2f61: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2f61]] 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=2F61 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F61 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2f61]] 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=2F61 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F61 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2f61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f61 OCA], [https://pdbe.org/2f61 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f61 RCSB], [https://www.ebi.ac.uk/pdbsum/2f61 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f61 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=2f61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f61 OCA], [https://pdbe.org/2f61 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f61 RCSB], [https://www.ebi.ac.uk/pdbsum/2f61 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f61 ProSAT]</span></td></tr>
</table>
</table>

Revision as of 10:43, 23 August 2023

Crystal structure of partially deglycosylated acid beta-glucosidaseCrystal structure of partially deglycosylated acid beta-glucosidase

Structural highlights

2f61 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 2.5Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

GLCM_HUMAN Defects in GBA are the cause of Gaucher disease (GD) [MIM:230800; also known as glucocerebrosidase deficiency. GD is the most prevalent lysosomal storage disease, characterized by accumulation of glucosylceramide in the reticulo-endothelial system. Different clinical forms are recognized depending on the presence (neuronopathic forms) or absence of central nervous system involvement, severity and age of onset.[1] [:][2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] Defects in GBA are the cause of Gaucher disease type 1 (GD1) [MIM:230800; also known as adult non-neuronopathic Gaucher disease. GD1 is characterized by hepatosplenomegaly with consequent anemia and thrombopenia, and bone involvement. The central nervous system is not involved.[:][48] [49] [50] [51] [52] [53] [54] [55] [56] [57] Defects in GBA are the cause of Gaucher disease type 2 (GD2) [MIM:230900; also known as acute neuronopathic Gaucher disease. GD2 is the most severe form and is universally progressive and fatal. It manifests soon after birth, with death generally occurring before patients reach two years of age.[58] [59] [60] [61] [62] [63] [64] [65] Defects in GBA are the cause of Gaucher disease type 3 (GD3) [MIM:231000; also known as subacute neuronopathic Gaucher disease. GD3 has central nervous manifestations.[66] [67] [68] [69] [70] [71] [72] Defects in GBA are the cause of Gaucher disease type 3C (GD3C) [MIM:231005; also known as pseudo-Gaucher disease or Gaucher-like disease.[73] [74] [75] [76] [77] [78] Defects in GBA are the cause of Gaucher disease perinatal lethal (GDPL) [MIM:608013. It is a distinct form of Gaucher disease type 2, characterized by fetal onset. Hydrops fetalis, in utero fetal death and neonatal distress are prominent features. When hydrops is absent, neurologic involvement begins in the first week and leads to death within 3 months. Hepatosplenomegaly is a major sign, and is associated with ichthyosis, arthrogryposis, and facial dysmorphism.[79] [80] [81] [82] [83] [84] Note=Perinatal lethal Gaucher disease is associated with non-immune hydrops fetalis, a generalized edema of the fetus with fluid accumulation in the body cavities due to non-immune causes. Non-immune hydrops fetalis is not a diagnosis in itself but a symptom, a feature of many genetic disorders, and the end-stage of a wide variety of disorders.[85] [86] [87] [88] [89] [90] Defects in GBA contribute to susceptibility to Parkinson disease (PARK) [MIM:168600. A complex neurodegenerative disorder characterized by bradykinesia, resting tremor, muscular rigidity and postural instability. Additional features are characteristic postural abnormalities, dysautonomia, dystonic cramps, and dementia. The pathology of Parkinson disease involves the loss of dopaminergic neurons in the substantia nigra and the presence of Lewy bodies (intraneuronal accumulations of aggregated proteins), in surviving neurons in various areas of the brain. The disease is progressive and usually manifests after the age of 50 years, although early-onset cases (before 50 years) are known. The majority of the cases are sporadic suggesting a multifactorial etiology based on environmental and genetic factors. However, some patients present with a positive family history for the disease. Familial forms of the disease usually begin at earlier ages and are associated with atypical clinical features.[91] [92] [93] [94] [95] [96]

