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| | ==Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal ion preference== | | ==Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal ion preference== |
| - | <StructureSection load='2zo9' size='340' side='right' caption='[[2zo9]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='2zo9' size='340' side='right'caption='[[2zo9]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2zo9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacter_aerogenes Enterobacter aerogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZO9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZO9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2zo9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_aerogenes Klebsiella aerogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZO9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZO9 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2dxn|2dxn]], [[2zoa|2zoa]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GpdQ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=548 Enterobacter aerogenes])</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=2zo9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zo9 OCA], [https://pdbe.org/2zo9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zo9 RCSB], [https://www.ebi.ac.uk/pdbsum/2zo9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zo9 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycerophosphodiester_phosphodiesterase Glycerophosphodiester phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.46 3.1.4.46] </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=2zo9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zo9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zo9 RCSB], [http://www.ebi.ac.uk/pdbsum/2zo9 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/GPDQ_KLEAE GPDQ_KLEAE] Catalyzes the hydrolysis of the 3'-5' phosphodiester bond of glycerophosphodiesters such as glycerophosphorylethanolamine (GPE), a typical phospholipid metabolite which is probably the natural substrate of the enzyme (PubMed:14711669). In addition, exhibits a broad substrate specificity and can catalyze the hydrolysis of various phosphomonoesters, diesters, triesters and phosphothiolates (PubMed:14711669, PubMed:168197, PubMed:17630782). Preferentially hydrolyzes the phosphate diesters over the phosphonate monoesters (PubMed:17630782). Can hydrolyze the model substrates p-nitrophenyl phosphate (pNPP), bis-(p-nitrophenyl phosphate) (bis(pNPP)) and ethyl p-nitrophenyl phosphate (EtpNPP) (PubMed:14711669, PubMed:168197, PubMed:17306828, PubMed:17630782, PubMed:18678932, PubMed:18831553). Also exhibits activity towards some organophosphate pesticides and is capable of hydrolyzing a close analog of EA 2192, the most toxic and persistent degradation product of the nerve agent VX (PubMed:14711669, PubMed:17630782).<ref>PMID:14711669</ref> <ref>PMID:168197</ref> <ref>PMID:17306828</ref> <ref>PMID:17630782</ref> <ref>PMID:18678932</ref> <ref>PMID:18831553</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zo/2zo9_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zo/2zo9_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </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=2zo9 ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 2zo9" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Phosphodiesterase|Phosphodiesterase]] | + | *[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Enterobacter aerogenes]] | + | [[Category: Klebsiella aerogenes]] |
| - | [[Category: Glycerophosphodiester phosphodiesterase]] | + | [[Category: Large Structures]] |
| - | [[Category: Carr, P D]] | + | [[Category: Carr PD]] |
| - | [[Category: Jackson, C J]] | + | [[Category: Jackson CJ]] |
| - | [[Category: Ollis, D L]] | + | [[Category: Ollis DL]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Iron]]
| + | |
| - | [[Category: Malonate]]
| + | |
| - | [[Category: Metalloenzyme]]
| + | |
| - | [[Category: Phosphodiesterase]]
| + | |
| Structural highlights
Function
