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1m04

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[[Image:1m04.gif|left|200px]]
 
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{{Structure
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==Mutant Streptomyces plicatus beta-hexosaminidase (D313N) in complex with product (GlcNAc)==
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|PDB= 1m04 |SIZE=350|CAPTION= <scene name='initialview01'>1m04</scene>, resolution 1.95&Aring;
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<StructureSection load='1m04' size='340' side='right'caption='[[1m04]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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<table><tr><td colspan='2'>[[1m04]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_plicatus Streptomyces plicatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M04 FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-N-acetylhexosaminidase Beta-N-acetylhexosaminidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.52 3.2.1.52] </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]] 1.95&#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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1m04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m04 OCA], [https://pdbe.org/1m04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m04 RCSB], [https://www.ebi.ac.uk/pdbsum/1m04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m04 ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1m01|1M01]], [[1m03|1M03]], [[1hp5|1hp5]], [[1jak|1jak]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m04 OCA], [http://www.ebi.ac.uk/pdbsum/1m04 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1m04 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/O85361_STRPL O85361_STRPL]
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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/m0/1m04_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=1m04 ConSurf].
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<div style="clear:both"></div>
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'''Mutant Streptomyces plicatus beta-hexosaminidase (D313N) in complex with product (GlcNAc)'''
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==See Also==
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*[[Beta-Hexosaminidase|Beta-Hexosaminidase]]
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*[[Beta-Hexosaminidase 3D structures|Beta-Hexosaminidase 3D structures]]
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==Overview==
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*[[Beta-N-acetylhexosaminidase 3D structures|Beta-N-acetylhexosaminidase 3D structures]]
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SpHex, a retaining family 20 glycosidase from Streptomyces plicatus, catalyzes the hydrolysis of N-acetyl-beta-hexosaminides. Accumulating evidence suggests that the hydrolytic mechanism involves substrate-assisted catalysis wherein the 2-acetamido substituent acts as a nucleophile to form an oxazolinium ion intermediate. The role of a conserved aspartate residue (D313) in the active site of SpHex was investigated through kinetic and structural analyses of two variant enzymes, D313A and D313N. Three-dimensional structures of the wild-type and variant enzymes in product complexes with N-acetyl-d-glucosamine revealed substantial differences. In the D313A variant the 2-acetamido group was found in two conformations of which only one is able to aid in catalysis through anchimeric assistance. The mutation D313N results in a steric clash in the active site between Asn-313 and the 2-acetamido group preventing the 2-acetamido group from providing anchimeric assistance, consistent with the large reduction in catalytic efficiency and the insensitivity of this variant to chemical rescue. By comparison, the D313A mutation results in a shift in a shift in the pH optimum and a modest decrease in activity that can be rescued by using azide as an exogenous nucleophile. These structural and kinetic data provide evidence that Asp-313 stabilizes the transition states flanking the oxazoline intermediate and also assists to correctly orient the 2-acetamido group for catalysis. Based on analogous conserved residues in the family 18 chitinases and family 56 hyaluronidases, the roles played by the Asp-313 residue is likely general for all hexosaminidases using a mechanism involving substrate-assisted catalysis.
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1M04 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_plicatus Streptomyces plicatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M04 OCA].
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==Reference==
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Aspartate 313 in the Streptomyces plicatus hexosaminidase plays a critical role in substrate-assisted catalysis by orienting the 2-acetamido group and stabilizing the transition state., Williams SJ, Mark BL, Vocadlo DJ, James MN, Withers SG, J Biol Chem. 2002 Oct 18;277(42):40055-65. Epub 2002 Aug 8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12171933 12171933]
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[[Category: Beta-N-acetylhexosaminidase]]
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[[Category: Single protein]]
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[[Category: Streptomyces plicatus]]
[[Category: Streptomyces plicatus]]
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[[Category: James, M N.G.]]
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[[Category: James MNG]]
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[[Category: Mark, B L.]]
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[[Category: Mark BL]]
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[[Category: Vocadlo, D J.]]
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[[Category: Vocadlo DJ]]
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[[Category: Williams, S J.]]
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[[Category: Williams SJ]]
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[[Category: Withers, S G.]]
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[[Category: Withers SG]]
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[[Category: family 20 glycosidase]]
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[[Category: hexosaminidase]]
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[[Category: substrate assisted catalysis]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:09:32 2008''
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Current revision

Mutant Streptomyces plicatus beta-hexosaminidase (D313N) in complex with product (GlcNAc)

PDB ID 1m04

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