2cbi

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[[Image:2cbi.gif|left|200px]]
 
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{{Structure
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==Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue of human O-GlcNAcase==
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|PDB= 2cbi |SIZE=350|CAPTION= <scene name='initialview01'>2cbi</scene>, resolution 2.25&Aring;
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<StructureSection load='2cbi' size='340' side='right'caption='[[2cbi]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Gol+Binding+Site+For+Chain+A'>AC1</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GBL:GAMMA-BUTYROLACTONE'>GBL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
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<table><tr><td colspan='2'>[[2cbi]] is a 2 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=2CBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CBI FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Hyalurononglucosaminidase Hyalurononglucosaminidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.35 3.2.1.35] </span>
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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]] 2.25&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GBL:GAMMA-BUTYROLACTONE'>GBL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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|DOMAIN=
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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=2cbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cbi OCA], [https://pdbe.org/2cbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cbi RCSB], [https://www.ebi.ac.uk/pdbsum/2cbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cbi ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2cbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cbi OCA], [http://www.ebi.ac.uk/pdbsum/2cbi PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2cbi RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/OGA_CLOP1 OGA_CLOP1] Biological function unknown. Capable of hydrolyzing the glycosidic link of O-GlcNAcylated proteins.
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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/cb/2cbi_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=2cbi 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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O-linked N-acetylglucosamine (O-GlcNAc) modification of specific serines/threonines on intracellular proteins in higher eukaryotes has been shown to directly regulate important processes such as the cell cycle, insulin sensitivity and transcription. The structure, molecular mechanisms of catalysis, protein substrate recognition/specificity of the eukaryotic O-GlcNAc transferase and hydrolase are largely unknown. Here we describe the crystal structure, enzymology and in vitro activity on human substrates of Clostridium perfringens NagJ, a close homologue of human O-GlcNAcase (OGA), representing the first family 84 glycoside hydrolase structure. The structure reveals a deep active site pocket highly conserved with the human enzyme, compatible with binding of O-GlcNAcylated peptides. Together with mutagenesis data, the structure supports a variant of the substrate-assisted catalytic mechanism, involving two aspartic acids and an unusually positioned tyrosine. Insights into recognition of substrate come from a complex with the transition state mimic O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino-N-phenylcarbamate (Ki=5.4 nM). Strikingly, the enzyme is inhibited by the pseudosubstrate peptide Ala-Cys(-S-GlcNAc)-Ala, and has OGA activity against O-GlcNAcylated human proteins, suggesting that the enzyme is a suitable model for further studies into the function of human OGA.
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'''STRUCTURE OF THE CLOSTRIDIUM PERFRINGENS NAGJ FAMILY 84 GLYCOSIDE HYDROLASE, A HOMOLOGUE OF HUMAN O-GLCNACASE'''
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Structural insights into the mechanism and inhibition of eukaryotic O-GlcNAc hydrolysis.,Rao FV, Dorfmueller HC, Villa F, Allwood M, Eggleston IM, van Aalten DM EMBO J. 2006 Apr 5;25(7):1569-78. Epub 2006 Mar 16. PMID:16541109<ref>PMID:16541109</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 2cbi" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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O-linked N-acetylglucosamine (O-GlcNAc) modification of specific serines/threonines on intracellular proteins in higher eukaryotes has been shown to directly regulate important processes such as the cell cycle, insulin sensitivity and transcription. The structure, molecular mechanisms of catalysis, protein substrate recognition/specificity of the eukaryotic O-GlcNAc transferase and hydrolase are largely unknown. Here we describe the crystal structure, enzymology and in vitro activity on human substrates of Clostridium perfringens NagJ, a close homologue of human O-GlcNAcase (OGA), representing the first family 84 glycoside hydrolase structure. The structure reveals a deep active site pocket highly conserved with the human enzyme, compatible with binding of O-GlcNAcylated peptides. Together with mutagenesis data, the structure supports a variant of the substrate-assisted catalytic mechanism, involving two aspartic acids and an unusually positioned tyrosine. Insights into recognition of substrate come from a complex with the transition state mimic O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino-N-phenylcarbamate (Ki=5.4 nM). Strikingly, the enzyme is inhibited by the pseudosubstrate peptide Ala-Cys(-S-GlcNAc)-Ala, and has OGA activity against O-GlcNAcylated human proteins, suggesting that the enzyme is a suitable model for further studies into the function of human OGA.
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*[[Hyaluronidase 3D structures|Hyaluronidase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2CBI 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=2CBI OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Structural insights into the mechanism and inhibition of eukaryotic O-GlcNAc hydrolysis., Rao FV, Dorfmueller HC, Villa F, Allwood M, Eggleston IM, van Aalten DM, EMBO J. 2006 Apr 5;25(7):1569-78. Epub 2006 Mar 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16541109 16541109]
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[[Category: Clostridium perfringens]]
[[Category: Clostridium perfringens]]
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[[Category: Hyalurononglucosaminidase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Allwood M]]
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[[Category: Aalten, D M.F Van.]]
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[[Category: Dorfmueller HC]]
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[[Category: Allwood, M.]]
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[[Category: Eggleston IM]]
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[[Category: Dorfmueller, H C.]]
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[[Category: Rao FV]]
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[[Category: Eggleston, I M.]]
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[[Category: Villa F]]
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[[Category: Rao, F V.]]
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[[Category: Van Aalten DMF]]
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[[Category: Villa, F.]]
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[[Category: carbohydrate]]
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[[Category: family 84 glycoside hydrolase]]
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[[Category: glycoside hydrolase]]
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[[Category: hyaluronidase]]
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[[Category: hydrolase]]
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[[Category: o-glcnac]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:19:09 2008''
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Current revision

Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue of human O-GlcNAcase

PDB ID 2cbi

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