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| - | [[Image:1yht.gif|left|200px]] | |
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| - | {{Structure
| + | ==Crystal structure analysis of Dispersin B== |
| - | |PDB= 1yht |SIZE=350|CAPTION= <scene name='initialview01'>1yht</scene>, resolution 2.00Å
| + | <StructureSection load='1yht' size='340' side='right'caption='[[1yht]], [[Resolution|resolution]] 2.00Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
| + | <table><tr><td colspan='2'>[[1yht]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aggregatibacter_actinomycetemcomitans Aggregatibacter actinomycetemcomitans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YHT 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]] 2Å</td></tr> |
| - | |GENE= dspB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=714 Aggregatibacter actinomycetemcomitans])
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=1yht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yht OCA], [https://pdbe.org/1yht PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yht RCSB], [https://www.ebi.ac.uk/pdbsum/1yht PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yht ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[1hp4|1HP4]], [[1o7a|1O7A]], [[1now|1NOW]], [[1qbb|1QBB]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yht OCA], [http://www.ebi.ac.uk/pdbsum/1yht PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yht RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/Q840G9_AGGAC Q840G9_AGGAC] |
| - | | + | == Evolutionary Conservation == |
| - | '''Crystal structure analysis of Dispersin B'''
| + | [[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/yh/1yht_consurf.spt"</scriptWhenChecked> |
| - | Bacteria in a biofilm are enmeshed in a self-synthesized extracellular polysaccharide matrix that holds the bacteria together in a mass and firmly attaches the bacterial mass to the underlying surface. A major component of the extracellular polysaccharide matrix in several phylogenetically diverse bacteria is PGA, a linear polymer of N-acetylglucosamine residues in beta(1,6)-linkage. PGA is produced by the Gram-negative periodontopathogen Actinobacillus actinomycetemcomitans as well as by the Gram-positive device-associated pathogen Staphylococcus epidermidis. We recently reported that A.actinomycetemcomitans produces a soluble glycoside hydrolase named dispersin B, which degrades PGA. Here, we present the crystal structure of dispersin B at 2.0A in complex with a glycerol and an acetate ion at the active site. The enzyme crystallizes in the orthorhombic space group C222(1) with cell dimensions a=41.02A, b=86.13A, c=185.77A. The core of the enzyme consists a (beta/alpha)(8) barrel topology similar to other beta-hexosaminidases but significant differences exist in the arrangement of loops hovering in the vicinity of the active site. The location and interactions of the glycerol and acetate moieties in conjunction with the sequence analysis suggest that dispersin B cleaves beta(1,6)-linked N-acetylglucosamine polymer using a catalytic machinery similar to other family 20 hexosaminidases which cleave beta(1,4)-linked N-acetylglucosamine residues.
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==About this Structure== | + | </jmolCheckbox> |
| - | 1YHT is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aggregatibacter_actinomycetemcomitans Aggregatibacter actinomycetemcomitans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHT 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=1yht ConSurf]. |
| - | | + | <div style="clear:both"></div> |
| - | ==Reference== | + | __TOC__ |
| - | Structural analysis of dispersin B, a biofilm-releasing glycoside hydrolase from the periodontopathogen Actinobacillus actinomycetemcomitans., Ramasubbu N, Thomas LM, Ragunath C, Kaplan JB, J Mol Biol. 2005 Jun 10;349(3):475-86. Epub 2005 Apr 14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15878175 15878175]
| + | </StructureSection> |
| | [[Category: Aggregatibacter actinomycetemcomitans]] | | [[Category: Aggregatibacter actinomycetemcomitans]] |
| - | [[Category: Beta-N-acetylhexosaminidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Single protein]]
| + | [[Category: Kaplan JB]] |
| - | [[Category: Kaplan, J B.]] | + | [[Category: Ragunath C]] |
| - | [[Category: Ragunath, C.]] | + | [[Category: Ramasubbu N]] |
| - | [[Category: Ramasubbu, N.]] | + | [[Category: Thomas LM]] |
| - | [[Category: Thomas, L M.]] | + | |
| - | [[Category: beta barrel]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:07:40 2008''
| + | |
