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2zoa

From Proteopedia

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Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) COLLECTED AT 1.280 ANGSTROM

Structural highlights

2zoa is a 2 chain structure with sequence from Klebsiella aerogenes. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.4Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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:168197, PubMed:14711669, 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.

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2zoa"

Categories: Klebsiella aerogenes | Large Structures | Carr PD | Jackson CJ | Ollis DL

@@ Line 1: / Line 1: @@
 ==Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) COLLECTED AT 1.280 ANGSTROM==
-<StructureSection load='2zoa' size='340' side='right' caption='[[2zoa]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='2zoa' size='340' side='right'caption='[[2zoa]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2zoa]] 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=2ZOA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZOA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2zoa]] 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=2ZOA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZOA FirstGlance]. <br>
-</td></tr><tr><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><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]] 2.4&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2zo9|2zo9]]</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><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=2zoa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zoa OCA], [https://pdbe.org/2zoa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zoa RCSB], [https://www.ebi.ac.uk/pdbsum/2zoa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zoa ProSAT]</span></td></tr>
-<tr><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>
+</table>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zoa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zoa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zoa RCSB], [http://www.ebi.ac.uk/pdbsum/2zoa PDBsum]</span></td></tr>
+== Function ==
-<table>
+[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:168197, PubMed:14711669, 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 ==
 [[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/zo/2zoa_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zo/2zoa_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].
+</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=2zoa ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2zoa" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Phosphodiesterase|Phosphodiesterase]]
+*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </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]]

2zoa

From Proteopedia

Current revision

Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) COLLECTED AT 1.280 ANGSTROM

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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