Function

GLCM_HUMAN

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

Acid beta-glucosidase (GCase) is a 497-amino acid, membrane-associated lysosomal exo-beta-glucosidase whose defective activity leads to the Gaucher disease phenotypes. To move toward a structure/function map for disease mutations, 52 selected single amino acid substitutions were introduced into GCase, expressed in an insect cell system, purified, and characterized for basic kinetic, stability, and activator response properties. The variant GCases from Gaucher disease patients and selected variant GCases from the mouse had decreased relative k(cat) and differential effects on active site binding and/or attachment of mechanism-based covalent (conduritol B epoxide) or reversible (deoxynojirimycin derivatives) inhibitors. A defect in negatively charged phospholipid activation was present in the majority of variant GCases but was increased in two, N370S and V394L. Deficits in saposin C enhancement of k(cat) were present in variant GCases involving residues 48-122, whereas approximately 2-fold increases were obtained with the L264I GCase. About 50% of variant GCases each had wild-type or increased sensitivity to in vitro cathepsin D digestion. Mapping of these properties onto the crystal structures of GCase indicated wide dispersion of functional properties that can affect catalytic function and stability. Site-directed mutagenesis of cysteine residues showed that the disulfide bonds, Cys(4)-Cys(16) and Cys(18)-Cys(23), and a free Cys(342) were essential for activity; the free Cys(126) and Cys(248) were not. Relative k(cat) was highly sensitive to a His substitution at Arg(496) but not at Arg(495). These studies and high phylogenetic conservation indicate localized and general structural effects of Gaucher disease mutations that were not obvious from the nature of the amino acid substitution, including those predicted to be nondisruptive (e.g. Val --> Leu). These results provide initial studies for the engineering of variant GCases and, potentially, molecular chaperones for therapeutic use.

Analyses of variant acid beta-glucosidases: effects of Gaucher disease mutations.,Liou B, Kazimierczuk A, Zhang M, Scott CR, Hegde RS, Grabowski GA J Biol Chem. 2006 Feb 17;281(7):4242-53. Epub 2005 Nov 17. PMID:16293621[97]

