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| - | {{Large structure}} | |
| - | {{STRUCTURE_2q51| PDB=2q51 | SCENE= }} | |
| - | ===Ensemble refinement of the protein crystal structure of an aspartoacylase from Homo sapiens=== | |
| - | {{ABSTRACT_PUBMED_17850744}} | |
| | | | |
| - | ==Disease== | + | ==Ensemble refinement of the protein crystal structure of an aspartoacylase from Homo sapiens== |
| - | [[http://www.uniprot.org/uniprot/ACY2_HUMAN ACY2_HUMAN]] Defects in ASPA are the cause of Canavan disease (CAND) [MIM:[http://omim.org/entry/271900 271900]]; also known as spongy degeneration of the brain. CAND is a rare neurodegenerative condition of infancy or childhood characterized by white matter vacuolization and demeylination that gives rise to a spongy appearance. The clinical features are onset in early infancy, atonia of neck muscles, hypotonia, hyperextension of legs and flexion of arms, blindness, severe mental defect, megalocephaly, and death by 18 months on the average.<ref>PMID:8252036</ref><ref>PMID:12706335</ref><ref>PMID:8023850</ref><ref>PMID:7668285</ref><ref>PMID:7599639</ref><ref>PMID:8659549</ref><ref>PMID:9452117</ref><ref>PMID:10564886</ref><ref>PMID:10407784</ref><ref>PMID:10909858</ref><ref>PMID:12638939</ref><ref>PMID:12205125</ref> | + | <StructureSection load='2q51' size='340' side='right'caption='[[2q51]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[2q51]] 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=2Q51 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q51 FirstGlance]. <br> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å, 16 models</td></tr> |
| | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2q51 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q51 OCA], [https://pdbe.org/2q51 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q51 RCSB], [https://www.ebi.ac.uk/pdbsum/2q51 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q51 ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Disease == |
| | + | [https://www.uniprot.org/uniprot/ACY2_HUMAN ACY2_HUMAN] Defects in ASPA are the cause of Canavan disease (CAND) [MIM:[https://omim.org/entry/271900 271900]; also known as spongy degeneration of the brain. CAND is a rare neurodegenerative condition of infancy or childhood characterized by white matter vacuolization and demeylination that gives rise to a spongy appearance. The clinical features are onset in early infancy, atonia of neck muscles, hypotonia, hyperextension of legs and flexion of arms, blindness, severe mental defect, megalocephaly, and death by 18 months on the average.<ref>PMID:8252036</ref> <ref>PMID:12706335</ref> <ref>PMID:8023850</ref> <ref>PMID:7668285</ref> <ref>PMID:7599639</ref> <ref>PMID:8659549</ref> <ref>PMID:9452117</ref> <ref>PMID:10564886</ref> <ref>PMID:10407784</ref> <ref>PMID:10909858</ref> <ref>PMID:12638939</ref> <ref>PMID:12205125</ref> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/ACY2_HUMAN ACY2_HUMAN] Catalyzes the deacetylation of N-acetylaspartic acid (NAA) to produce acetate and L-aspartate. NAA occurs in high concentration in brain and its hydrolysis NAA plays a significant part in the maintenance of intact white matter. In other tissues it act as a scavenger of NAA from body fluids. |
| | + | == Evolutionary Conservation == |
| | + | [[Image:Consurf_key_small.gif|200px|right]] |
| | + | Check<jmol> |
| | + | <jmolCheckbox> |
| | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q5/2q51_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2q51 ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement. |
| | | | |
| - | ==Function==
| + | Ensemble refinement of protein crystal structures: validation and application.,Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr Structure. 2007 Sep;15(9):1040-52. PMID:17850744<ref>PMID:17850744</ref> |
| - | [[http://www.uniprot.org/uniprot/ACY2_HUMAN ACY2_HUMAN]] Catalyzes the deacetylation of N-acetylaspartic acid (NAA) to produce acetate and L-aspartate. NAA occurs in high concentration in brain and its hydrolysis NAA plays a significant part in the maintenance of intact white matter. In other tissues it act as a scavenger of NAA from body fluids.
| + | |
| | | | |
| - | ==About this Structure==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | [[2q51]] is a 2 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=2Q51 OCA].
