4pyh

From Proteopedia

(Difference between revisions)

Revision as of 07:37, 8 February 2023

Phospho-glucan bound structure of starch phosphatase Starch EXcess4 reveals the mechanism for C6-specificty

Structural highlights

4pyh is a 1 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9]

Publication Abstract from PubMed

Plants use the insoluble polyglucan starch as their primary glucose storage molecule. Reversible phosphorylation, at the C6 and C3 positions of glucose moieties, is the only known natural modification of starch and is the key regulatory mechanism controlling its diurnal breakdown in plant leaves. The glucan phosphatase Starch Excess4 (SEX4) is a position-specific starch phosphatase that is essential for reversible starch phosphorylation; its absence leads to a dramatic accumulation of starch in Arabidopsis, but the basis for its function is unknown. Here we describe the crystal structure of SEX4 bound to maltoheptaose and phosphate to a resolution of 1.65 A. SEX4 binds maltoheptaose via a continuous binding pocket and active site that spans both the carbohydrate-binding module (CBM) and the dual-specificity phosphatase (DSP) domain. This extended interface is composed of aromatic and hydrophilic residues that form a specific glucan-interacting platform. SEX4 contains a uniquely adapted DSP active site that accommodates a glucan polymer and is responsible for positioning maltoheptaose in a C6-specific orientation. We identified two DSP domain residues that are responsible for SEX4 site-specific activity and, using these insights, we engineered a SEX4 double mutant that completely reversed specificity from the C6 to the C3 position. Our data demonstrate that the two domains act in consort, with the CBM primarily responsible for engaging glucan chains, whereas the DSP integrates them in the catalytic site for position-specific dephosphorylation. These data provide important insights into the structural basis of glucan phosphatase site-specific activity and open new avenues for their biotechnological utilization.

Phosphoglucan-bound structure of starch phosphatase Starch Excess4 reveals the mechanism for C6 specificity.,Meekins DA, Raththagala M, Husodo S, White CJ, Guo HF, Kotting O, Vander Kooi CW, Gentry MS 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^[10]

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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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

1 Structural highlights
2 Function
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/4pyh"

Categories: Arabidopsis thaliana | Large Structures | Meekins DA | Vander Kooi CW

@@ Line 1: / Line 1: @@
 ==Phospho-glucan bound structure of starch phosphatase Starch EXcess4 reveals the mechanism for C6-specificty==
-<StructureSection load='4pyh' size='340' side='right' caption='[[4pyh]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
+<StructureSection load='4pyh' size='340' side='right'caption='[[4pyh]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4pyh]] is a 1 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=4PYH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PYH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4pyh]] is a 1 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=4PYH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PYH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PRD_900035:alpha-maltohexaose'>PRD_900035</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3nme|3nme]], [[4kyq|4kyq]], [[4kyr|4kyr]]</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=4pyh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pyh OCA], [https://pdbe.org/4pyh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pyh RCSB], [https://www.ebi.ac.uk/pdbsum/4pyh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pyh ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DSP4, PTPKIS1, SEX4, At3g52180, F4F15.290 ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4pyh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pyh OCA], [http://pdbe.org/4pyh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pyh RCSB], [http://www.ebi.ac.uk/pdbsum/4pyh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pyh 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/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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Kooi, C W.Vander]]
+[[Category: Large Structures]]
-[[Category: Meekins, D A]]
+[[Category: Meekins DA]]
-[[Category: Carbohydrate binding]]
+[[Category: Vander Kooi CW]]
-[[Category: Chloroplast]]
-[[Category: Dual-specificity phosphatase]]
-[[Category: Hydrolase]]
-[[Category: Starch phosphatase]]

4pyh

From Proteopedia

Revision as of 07:37, 8 February 2023

Phospho-glucan bound structure of starch phosphatase Starch EXcess4 reveals the mechanism for C6-specificty

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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