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

See Also

References

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  2. Neumann J, Bras J, Deas E, O'Sullivan SS, Parkkinen L, Lachmann RH, Li A, Holton J, Guerreiro R, Paudel R, Segarane B, Singleton A, Lees A, Hardy J, Houlden H, Revesz T, Wood NW. Glucocerebrosidase mutations in clinical and pathologically proven Parkinson's disease. Brain. 2009 Jul;132(Pt 7):1783-94. doi: 10.1093/brain/awp044. Epub 2009 Mar 13. PMID:19286695 doi:10.1093/brain/awp044
  3. Liou B, Kazimierczuk A, Zhang M, Scott CR, Hegde RS, Grabowski GA. Analyses of variant acid beta-glucosidases: effects of Gaucher disease mutations. J Biol Chem. 2006 Feb 17;281(7):4242-53. Epub 2005 Nov 17. PMID:16293621 doi:10.1074/jbc.M511110200
  4. Beutler E, Gelbart T. Gaucher disease associated with a unique KpnI restriction site: identification of the amino-acid substitution. Ann Hum Genet. 1990 May;54(Pt 2):149-53. PMID:1974409
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  15. Cormand B, Vilageliu L, Balcells S, Gonzalez-Duarte R, Chabas A, Grinberg D. Two novel (1098insA and Y313H) and one rare (R359Q) mutations detected in exon 8 of the beta-glucocerebrosidase gene in Gaucher's disease patients. Hum Mutat. 1996;7(3):272-4. PMID:8829663 doi:<272::AID-HUMU14>3.0.CO;2-# 10.1002/(SICI)1098-1004(1996)7:3<272::AID-HUMU14>3.0.CO;2-#
  16. Amaral O, Pinto E, Fortuna M, Lacerda L, Sa Miranda MC. Type 1 Gaucher disease: identification of N396T and prevalence of glucocerebrosidase mutations in the Portuguese. Hum Mutat. 1996;8(3):280-1. PMID:8889591 doi:<280::AID-HUMU15>3.0.CO;2-Z 10.1002/(SICI)1098-1004(1996)8:3<280::AID-HUMU15>3.0.CO;2-Z
  17. Seeman PJ, Finckh U, Hoppner J, Lakner V, Liebisch I, Grau G, Rolfs A. Two new missense mutations in a non-Jewish Caucasian family with type 3 Gaucher disease. Neurology. 1996 Apr;46(4):1102-7. PMID:8780099
  18. Cormand B, Grinberg D, Gort L, Fiumara A, Barone R, Vilageliu L, Chabas A. Two new mild homozygous mutations in Gaucher disease patients: clinical signs and biochemical analyses. Am J Med Genet. 1997 Jun 27;70(4):437-43. PMID:9182788
  19. Choy FY, Humphries ML, Shi H. Identification of two novel and four uncommon missense mutations among chinese Gaucher disease patients. Am J Med Genet. 1997 Aug 8;71(2):172-8. PMID:9217217
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  28. Parenti G, Filocamo M, Titomanlio L, Rizzolo G, Silvestro E, Perretti A, Gatti R, Andria G. A novel mutation of the beta-glucocerebrosidase gene associated with neurologic manifestations in three sibs. Clin Genet. 1998 Apr;53(4):281-5. PMID:9650766
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  30. Choy FY, Humphries ML, Ben-Yoseph Y. A novel mutation (V191G) in a German-British type 1 Gaucher disease patient. Mutations in brief no. 131. Online. Hum Mutat. 1998;11(5):411-2. PMID:10206680 doi:<411::AID-HUMU11>3.0.CO;2-2 10.1002/(SICI)1098-1004(1998)11:5<411::AID-HUMU11>3.0.CO;2-2
  31. Wasserstein MP, Martignetti JA, Zeitlin R, Lumerman H, Solomon M, Grace ME, Desnick RJ. Type 1 Gaucher disease presenting with extensive mandibular lytic lesions: identification and expression of a novel acid beta-glucosidase mutation. Am J Med Genet. 1999 Jun 4;84(4):334-9. PMID:10340647
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  42. Salvioli R, Tatti M, Scarpa S, Moavero SM, Ciaffoni F, Felicetti F, Kaneski CR, Brady RO, Vaccaro AM. The N370S (Asn370-->Ser) mutation affects the capacity of glucosylceramidase to interact with anionic phospholipid-containing membranes and saposin C. Biochem J. 2005 Aug 15;390(Pt 1):95-103. PMID:15826241 doi:BJ20050325
  43. Miocic S, Filocamo M, Dominissini S, Montalvo AL, Vlahovicek K, Deganuto M, Mazzotti R, Cariati R, Bembi B, Pittis MG. Identification and functional characterization of five novel mutant alleles in 58 Italian patients with Gaucher disease type 1. Hum Mutat. 2005 Jan;25(1):100. PMID:15605411 doi:10.1002/humu.9301
