3gvq

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UROD single-chain dimerUROD single-chain dimer

Structural highlights

3gvq 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.
Method:X-ray diffraction, Resolution 2.1Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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; EC 4.1.1.37), the fifth enzyme of the heme biosynthetic pathway, is required for the production of heme, vitamin B12, siroheme, and chlorophyll precursors. URO-D catalyzes the sequential decarboxylation of four acetate side chains in the pyrrole groups of uroporphyrinogen to produce coproporphyrinogen. URO-D is a stable homodimer, with the active-site clefts of the two subunits adjacent to each other. It has been hypothesized that the two catalytic centers interact functionally, perhaps by shuttling of reaction intermediates between subunits. We tested this hypothesis by construction of a single-chain protein (single-chain URO-D) in which the two subunits were connected by a flexible linker. The crystal structure of this protein was shown to be superimposable with wild-type activity and to have comparable catalytic activity. Mutations that impaired one or the other of the two active sites of single-chain URO-D resulted in approximately half of wild-type activity. The distributions of reaction intermediates were the same for mutant and wild-type sequences and were unaltered in a competition experiment using I and III isomer substrates. These observations indicate that communication between active sites is not required for enzyme function and suggest that the dimeric structure of URO-D is required to achieve conformational stability and to create a large active-site cleft.

Substrate shuttling between active sites of uroporphyrinogen decarboxylase is not required to generate coproporphyrinogen.,Phillips JD, Warby CA, Whitby FG, Kushner JP, Hill CP J Mol Biol. 2009 Jun 5;389(2):306-14. Epub 2009 Apr 10. PMID:19362562[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, Warby CA, Whitby FG, Kushner JP, Hill CP. Substrate shuttling between active sites of uroporphyrinogen decarboxylase is not required to generate coproporphyrinogen. J Mol Biol. 2009 Jun 5;389(2):306-14. Epub 2009 Apr 10. PMID:19362562 doi:10.1016/j.jmb.2009.04.013

3gvq, resolution 2.10Å

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