2epo: Difference between revisions

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OCA

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-[[Image:2epo.jpg|left|200px]]<br /><applet load="2epo" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2epo, resolution 1.56&Aring;" />
-'''N-acetyl-B-D-glucosaminidase (GCNA) from Streptococcus gordonii'''<br />
-==Overview==
+==N-acetyl-B-D-glucosaminidase (GCNA) from Streptococcus gordonii==
-The crystal structure of GcnA, an N-acetyl-beta-D-glucosaminidase from Streptococcus gordonii, was solved by multiple wavelength anomalous dispersion phasing using crystals of selenomethionine-substituted protein. GcnA is a homodimer with subunits each comprised of three domains. The structure of the C-terminal alpha-helical domain has not been observed previously and forms a large dimerisation interface. The fold of the N-terminal domain is observed in all structurally related glycosidases although its function is unknown. The central domain has a canonical (beta/alpha)(8) TIM-barrel fold which harbours the active site. The primary sequence and structure of this central domain identifies the enzyme as a family 20 glycosidase. Key residues implicated in catalysis have different conformations in two different crystal forms, which probably represent active and inactive conformations of the enzyme. The catalytic mechanism for this class of glycoside hydrolase, where the substrate rather than the enzyme provides the cleavage-inducing nucleophile, has been confirmed by the structure of GcnA complexed with a putative reaction intermediate analogue, N-acetyl-beta-D-glucosamine-thiazoline. The catalytic mechanism is discussed in light of these and other family 20 structures.
+<StructureSection load='2epo' size='340' side='right'caption='[[2epo]], [[Resolution|resolution]] 1.56&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[2epo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_gordonii Streptococcus gordonii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EPO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EPO FirstGlance]. <br>
-EPO is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_gordonii Streptococcus gordonii] with <scene name='pdbligand=ACY:'>ACY</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Known structural/functional Sites: <scene name='pdbsite=AC1:Acy+Binding+Site+For+Residue+A+660'>AC1</scene> and <scene name='pdbsite=AC2:Acy+Binding+Site+For+Residue+B+1660'>AC2</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EPO OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.56&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2epo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2epo OCA], [https://pdbe.org/2epo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2epo RCSB], [https://www.ebi.ac.uk/pdbsum/2epo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2epo ProSAT]</span></td></tr>
-Structure of N-acetyl-beta-D-glucosaminidase (GcnA) from the endocarditis pathogen Streptococcus gordonii and its complex with the mechanism-based inhibitor NAG-thiazoline., Langley DB, Harty DW, Jacques NA, Hunter N, Guss JM, Collyer CA, J Mol Biol. 2008 Mar 14;377(1):104-16. Epub 2007 Sep 16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18237743 18237743]
+</table>
-[[Category: Beta-N-acetylhexosaminidase]]
+== Function ==
-[[Category: Single protein]]
+[https://www.uniprot.org/uniprot/Q6ST21_STRGN Q6ST21_STRGN]
+== 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/ep/2epo_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2epo ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Streptococcus gordonii]]
-[[Category: Langley, D B.]]
+[[Category: Langley DB]]
-[[Category: ACY]]
-[[Category: family 20]]
-[[Category: gcna]]
-[[Category: glucosaminidase]]
-[[Category: glycoside hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Mar 14 09:30:47 2008''