3hwp
From Proteopedia
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure and computational analyses provide insights into the catalytic mechanism of 2, 4-diacetylphloroglucinol hydrolase PhlG from Pseudomonas fluorescens== | |
| + | <StructureSection load='3hwp' size='340' side='right'caption='[[3hwp]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3hwp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_protegens_Pf-5 Pseudomonas protegens Pf-5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HWP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HWP FirstGlance]. <br> | ||
| + | </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> | ||
| + | <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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3hwp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hwp OCA], [https://pdbe.org/3hwp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hwp RCSB], [https://www.ebi.ac.uk/pdbsum/3hwp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hwp ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/PHLG_PSEF5 PHLG_PSEF5] Hydrolase that specifically degrades the potent antimicrobial compound 2,4-diacetylphloroglucinol (DAPG) to equimolar amounts of mildly toxic monoacetylphloroglucinol (MAPG) and acetate.<ref>PMID:20018877</ref> | ||
| + | == 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/hw/3hwp_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3hwp ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 2,4-Diacetylphloroglucinol hydrolase PhlG from Pseudomonas fluorescens catalyzes hydrolytic carbon-carbon (C-C) bond cleavage of the antibiotic 2,4-diacetylphloroglucinol to form monoacetylphloroglucinol, a rare class of reactions in chemistry and biochemistry. To investigate the catalytic mechanism of this enzyme, we determined the three-dimensional structure of PhlG at 2.0 A resolution using x-ray crystallography and MAD methods. The overall structure includes a small N-terminal domain mainly involved in dimerization and a C-terminal domain of Bet v1-like fold, which distinguishes PhlG from the classical alpha/beta-fold hydrolases. A dumbbell-shaped substrate access tunnel was identified to connect a narrow interior amphiphilic pocket to the exterior solvent. The tunnel is likely to undergo a significant conformational change upon substrate binding to the active site. Structural analysis coupled with computational docking studies, site-directed mutagenesis, and enzyme activity analysis revealed that cleavage of the 2,4-diacetylphloroglucinol C-C bond proceeds via nucleophilic attack by a water molecule, which is coordinated by a zinc ion. In addition, residues Tyr(121), Tyr(229), and Asn(132), which are predicted to be hydrogen-bonded to the hydroxyl groups and unhydrolyzed acetyl group, can finely tune and position the bound substrate in a reactive orientation. Taken together, these results revealed the active sites and zinc-dependent hydrolytic mechanism of PhlG and explained its substrate specificity as well. | ||
| - | + | Crystal structure and computational analyses provide insights into the catalytic mechanism of 2,4-diacetylphloroglucinol hydrolase PhlG from Pseudomonas fluorescens.,He YX, Huang L, Xue Y, Fei X, Teng YB, Rubin-Pitel SB, Zhao H, Zhou CZ J Biol Chem. 2010 Feb 12;285(7):4603-11. Epub 2009 Dec 16. PMID:20018877<ref>PMID:20018877</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 3hwp" style="background-color:#fffaf0;"></div> | |
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Pseudomonas protegens Pf-5]] | ||
| + | [[Category: Fei X]] | ||
| + | [[Category: He Y-X]] | ||
| + | [[Category: Huang L]] | ||
| + | [[Category: Teng Y-B]] | ||
| + | [[Category: Xue Y]] | ||
| + | [[Category: Zhou C-Z]] | ||
Current revision
Crystal structure and computational analyses provide insights into the catalytic mechanism of 2, 4-diacetylphloroglucinol hydrolase PhlG from Pseudomonas fluorescens
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Categories: Large Structures | Pseudomonas protegens Pf-5 | Fei X | He Y-X | Huang L | Teng Y-B | Xue Y | Zhou C-Z
