophobic residues and allows formation of hydrogen bonding interactions between a carboxylate oxygen atom of the invariant Asp86 residue and the pyrrole NH groups. Structural and biochemical analyses of URO-D proteins mutated at Asp86 support the conclusion that this residue makes important contributions to binding and likely promotes catalysis by stabilizing a positive charge on a reaction intermediate. The central coordination geometry of Asp86 allows the initial substrates and the various partially decarboxylated intermediates to be bound with equivalent activating interactions, and thereby explains how all four of the substrate acetate groups can be decarboxylated at the same catalytic center.

Structural basis for tetrapyrrole coordination by uroporphyrinogen decarboxylase.,Phillips JD, Whitby FG, Kushner JP, Hill CP EMBO J. 2003 Dec 1;22(23):6225-33. PMID:14633982[21]

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

References

  1. ↑ Garey JR, Harrison LM, Franklin KF, Metcalf KM, Radisky ES, Kushner JP. Uroporphyrinogen decarboxylase: a splice site mutation causes the deletion of exon 6 in multiple families with porphyria cutanea tarda. J Clin Invest. 1990 Nov;86(5):1416-22. PMID:2243121 doi:http://dx.doi.org/10.1172/JCI114856
  2. ↑ Phillips JD, Parker TL, Schubert HL, Whitby FG, Hill CP, Kushner JP. Functional consequences of naturally occurring mutations in human uroporphyrinogen decarboxylase. Blood. 2001 Dec 1;98(12):3179-85. PMID:11719352
  3. ↑ Garey JR, Hansen JL, Harrison LM, Kennedy JB, Kushner JP. A point mutation in the coding region of uroporphyrinogen decarboxylase associated with familial porphyria cutanea tarda. Blood. 1989 Mar;73(4):892-5. PMID:2920211
  4. ↑ Roberts AG, Elder GH, De Salamanca RE, Herrero C, Lecha M, Mascaro JM. A mutation (G281E) of the human uroporphyrinogen decarboxylase gene causes both hepatoerythropoietic porphyria and overt familial porphyria cutanea tarda: biochemical and genetic studies on Spanish patients. J Invest Dermatol. 1995 Apr;104(4):500-2. PMID:7706766
  5. ↑ McManus JF, Begley CG, Sassa S, Ratnaike S. Five new mutations in the uroporphyrinogen decarboxylase gene identified in families with cutaneous porphyria. Blood. 1996 Nov 1;88(9):3589-600. PMID:8896428
  6. ↑ Mendez M, Sorkin L, Rossetti MV, Astrin KH, del C Batlle AM, Parera VE, Aizencang G, Desnick RJ. Familial porphyria cutanea tarda: characterization of seven novel uroporphyrinogen decarboxylase mutations and frequency of common hemochromatosis alleles. Am J Hum Genet. 1998 Nov;63(5):1363-75. PMID:9792863
  7. ↑ McManus JF, Begley CG, Sassa S, Ratnaike S. Three new mutations in the uroporphyrinogen decarboxylase gene in familial porphyria cutanea tarda. Mutation in brief no. 237. Online. Hum Mutat. 1999;13(5):412. PMID:10338097 doi:<412::AID-HUMU11>3.0.CO;2-T 10.1002/(SICI)1098-1004(1999)13:5<412::AID-HUMU11>3.0.CO;2-T
  8. ↑ Christiansen L, Ged C, Hombrados I, Brons-Poulsen J, Fontanellas A, de Verneuil H, Horder M, Petersen NE. Screening for mutations in the uroporphyrinogen decarboxylase gene using denaturing gradient gel electrophoresis. Identification and characterization of six novel mutations associated with familial PCT. Hum Mutat. 1999;14(3):222-32. PMID:10477430 doi:<222::AID-HUMU5>3.0.CO;2-V 10.1002/(SICI)1098-1004(1999)14:3<222::AID-HUMU5>3.0.CO;2-V