  44. Aharon-Peretz J, Badarny S, Rosenbaum H, Gershoni-Baruch R. Mutations in the glucocerebrosidase gene and Parkinson disease: phenotype-genotype correlation. Neurology. 2005 Nov 8;65(9):1460-1. Epub 2005 Sep 7. PMID:16148263 doi:10.1212/01.wnl.0000176987.47875.28
  45. Tan EK, Tong J, Fook-Chong S, Yih Y, Wong MC, Pavanni R, Zhao Y. Glucocerebrosidase mutations and risk of Parkinson disease in Chinese patients. Arch Neurol. 2007 Jul;64(7):1056-8. PMID:17620502 doi:10.1001/archneur.64.7.1056
  46. Mata IF, Samii A, Schneer SH, Roberts JW, Griffith A, Leis BC, Schellenberg GD, Sidransky E, Bird TD, Leverenz JB, Tsuang D, Zabetian CP. Glucocerebrosidase gene mutations: a risk factor for Lewy body disorders. Arch Neurol. 2008 Mar;65(3):379-82. doi: 10.1001/archneurol.2007.68. PMID:18332251 doi:10.1001/archneurol.2007.68
  47. Sidransky E, Nalls MA, Aasly JO, Aharon-Peretz J, Annesi G, Barbosa ER, Bar-Shira A, Berg D, Bras J, Brice A, Chen CM, Clark LN, Condroyer C, De Marco EV, Durr A, Eblan MJ, Fahn S, Farrer MJ, Fung HC, Gan-Or Z, Gasser T, Gershoni-Baruch R, Giladi N, Griffith A, Gurevich T, Januario C, Kropp P, Lang AE, Lee-Chen GJ, Lesage S, Marder K, Mata IF, Mirelman A, Mitsui J, Mizuta I, Nicoletti G, Oliveira C, Ottman R, Orr-Urtreger A, Pereira LV, Quattrone A, Rogaeva E, Rolfs A, Rosenbaum H, Rozenberg R, Samii A, Samaddar T, Schulte C, Sharma M, Singleton A, Spitz M, Tan EK, Tayebi N, Toda T, Troiano AR, Tsuji S, Wittstock M, Wolfsberg TG, Wu YR, Zabetian CP, Zhao Y, Ziegler SG. Multicenter analysis of glucocerebrosidase mutations in Parkinson's disease. N Engl J Med. 2009 Oct 22;361(17):1651-61. doi: 10.1056/NEJMoa0901281. PMID:19846850 doi:10.1056/NEJMoa0901281
  48. Neumann J, Bras J, Deas E, O'Sullivan SS, Parkkinen L, Lachmann RH, Li A, Holton J, Guerreiro R, Paudel R, Segarane B, Singleton A, Lees A, Hardy J, Houlden H, Revesz T, Wood NW. Glucocerebrosidase mutations in clinical and pathologically proven Parkinson's disease. Brain. 2009 Jul;132(Pt 7):1783-94. doi: 10.1093/brain/awp044. Epub 2009 Mar 13. PMID:19286695 doi:10.1093/brain/awp044
  49. Amaral O, Pinto E, Fortuna M, Lacerda L, Sa Miranda MC. Type 1 Gaucher disease: identification of N396T and prevalence of glucocerebrosidase mutations in the Portuguese. Hum Mutat. 1996;8(3):280-1. PMID:8889591 doi:<280::AID-HUMU15>3.0.CO;2-Z 10.1002/(SICI)1098-1004(1996)8:3<280::AID-HUMU15>3.0.CO;2-Z
  50. Choy FY, Humphries ML, Ben-Yoseph Y. A novel mutation (V191G) in a German-British type 1 Gaucher disease patient. Mutations in brief no. 131. Online. Hum Mutat. 1998;11(5):411-2. PMID:10206680 doi:<411::AID-HUMU11>3.0.CO;2-2 10.1002/(SICI)1098-1004(1998)11:5<411::AID-HUMU11>3.0.CO;2-2
  51. Wasserstein MP, Martignetti JA, Zeitlin R, Lumerman H, Solomon M, Grace ME, Desnick RJ. Type 1 Gaucher disease presenting with extensive mandibular lytic lesions: identification and expression of a novel acid beta-glucosidase mutation. Am J Med Genet. 1999 Jun 4;84(4):334-9. PMID:10340647
  52. Bembi B, Zambito Marsala S, Sidransky E, Ciana G, Carrozzi M, Zorzon M, Martini C, Gioulis M, Pittis MG, Capus L. Gaucher's disease with Parkinson's disease: clinical and pathological aspects. Neurology. 2003 Jul 8;61(1):99-101. PMID:12847165
  53. Miocic S, Filocamo M, Dominissini S, Montalvo AL, Vlahovicek K, Deganuto M, Mazzotti R, Cariati R, Bembi B, Pittis MG. Identification and functional characterization of five novel mutant alleles in 58 Italian patients with Gaucher disease type 1. Hum Mutat. 2005 Jan;25(1):100. PMID:15605411 doi:10.1002/humu.9301
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  55. Tan EK, Tong J, Fook-Chong S, Yih Y, Wong MC, Pavanni R, Zhao Y. Glucocerebrosidase mutations and risk of Parkinson disease in Chinese patients. Arch Neurol. 2007 Jul;64(7):1056-8. PMID:17620502 doi:10.1001/archneur.64.7.1056
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