2vc9

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[[Image:2vc9.jpg|left|200px]]
 
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==Family 89 Glycoside Hydrolase from Clostridium perfringens in complex with 2-acetamido-1,2-dideoxynojirmycin==
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The line below this paragraph, containing "STRUCTURE_2vc9", creates the "Structure Box" on the page.
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<StructureSection load='2vc9' size='340' side='right'caption='[[2vc9]], [[Resolution|resolution]] 2.36&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'>[[2vc9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VC9 FirstGlance]. <br>
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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]] 2.36&#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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NOK:2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN'>NOK</scene></td></tr>
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{{STRUCTURE_2vc9| PDB=2vc9 | 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=2vc9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vc9 OCA], [https://pdbe.org/2vc9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vc9 RCSB], [https://www.ebi.ac.uk/pdbsum/2vc9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vc9 ProSAT]</span></td></tr>
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</table>
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'''FAMILY 89 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH 2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN'''
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== Function ==
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[https://www.uniprot.org/uniprot/A0A0H2YU91_CLOP1 A0A0H2YU91_CLOP1]
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== Evolutionary Conservation ==
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==Overview==
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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/vc/2vc9_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=2vc9 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 ==
Mucopolysaccharidosis III (MPS III) has four forms (A-D) that result from buildup of an improperly degraded glycosaminoglycan in lysosomes. MPS IIIB is attributable to the decreased activity of a lysosomal alpha-N-acetylglucosaminidase (NAGLU). Here, we describe the structure, catalytic mechanism, and inhibition of CpGH89 from Clostridium perfringens, a close bacterial homolog of NAGLU. The structure enables the generation of a homology model of NAGLU, an enzyme that has resisted structural studies despite having been studied for &gt;20 years. This model reveals which mutations giving rise to MPS IIIB map to the active site and which map to regions distant from the active site. The identification of potent inhibitors of CpGH89 and the structures of these inhibitors in complex with the enzyme suggest small-molecule candidates for use as chemical chaperones. These studies therefore illuminate the genetic basis of MPS IIIB, provide a clear biochemical rationale for the necessary sequential action of heparan-degrading enzymes, and open the door to the design and optimization of chemical chaperones for treating MPS IIIB.
Mucopolysaccharidosis III (MPS III) has four forms (A-D) that result from buildup of an improperly degraded glycosaminoglycan in lysosomes. MPS IIIB is attributable to the decreased activity of a lysosomal alpha-N-acetylglucosaminidase (NAGLU). Here, we describe the structure, catalytic mechanism, and inhibition of CpGH89 from Clostridium perfringens, a close bacterial homolog of NAGLU. The structure enables the generation of a homology model of NAGLU, an enzyme that has resisted structural studies despite having been studied for &gt;20 years. This model reveals which mutations giving rise to MPS IIIB map to the active site and which map to regions distant from the active site. The identification of potent inhibitors of CpGH89 and the structures of these inhibitors in complex with the enzyme suggest small-molecule candidates for use as chemical chaperones. These studies therefore illuminate the genetic basis of MPS IIIB, provide a clear biochemical rationale for the necessary sequential action of heparan-degrading enzymes, and open the door to the design and optimization of chemical chaperones for treating MPS IIIB.
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==About this Structure==
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Structural and mechanistic insight into the basis of mucopolysaccharidosis IIIB.,Ficko-Blean E, Stubbs KA, Nemirovsky O, Vocadlo DJ, Boraston AB Proc Natl Acad Sci U S A. 2008 May 6;105(18):6560-5. Epub 2008 Apr 28. PMID:18443291<ref>PMID:18443291</ref>
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2VC9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VC9 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structural and mechanistic insight into the basis of mucopolysaccharidosis IIIB., Ficko-Blean E, Stubbs KA, Nemirovsky O, Vocadlo DJ, Boraston AB, Proc Natl Acad Sci U S A. 2008 May 6;105(18):6560-5. Epub 2008 Apr 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18443291 18443291]
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</div>
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[[Category: Alpha-N-acetylglucosaminidase]]
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<div class="pdbe-citations 2vc9" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Clostridium perfringens]]
[[Category: Clostridium perfringens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Berg, O.]]
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[[Category: Berg O]]
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[[Category: Boraston, A B.]]
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[[Category: Boraston AB]]
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[[Category: Ficko-Blean, E.]]
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[[Category: Ficko-Blean E]]
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[[Category: Stubbs, K A.]]
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[[Category: Stubbs KA]]
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[[Category: Vocadlo, D J.]]
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[[Category: Vocadlo DJ]]
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[[Category: 2-acetamido-1]]
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[[Category: 2-dideoxynojirmycin]]
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[[Category: Alpha-n-acetylglucosaminidase]]
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[[Category: Family 89 glycoside hydrolase]]
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[[Category: Gh89]]
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[[Category: Hydrolase]]
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[[Category: Mucopolysaccharidosis]]
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[[Category: Naglu]]
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[[Category: Sanfilippo disease]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 14 11:39:40 2008''
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Current revision

Family 89 Glycoside Hydrolase from Clostridium perfringens in complex with 2-acetamido-1,2-dideoxynojirmycin

PDB ID 2vc9

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