  9. ↑ Brady JJ, Jackson HA, Roberts AG, Morgan RR, Whatley SD, Rowlands GL, Darby C, Shudell E, Watson R, Paiker J, Worwood MW, Elder GH. Co-inheritance of mutations in the uroporphyrinogen decarboxylase and hemochromatosis genes accelerates the onset of porphyria cutanea tarda. J Invest Dermatol. 2000 Nov;115(5):868-74. PMID:11069625 doi:jid148
  10. ↑ Cappellini MD, Martinez di Montemuros F, Tavazzi D, Fargion S, Pizzuti A, Comino A, Cainelli T, Fiorelli G. Seven novel point mutations in the uroporphyrinogen decarboxylase (UROD) gene in patients with familial porphyria cutanea tarda (f-PCT). Hum Mutat. 2001 Apr;17(4):350. PMID:11295834 doi:10.1002/humu.35
  11. ↑ McManus JF, Begley CG, Sassa S, Ratnaike S. Five new mutations in the uroporphyrinogen decarboxylase gene identified in families with cutaneous porphyria. Blood. 1996 Nov 1;88(9):3589-600. PMID:8896428
  12. ↑ Moran-Jimenez MJ, Ged C, Romana M, Enriquez De Salamanca R, Taieb A, Topi G, D'Alessandro L, de Verneuil H. Uroporphyrinogen decarboxylase: complete human gene sequence and molecular study of three families with hepatoerythropoietic porphyria. Am J Hum Genet. 1996 Apr;58(4):712-21. PMID:8644733
  13. ↑ de Verneuil H, Grandchamp B, Beaumont C, Picat C, Nordmann Y. Uroporphyrinogen decarboxylase structural mutant (Gly281----Glu) in a case of porphyria. Science. 1986 Nov 7;234(4777):732-4. PMID:3775362
  14. ↑ Romana M, Grandchamp B, Dubart A, Amselem S, Chabret C, Nordmann Y, Goossens M, Romeo PH. Identification of a new mutation responsible for hepatoerythropoietic porphyria. Eur J Clin Invest. 1991 Apr;21(2):225-9. PMID:1905636
  15. ↑ de Verneuil H, Bourgeois F, de Rooij F, Siersema PD, Wilson JH, Grandchamp B, Nordmann Y. Characterization of a new mutation (R292G) and a deletion at the human uroporphyrinogen decarboxylase locus in two patients with hepatoerythropoietic porphyria. Hum Genet. 1992 Jul;89(5):548-52. PMID:1634232
  16. ↑ Meguro K, Fujita H, Ishida N, Akagi R, Kurihara T, Galbraith RA, Kappas A, Zabriskie JB, Toback AC, Harber LC, et al.. Molecular defects of uroporphyrinogen decarboxylase in a patient with mild hepatoerythropoietic porphyria. J Invest Dermatol. 1994 May;102(5):681-5. PMID:8176248
  17. ↑ Ged C, Ozalla D, Herrero C, Lecha M, Mendez M, de Verneuil H, Mascaro JM. Description of a new mutation in hepatoerythropoietic porphyria and prenatal exclusion of a homozygous fetus. Arch Dermatol. 2002 Jul;138(7):957-60. PMID:12071824
  18. ↑ Armstrong DK, Sharpe PC, Chambers CR, Whatley SD, Roberts AG, Elder GH. Hepatoerythropoietic porphyria: a missense mutation in the UROD gene is associated with mild disease and an unusual porphyrin excretion pattern. Br J Dermatol. 2004 Oct;151(4):920-3. PMID:15491440 doi:BJD6101
  19. ↑ Phillips JD, Whitby FG, Stadtmueller BM, Edwards CQ, Hill CP, Kushner JP. Two novel uroporphyrinogen decarboxylase (URO-D) mutations causing hepatoerythropoietic porphyria (HEP). Transl Res. 2007 Feb;149(2):85-91. PMID:17240319 doi:10.1016/j.trsl.2006.08.006
  20. ↑ To-Figueras J, Phillips JD, Gonzalez-Lopez JM, Badenas C, Madrigal I, Gonzalez-Romaris EM, Ramos C, Aguirre JM, Herrero C. Hepatoerythropoietic porphyria due to a novel mutation in the uroporphyrinogen decarboxylase gene. Br J Dermatol. 2011 Sep;165(3):499-505. doi: 10.1111/j.1365-2133.2011.10453.x., Epub 2011 Aug 18. PMID:21668429 doi:10.1111/j.1365-2133.2011.10453.x
  21. ↑ Phillips JD, Whitby FG, Kushner JP, Hill CP. Structural basis for tetrapyrrole coordination by uroporphyrinogen decarboxylase. EMBO J. 2003 Dec 1;22(23):6225-33. PMID:14633982 doi:10.1093/emboj/cdg606

1r3r, resolution 1.85Å

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