GPDQ_KLEAE Catalyzes the hydrolysis of the 3'-5' phosphodiester bond of glycerophosphodiesters such as glycerophosphorylethanolamine (GPE), a typical phospholipid metabolite which is probably the natural substrate of the enzyme (PubMed:14711669). In addition, exhibits a broad substrate specificity and can catalyze the hydrolysis of various phosphomonoesters, diesters, triesters and phosphothiolates (PubMed:14711669, PubMed:168197, PubMed:17630782). Preferentially hydrolyzes the phosphate diesters over the phosphonate monoesters (PubMed:17630782). Can hydrolyze the model substrates p-nitrophenyl phosphate (pNPP), bis-(p-nitrophenyl phosphate) (bis(pNPP)) and ethyl p-nitrophenyl phosphate (EtpNPP) (PubMed:14711669, PubMed:168197, PubMed:17306828, PubMed:17630782, PubMed:18678932, PubMed:18831553). Also exhibits activity towards some organophosphate pesticides and is capable of hydrolyzing a close analog of EA 2192, the most toxic and persistent degradation product of the nerve agent VX (PubMed:14711669, PubMed:17630782).[1] [2] [3] [4] [5] [6]
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
The structure of a malonate-bound form of the glycerophosphodiesterase from Enterobacter aerogenes, GpdQ, has been refined at a resolution of 2.2 A to a final R factor of 17.1%. The structure was originally solved to 2.9 A resolution using SAD phases from Zn2+ metal ions introduced into the active site of the apoenzyme [Jackson et al. (2007), J. Mol. Biol. 367, 1047-1062]. However, the 2.9 A resolution was insufficient to discern significant details of the architecture of the binuclear metal centre that constitutes the active site. Furthermore, kinetic analysis revealed that the enzyme lost a significant amount of activity in the presence of Zn2+, suggesting that it is unlikely to be a catalytically relevant metal ion. In this communication, a higher resolution structure of GpdQ is presented in which malonate is visibly coordinated in the active site and analysis of the native metal-ion preference is presented using atomic absorption spectroscopy and anomalous scattering. Catalytic implications of the structure and its Fe2+ metal-ion preference are discussed.
Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference.,Jackson CJ, Hadler KS, Carr PD, Oakley AJ, Yip S, Schenk G, Ollis DL Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Aug 1;64(Pt, 8):681-5. Epub 2008 Jul 5. PMID:18678932[7]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ McLoughlin SY, Jackson C, Liu JW, Ollis DL. Growth of Escherichia coli coexpressing phosphotriesterase and glycerophosphodiester phosphodiesterase, using paraoxon as the sole phosphorus source. Appl Environ Microbiol. 2004 Jan;70(1):404-12. PMID:14711669 doi:10.1128/AEM.70.1.404-412.2004
- ↑ Gerlt JA, Whitman GJ. Purification and properties of a phosphohydrolase from Enterobacter aerogenes. J Biol Chem. 1975 Jul 10;250(13):5053-8 PMID:168197
- ↑ Jackson CJ, Carr PD, Liu JW, Watt SJ, Beck JL, Ollis DL. The structure and function of a novel glycerophosphodiesterase from Enterobacter aerogenes. J Mol Biol. 2007 Apr 6;367(4):1047-62. Epub 2007 Jan 20. PMID:17306828 doi:10.1016/j.jmb.2007.01.032
- ↑ Ghanem E, Li Y, Xu C, Raushel FM. Characterization of a phosphodiesterase capable of hydrolyzing EA 2192, the most toxic degradation product of the nerve agent VX. Biochemistry. 2007 Aug 7;46(31):9032-40. PMID:17630782 doi:10.1021/bi700561k
- ↑ Jackson CJ, Hadler KS, Carr PD, Oakley AJ, Yip S, Schenk G, Ollis DL. Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Aug 1;64(Pt, 8):681-5. Epub 2008 Jul 5. PMID:18678932 doi:10.1107/S1744309108017600
- ↑ Hadler KS, Tanifum EA, Yip SH, Mitic N, Guddat LW, Jackson CJ, Gahan LR, Nguyen K, Carr PD, Ollis DL, Hengge AC, Larrabee JA, Schenk G. Substrate-Promoted Formation of a Catalytically Competent Binuclear Center and Regulation of Reactivity in a Glycerophosphodiesterase from Enterobacter aerogenes. J Am Chem Soc. 2008 Oct 3. PMID:18831553 doi:http://dx.doi.org/10.1021/ja803346w
- ↑ Jackson CJ, Hadler KS, Carr PD, Oakley AJ, Yip S, Schenk G, Ollis DL. Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Aug 1;64(Pt, 8):681-5. Epub 2008 Jul 5. PMID:18678932 doi:10.1107/S1744309108017600
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