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3igu

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{{Seed}}
 
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[[Image:3igu.png|left|200px]]
 
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==Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate==
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The line below this paragraph, containing "STRUCTURE_3igu", creates the "Structure Box" on the page.
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<StructureSection load='3igu' size='340' side='right'caption='[[3igu]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3igu]] 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=3IGU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IGU FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7JZ:2-DEOXY-2,2-DIFLUORO-BETA-D-LYXO-HEXOPYRANOSE'>7JZ</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
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{{STRUCTURE_3igu| PDB=3igu | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3igu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3igu OCA], [https://pdbe.org/3igu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3igu RCSB], [https://www.ebi.ac.uk/pdbsum/3igu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3igu ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/NAGAB_HUMAN NAGAB_HUMAN] Defects in NAGA are the cause of Schindler disease (SCHIND) [MIM:[https://omim.org/entry/609241 609241]. Schindler disease is a form of NAGA deficiency characterized by early onset neuroaxonal dystrophy and neurological signs (convulsion during fever, epilepsy, psychomotor retardation and hypotonia). NAGA deficiency is typically classified in three main phenotypes: NAGA deficiency type I (Schindler disease or Schindler disease type I) with severe manifestations; NAGA deficiency type II (Kanzazi disease or Schindler disease type II) which is mild; NAGA deficiency type III (Schindler disease type III) characterized by mild-to-moderate neurologic manifestations. NAGA deficiency results in the increased urinary excretion of glycopeptides and oligosaccharides containing alpha-N-acetylgalactosaminyl moieties. Inheritance is autosomal recessive.<ref>PMID:2243144</ref> <ref>PMID:8782044</ref> Defects in NAGA are the cause of Kanzaki disease (KANZD) [MIM:[https://omim.org/entry/609242 609242]; also known as NAGA deficiency type II or Schindler disease type II. Kanzaki disease is an autosomal recessive disorder characterized by late onset, angiokeratoma corporis diffusum and mild intellectual impairment.<ref>PMID:8040340</ref> <ref>PMID:11251574</ref>
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== Function ==
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[https://www.uniprot.org/uniprot/NAGAB_HUMAN NAGAB_HUMAN] Removes terminal alpha-N-acetylgalactosamine residues from glycolipids and glycopeptides. Required for the breakdown of glycolipids.<ref>PMID:9741689</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ig/3igu_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3igu ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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alpha-N-acetylgalactosaminidase (alpha-NAGAL; E.C. 3.2.1.49) is a lysosomal exoglycosidase that cleaves terminal alpha-N-acetylgalactosamine residues from glycopeptides and glycolipids. In humans, a deficiency of alpha-NAGAL activity results in the lysosomal storage disorders Schindler disease and Kanzaki disease. To better understand the molecular defects in the diseases, we determined the crystal structure of human alpha-NAGAL after expressing wild-type and glycosylation-deficient glycoproteins in recombinant insect cell expression systems. We measured the enzymatic parameters of our purified wild-type and mutant enzymes, establishing their enzymatic equivalence. To investigate the binding specificity and catalytic mechanism of the human alpha-NAGAL enzyme, we determined three crystallographic complexes with different catalytic products bound in the active site of the enzyme. To better understand how individual defects in the alpha-NAGAL glycoprotein lead to Schindler disease, we analyzed the effect of disease-causing mutations on the three-dimensional structure.
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===Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate===
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The 1.9 a structure of human alpha-N-acetylgalactosaminidase: The molecular basis of Schindler and Kanzaki diseases.,Clark NE, Garman SC J Mol Biol. 2009 Oct 23;393(2):435-47. Epub 2009 Aug 14. PMID:19683538<ref>PMID:19683538</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3igu" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19683538}}, adds the Publication Abstract to the page
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*[[Galactosidase 3D structures|Galactosidase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19683538 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19683538}}
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__TOC__
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</StructureSection>
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==Disease==
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Known disease associated with this structure: Kanzaki disease OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=104170 104170]], Schindler disease, type I OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=104170 104170]], Schindler disease, type III OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=104170 104170]]
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==About this Structure==
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3IGU is a 2 chains structure of sequences 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=3IGU OCA].
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==Reference==
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<ref group="xtra">PMID:19683538</ref><references group="xtra"/>
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[[Category: Alpha-N-acetylgalactosaminidase]]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Clark, N E.]]
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[[Category: Large Structures]]
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[[Category: Garman, S C.]]
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[[Category: Clark NE]]
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[[Category: Carbohydrate-binding protein]]
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[[Category: Garman SC]]
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[[Category: Disease mutation]]
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[[Category: Disulfide bond]]
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[[Category: Epilepsy]]
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[[Category: Glycoprotein]]
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[[Category: Glycosidase]]
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[[Category: Hydrolase]]
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[[Category: Kanzaki disease]]
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[[Category: Lysosomal enzyme]]
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[[Category: Lysosome]]
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[[Category: Phosphoprotein]]
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[[Category: Schindler disease]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 28 12:12:23 2009''
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Current revision

Crystal structure of human alpha-N-acetylgalactosaminidase, covalent intermediate

PDB ID 3igu

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