2epo: Difference between revisions

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-[[Image:2epo.jpg|left|200px]]
- {{Structure
+==N-acetyl-B-D-glucosaminidase (GCNA) from Streptococcus gordonii==
-|PDB= 2epo |SIZE=350|CAPTION= <scene name='initialview01'>2epo</scene>, resolution 1.56&Aring;
+<StructureSection load='2epo' size='340' side='right'caption='[[2epo]], [[Resolution|resolution]] 1.56&Aring;' scene=''>
-|SITE= <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>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>
+<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>
-|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>
+</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>
-|GENE= gcna ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1302 Streptococcus gordonii])
+<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>
-|DOMAIN=
+<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>
-|RELATEDENTRY=[[2epk|2epk]], [[2epl|2epl]], [[2epm|2epm]], [[2epn|2epn]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2epo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2epo OCA], [http://www.ebi.ac.uk/pdbsum/2epo PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2epo RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/Q6ST21_STRGN Q6ST21_STRGN]
+== Evolutionary Conservation ==
-'''N-acetyl-B-D-glucosaminidase (GCNA) from Streptococcus gordonii'''
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
-==Overview==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ep/2epo_consurf.spt"</scriptWhenChecked>
-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.
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==About this Structure==
+  </jmolCheckbox>
-EPO is a [[Single protein]] structure of sequence from [http://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].
+</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>
-==Reference==
+__TOC__
-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://www.ncbi.nlm.nih.gov/pubmed/18237743 18237743]
+</StructureSection>
-[[Category: Beta-N-acetylhexosaminidase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
 [[Category: Streptococcus gordonii]]
-[[Category: Langley, D B.]]
+[[Category: Langley DB]]
-[[Category: family 20]]
-[[Category: gcna]]
-[[Category: glucosaminidase]]
-[[Category: glycoside hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:52:17 2008''