3nme

From Proteopedia

(Difference between revisions)

Current revision

Structure of a plant phosphatase

Structural highlights

3nme is a 2 chain structure with sequence from Arabidopsis thaliana. 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

DSPG4_ARATH Starch granule-associated phosphoglucan phosphatase involved in the control of starch accumulation. Acts as a major regulator of the initial steps of starch degradation at the granule surface. Functions during the day by dephosphorylating the night-accumulated phospho-oligosaccharides. Can release phosphate from both the C6 and the C3 positions, but dephosphorylates preferentially the C6 position (PubMed:20018599, PubMed:26231210).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11]

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

Living organisms utilize carbohydrates as essential energy storage molecules. Starch is the predominant carbohydrate storage molecule in plants while glycogen is utilized in animals. Starch is a water-insoluble polymer that requires the concerted activity of kinases and phosphatases to solubilize the outer surface of the glucan and mediate starch catabolism. All known plant genomes encode the glucan phosphatase Starch Excess4 (SEX4). SEX4 can dephosphorylate both the starch granule surface and soluble phosphoglucans and is necessary for processive starch metabolism. The physical basis for the function of SEX4 as a glucan phosphatase is currently unclear. Herein, we report the crystal structure of SEX4, containing phosphatase, carbohydrate-binding, and C-terminal domains. The three domains of SEX4 fold into a compact structure with extensive interdomain interactions. The C-terminal domain of SEX4 integrally folds into the core of the phosphatase domain and is essential for its stability. The phosphatase and carbohydrate-binding domains directly interact and position the phosphatase active site toward the carbohydrate-binding site in a single continuous pocket. Mutagenesis of the phosphatase domain residue F167, which forms the base of this pocket and bridges the two domains, selectively affects the ability of SEX4 to function as a glucan phosphatase. Together, these results reveal the unique tertiary architecture of SEX4 that provides the physical basis for its function as a glucan phosphatase.

Structural basis for the glucan phosphatase activity of Starch Excess4.,Vander Kooi CW, Taylor AO, Pace RM, Meekins DA, Guo HF, Kim Y, Gentry MS Proc Natl Acad Sci U S A. 2010 Aug 31;107(35):15379-84. Epub 2010 Aug 2. PMID:20679247^[12]

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

References

↑ Niittyla T, Comparot-Moss S, Lue WL, Messerli G, Trevisan M, Seymour MD, Gatehouse JA, Villadsen D, Smith SM, Chen J, Zeeman SC, Smith AM. Similar protein phosphatases control starch metabolism in plants and glycogen metabolism in mammals. J Biol Chem. 2006 Apr 28;281(17):11815-8. Epub 2006 Mar 2. PMID:16513634 doi:10.1074/jbc.M600519200
↑ Kerk D, Conley TR, Rodriguez FA, Tran HT, Nimick M, Muench DG, Moorhead GB. A chloroplast-localized dual-specificity protein phosphatase in Arabidopsis contains a phylogenetically dispersed and ancient carbohydrate-binding domain, which binds the polysaccharide starch. Plant J. 2006 May;46(3):400-13. PMID:16623901 doi:10.1111/j.1365-313X.2006.02704.x
↑ Sokolov LN, Dominguez-Solis JR, Allary AL, Buchanan BB, Luan S. A redox-regulated chloroplast protein phosphatase binds to starch diurnally and functions in its accumulation. Proc Natl Acad Sci U S A. 2006 Jun 20;103(25):9732-7. Epub 2006 Jun 13. PMID:16772378 doi:10.1073/pnas.0603329103
↑ Kotting O, Santelia D, Edner C, Eicke S, Marthaler T, Gentry MS, Comparot-Moss S, Chen J, Smith AM, Steup M, Ritte G, Zeeman SC. STARCH-EXCESS4 is a laforin-like Phosphoglucan phosphatase required for starch degradation in Arabidopsis thaliana. Plant Cell. 2009 Jan;21(1):334-46. doi: 10.1105/tpc.108.064360. Epub 2009 Jan 13. PMID:19141707 doi:10.1105/tpc.108.064360
↑ Hsu S, Kim Y, Li S, Durrant ES, Pace RM, Woods VL Jr, Gentry MS. Structural insights into glucan phosphatase dynamics using amide hydrogen-deuterium exchange mass spectrometry. Biochemistry. 2009 Oct 20;48(41):9891-902. doi: 10.1021/bi9008853. PMID:19754155 doi:10.1021/bi9008853
↑ Hejazi M, Fettke J, Kotting O, Zeeman SC, Steup M. The Laforin-like dual-specificity phosphatase SEX4 from Arabidopsis hydrolyzes both C6- and C3-phosphate esters introduced by starch-related dikinases and thereby affects phase transition of alpha-glucans. Plant Physiol. 2010 Feb;152(2):711-22. doi: 10.1104/pp.109.149914. Epub 2009 Dec , 16. PMID:20018599 doi:10.1104/pp.109.149914
↑ Vander Kooi CW, Taylor AO, Pace RM, Meekins DA, Guo HF, Kim Y, Gentry MS. Structural basis for the glucan phosphatase activity of Starch Excess4. Proc Natl Acad Sci U S A. 2010 Aug 31;107(35):15379-84. Epub 2010 Aug 2. PMID:20679247 doi:10.1073/pnas.1009386107
↑ Santelia D, Kotting O, Seung D, Schubert M, Thalmann M, Bischof S, Meekins DA, Lutz A, Patron N, Gentry MS, Allain FH, Zeeman SC. The phosphoglucan phosphatase like sex Four2 dephosphorylates starch at the C3-position in Arabidopsis. Plant Cell. 2011 Nov;23(11):4096-111. doi: 10.1105/tpc.111.092155. Epub 2011 Nov , 18. PMID:22100529 doi:10.1105/tpc.111.092155
↑ Weise SE, Aung K, Jarou ZJ, Mehrshahi P, Li Z, Hardy AC, Carr DJ, Sharkey TD. Engineering starch accumulation by manipulation of phosphate metabolism of starch. Plant Biotechnol J. 2012 Jun;10(5):545-54. doi: 10.1111/j.1467-7652.2012.00684.x., Epub 2012 Feb 9. PMID:22321580 doi:10.1111/j.1467-7652.2012.00684.x
↑ Meekins DA, Raththagala M, Husodo S, White CJ, Guo HF, Kotting O, Vander Kooi CW, Gentry MS. Phosphoglucan-bound structure of starch phosphatase Starch Excess4 reveals the mechanism for C6 specificity. Proc Natl Acad Sci U S A. 2014 May 20;111(20):7272-7. doi:, 10.1073/pnas.1400757111. Epub 2014 May 5. PMID:24799671 doi:http://dx.doi.org/10.1073/pnas.1400757111
↑ Meekins DA, Raththagala M, Auger KD, Turner BD, Santelia D, Kötting O, Gentry MS, Vander Kooi CW. Mechanistic Insights into Glucan Phosphatase Activity against Polyglucan Substrates. J Biol Chem. 2015 Sep 18;290(38):23361-70. PMID:26231210 doi:10.1074/jbc.M115.658203
↑ Vander Kooi CW, Taylor AO, Pace RM, Meekins DA, Guo HF, Kim Y, Gentry MS. Structural basis for the glucan phosphatase activity of Starch Excess4. Proc Natl Acad Sci U S A. 2010 Aug 31;107(35):15379-84. Epub 2010 Aug 2. PMID:20679247 doi:10.1073/pnas.1009386107