| + | </div> |
| | + | <div class="pdbe-citations 2q51" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Aspartoacylase|Aspartoacylase]] | + | *[[Aminoacylase 3D structures|Aminoacylase 3D structures]] |
| - | | + | *[[Aspartoacylase 3D structures|Aspartoacylase 3D structures]] |
| - | ==Reference== | + | == References == |
| - | <ref group="xtra">PMID:017850744</ref><ref group="xtra">PMID:017194761</ref><references group="xtra"/><references/>
| + | <references/> |
| - | [[Category: Aspartoacylase]]
| + | __TOC__ |
| | + | </StructureSection> |
| | [[Category: Homo sapiens]] | | [[Category: Homo sapiens]] |
| - | [[Category: CESG, Center for Eukaryotic Structural Genomics.]] | + | [[Category: Large Structures]] |
| - | [[Category: Kondrashov, D A.]] | + | [[Category: Kondrashov DA]] |
| - | [[Category: Levin, E J.]] | + | [[Category: Levin EJ]] |
| - | [[Category: Phillips, G N.]] | + | [[Category: Phillips Jr GN]] |
| - | [[Category: Wesenberg, G E.]] | + | [[Category: Wesenberg GE]] |
| - | [[Category: Acy2]]
| + | |
| - | [[Category: Aminoacylase-2]]
| + | |
| - | [[Category: Aspa]]
| + | |
| - | [[Category: Aspartoacylase family]]
| + | |
| - | [[Category: Canavan disease]]
| + | |
| - | [[Category: Center for eukaryotic structural genomic]]
| + | |
| - | [[Category: Cesg]]
| + | |
| - | [[Category: Ensemble refinement]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: N-acetyl-l-aspartate]]
| + | |
| - | [[Category: Protein structure initiative]]
| + | |
| - | [[Category: Psi]]
| + | |
| - | [[Category: Refinement methodology development]]
| + | |
| - | [[Category: Structural genomic]]
| + | |
| - | [[Category: Zinc-dependent hydrolase]]
| + | |
| Structural highlights
Disease
ACY2_HUMAN Defects in ASPA are the cause of Canavan disease (CAND) [MIM:271900; also known as spongy degeneration of the brain. CAND is a rare neurodegenerative condition of infancy or childhood characterized by white matter vacuolization and demeylination that gives rise to a spongy appearance. The clinical features are onset in early infancy, atonia of neck muscles, hypotonia, hyperextension of legs and flexion of arms, blindness, severe mental defect, megalocephaly, and death by 18 months on the average.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]
Function
ACY2_HUMAN Catalyzes the deacetylation of N-acetylaspartic acid (NAA) to produce acetate and L-aspartate. NAA occurs in high concentration in brain and its hydrolysis NAA plays a significant part in the maintenance of intact white matter. In other tissues it act as a scavenger of NAA from body fluids.
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
X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.
Ensemble refinement of protein crystal structures: validation and application.,Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr Structure. 2007 Sep;15(9):1040-52. PMID:17850744[13]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kaul R, Gao GP, Balamurugan K, Matalon R. Cloning of the human aspartoacylase cDNA and a common missense mutation in Canavan disease. Nat Genet. 1993 Oct;5(2):118-23. PMID:8252036 doi:http://dx.doi.org/10.1038/ng1093-118
- ↑ Moore RA, Le Coq J, Faehnle CR, Viola RE. Purification and preliminary characterization of brain aspartoacylase. Arch Biochem Biophys. 2003 May 1;413(1):1-8. PMID:12706335
- ↑ Kaul R, Gao GP, Aloya M, Balamurugan K, Petrosky A, Michals K, Matalon R. Canavan disease: mutations among Jewish and non-Jewish patients. Am J Hum Genet. 1994 Jul;55(1):34-41. PMID:8023850
- ↑ Shaag A, Anikster Y, Christensen E, Glustein JZ, Fois A, Michelakakis H, Nigro F, Pronicka E, Ribes A, Zabot MT, et al.. The molecular basis of canavan (aspartoacylase deficiency) disease in European non-Jewish patients. Am J Hum Genet. 1995 Sep;57(3):572-80. PMID:7668285
- ↑ Kaul R, Gao GP, Michals K, Whelan DT, Levin S, Matalon R. Novel (cys152 > arg) missense mutation in an Arab patient with Canavan disease. Hum Mutat. 1995;5(3):269-71. PMID:7599639 doi:http://dx.doi.org/10.1002/humu.1380050313
- ↑ Kaul R, Gao GP, Matalon R, Aloya M, Su Q, Jin M, Johnson AB, Schutgens RB, Clarke JT. Identification and expression of eight novel mutations among non-Jewish patients with Canavan disease. Am J Hum Genet. 1996 Jul;59(1):95-102. PMID:8659549
- ↑ Kobayashi K, Tsujino S, Ezoe T, Hamaguchi H, Nihei K, Sakuragawa N. Missense mutation (I143T) in a Japanese patient with Canavan disease. Hum Mutat. 1998;Suppl 1:S308-9. PMID:9452117
- ↑ Rady PL, Vargas T, Tyring SK, Matalon R, Langenbeck U. Novel missense mutation (Y231C) in a turkish patient with canavan disease. Am J Med Genet. 1999 Nov 26;87(3):273-5. PMID:10564886
- ↑ Elpeleg ON, Shaag A. The spectrum of mutations of the aspartoacylase gene in Canavan disease in non-Jewish patients. J Inherit Metab Dis. 1999 Jun;22(4):531-4. PMID:10407784
- ↑ Sistermans EA, de Coo RF, van Beerendonk HM, Poll-The BT, Kleijer WJ, van Oost BA. Mutation detection in the aspartoacylase gene in 17 patients with Canavan disease: four new mutations in the non-Jewish population. Eur J Hum Genet. 2000 Jul;8(7):557-60. PMID:10909858 doi:10.1038/sj.ejhg.5200477
- ↑ Zeng BJ, Wang ZH, Ribeiro LA, Leone P, De Gasperi R, Kim SJ, Raghavan S, Ong E, Pastores GM, Kolodny EH. Identification and characterization of novel mutations of the aspartoacylase gene in non-Jewish patients with Canavan disease. J Inherit Metab Dis. 2002 Nov;25(7):557-70. PMID:12638939
- ↑ Olsen TR, Tranebjaerg L, Kvittingen EA, Hagenfeldt L, Moller C, Nilssen O. Two novel aspartoacylase gene (ASPA) missense mutations specific to Norwegian and Swedish patients with Canavan disease. J Med Genet. 2002 Sep;39(9):e55. PMID:12205125
- ↑ Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Ensemble refinement of protein crystal structures: validation and application. Structure. 2007 Sep;15(9):1040-52. PMID:17850744 doi:http://dx.doi.org/10.1016/j.str.2007.06.019
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