3g5i
From Proteopedia
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| - | [[ | + | ==Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor== |
| + | <StructureSection load='3g5i' size='340' side='right' caption='[[3g5i]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3g5i]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G5I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G5I FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DNB:(2S,3S,4R,5R)-2-(3,4-DIAMINOPHENYL)-5-(HYDROXYMETHYL)PYRROLIDINE-3,4-DIOL'>DNB</scene></td></tr> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1yoe|1yoe]], [[1q8f|1q8f]]</td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ybeK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8] </span></td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3g5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g5i OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g5i RCSB], [http://www.ebi.ac.uk/pdbsum/3g5i PDBsum]</span></td></tr> | ||
| + | </table> | ||
| + | == 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/g5/3g5i_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/chain_selection.php?pdb_ID=2ata ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Nucleoside hydrolases (NHs) are enzymes that catalyze the excision of the N-glycosidic bond in nucleosides to allow recycling of the nitrogenous bases. The fine details of the catalytic mechanism and the structural features imposing the substrate specificity of the various members of the NH family are still debated. Here we present the functional characterization of the Escherichia coli YbeK (RihA) protein as a pyrimidine nucleoside-preferring NH and its first crystal structure to 1.8 A resolution. The enzyme active site is occupied by either the alpha or beta anomer of ribose and provides the first structural description of the binding of the NH reaction product. While the amino acid residues involved in ribosyl binding are strictly conserved in pyrimidine-specific NHs, the residues involved in specific interactions with the nitrogenous bases differ considerably. Further comparison of the active site architecture of YbeK with the related NHs establishes structural determinants involved in triggering the conformational transition between the open and closed structures and suggests a mechanism for product release. | ||
| - | + | New insights into the mechanism of nucleoside hydrolases from the crystal structure of the Escherichia coli YbeK protein bound to the reaction product.,Muzzolini L, Versees W, Tornaghi P, Van Holsbeke E, Steyaert J, Degano M Biochemistry. 2006 Jan 24;45(3):773-82. PMID:16411753<ref>PMID:16411753</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | == References == | |
| - | + | <references/> | |
| - | + | __TOC__ | |
| - | + | </StructureSection> | |
| - | + | ||
| - | == | + | |
| - | < | + | |
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Ribosylpyrimidine nucleosidase]] | [[Category: Ribosylpyrimidine nucleosidase]] | ||
| - | [[Category: Degano, M | + | [[Category: Degano, M]] |
| - | [[Category: Garau, G | + | [[Category: Garau, G]] |
| - | [[Category: Muzzolini, L | + | [[Category: Muzzolini, L]] |
| - | [[Category: Tornaghi, P | + | [[Category: Tornaghi, P]] |
[[Category: Glycosidase]] | [[Category: Glycosidase]] | ||
[[Category: Hydrolase]] | [[Category: Hydrolase]] | ||
Revision as of 10:26, 3 December 2014
Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor
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