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

Categories: Arabidopsis thaliana | Large Structures | Vander Kooi CW

@@ Line 1: / Line 1: @@
 ==Structure of a plant phosphatase==
-<StructureSection load='3nme' size='340' side='right' caption='[[3nme]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='3nme' size='340' side='right'caption='[[3nme]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3nme]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NME FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3nme]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NME FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.4&#8491;</td></tr>
-<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At3g52180 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=3nme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nme OCA], [https://pdbe.org/3nme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nme RCSB], [https://www.ebi.ac.uk/pdbsum/3nme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nme ProSAT]</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=3nme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nme OCA], [http://pdbe.org/3nme PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nme RCSB], [http://www.ebi.ac.uk/pdbsum/3nme PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nme ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DSP4_ARATH DSP4_ARATH]] Starch granule-associated phosphoglucan phosphatase involved in the control of starch accumulation. Acts as major regulator of the initial steps of starch degradation at the granule surface. Functions during the day by dephosphorylating the night-accumulated phospho-oligosaccharides. Can release phosphate from both the C6 and the C3 positions.<ref>PMID:16513634</ref> <ref>PMID:16623901</ref> <ref>PMID:16772378</ref> <ref>PMID:19754155</ref> <ref>PMID:19141707</ref> <ref>PMID:20018599</ref> <ref>PMID:22100529</ref> <ref>PMID:22321580</ref> <ref>PMID:20679247</ref>
+[https://www.uniprot.org/uniprot/DSPG4_ARATH DSPG4_ARATH] Starch granule-associated phosphoglucan phosphatase involved in the control of starch accumulation. Acts as a major regulator of the initial steps of starch degradation at the granule surface. Functions during the day by dephosphorylating the night-accumulated phospho-oligosaccharides. Can release phosphate from both the C6 and the C3 positions, but dephosphorylates preferentially the C6 position (PubMed:20018599, PubMed:26231210).<ref>PMID:16513634</ref> <ref>PMID:16623901</ref> <ref>PMID:16772378</ref> <ref>PMID:19141707</ref> <ref>PMID:19754155</ref> <ref>PMID:20018599</ref> <ref>PMID:20679247</ref> <ref>PMID:22100529</ref> <ref>PMID:22321580</ref> <ref>PMID:24799671</ref> <ref>PMID:26231210</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/nm/3nme_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nm/3nme_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>
   </jmolCheckbox>
@@ Line 34: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Kooi, C W.Vander]]
+[[Category: Large Structures]]
-[[Category: Carbohydrate binding]]
+[[Category: Vander Kooi CW]]
-[[Category: Dual specificity phosphatase]]
-[[Category: Hydrolase]]
-[[Category: Phosphatase]]

3nme

From Proteopedia

Current revision

Structure of a plant phosphatase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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