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3hwp

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Revision as of 20:10, 11 August 2016

Crystal structure and computational analyses provide insights into the catalytic mechanism of 2, 4-diacetylphloroglucinol hydrolase PhlG from Pseudomonas fluorescens

Structural highlights

3hwp is a 2 chain structure with sequence from Psef5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
NonStd Res:
Gene:	PhlG (PSEF5)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ He YX, Huang L, Xue Y, Fei X, Teng YB, Rubin-Pitel SB, Zhao H, Zhou CZ. Crystal structure and computational analyses provide insights into the catalytic mechanism of 2,4-diacetylphloroglucinol hydrolase PhlG from Pseudomonas fluorescens. J Biol Chem. 2010 Feb 12;285(7):4603-11. Epub 2009 Dec 16. PMID:20018877 doi:10.1074/jbc.M109.044180

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3hwp"

@@ Line 1: / Line 1: @@
 ==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]] 2.00&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PhlG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=220664 PSEF5])</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=3hwp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hwp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hwp RCSB], [http://www.ebi.ac.uk/pdbsum/3hwp PDBsum]</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=3hwp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hwp OCA], [http://pdbe.org/3hwp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hwp RCSB], [http://www.ebi.ac.uk/pdbsum/3hwp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hwp ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 16: / Line 17: @@
     <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].
+</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;">
@@ Line 26: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3hwp" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

3hwp

From Proteopedia

Revision as of 20:10, 11 August 2016

Crystal structure and computational analyses provide insights into the catalytic mechanism of 2, 4-diacetylphloroglucinol hydrolase PhlG from Pseudomonas fluorescens

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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