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7mog

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Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) Cys150Ser in complex with 5-PCF2 Am-InsP5, an analogue of 5-InsP7

Structural highlights

7mog 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 1.8Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DSP1_ARATH Possesses phosphotyrosine phosphatase activity in vitro. Hydrolyzes para-nitrophenyl phosphate in vitro (PubMed:21409566, PubMed:18433060). Hydrolyzes O-methylfluorescein phosphate in vitro (PubMed:21409566). Hydrolyzes polyphosphate and ATP in vitro (PubMed:18433060). Dephosphorylates the phosphoinositides PI(3,4,5)P3, PI(3,5)P2, but not PI(3)P, PI(3,4)P2 or PI(4,5)P2 (PubMed:17976645).^[1] ^[2] ^[3]

Publication Abstract from PubMed

Structural snapshots of protein/ligand complexes are a prerequisite for gaining atomic level insight into enzymatic reaction mechanisms. An important group of enzymes has been deprived of this analytical privilege: members of the protein tyrosine phosphatase (PTP) superfamily with catalytic WPD-loops lacking the indispensable general-acid/base within a tryptophan-proline-aspartate/glutamate context. Here, we provide the ligand/enzyme crystal complexes for one such PTP outlier: Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1 (AtPFA-DSP1), herein unveiled as a regioselective and efficient phosphatase towards inositol pyrophosphate (PP-InsP) signaling molecules. Although the WPD loop is missing its canonical tripeptide motif, this structural element contributes to catalysis by assisting PP-InsP delivery into the catalytic pocket, for a choreographed exchange with phosphate reaction product. Subsequently, an intramolecular proton donation by PP-InsP substrate is posited to substitute functionally for the absent aspartate/glutamate general-acid. Overall, we expand mechanistic insight into adaptability of the conserved PTP structural elements.

A structural expose of noncanonical molecular reactivity within the protein tyrosine phosphatase WPD loop.,Wang H, Perera L, Jork N, Zong G, Riley AM, Potter BVL, Jessen HJ, Shears SB Nat Commun. 2022 Apr 25;13(1):2231. doi: 10.1038/s41467-022-29673-y. PMID:35468885^[4]

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

References

↑ Roma-Mateo C, Rios P, Tabernero L, Attwood TK, Pulido R. A novel phosphatase family, structurally related to dual-specificity phosphatases, that displays unique amino acid sequence and substrate specificity. J Mol Biol. 2007 Dec 7;374(4):899-909. doi: 10.1016/j.jmb.2007.10.008. Epub 2007 , Oct 11. PMID:17976645 doi:http://dx.doi.org/10.1016/j.jmb.2007.10.008
↑ Aceti DJ, Bitto E, Yakunin AF, Proudfoot M, Bingman CA, Frederick RO, Sreenath HK, Vojtik FC, Wrobel RL, Fox BG, Markley JL, Phillips GN Jr. Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000. Proteins. 2008 Oct;73(1):241-53. PMID:18433060 doi:10.1002/prot.22041
↑ Roma-Mateo C, Sacristan-Reviriego A, Beresford NJ, Caparros-Martin JA, Culianez-Macia FA, Martin H, Molina M, Tabernero L, Pulido R. Phylogenetic and genetic linkage between novel atypical dual-specificity phosphatases from non-metazoan organisms. Mol Genet Genomics. 2011 Apr;285(4):341-54. doi: 10.1007/s00438-011-0611-6. Epub , 2011 Mar 16. PMID:21409566 doi:http://dx.doi.org/10.1007/s00438-011-0611-6
↑ Wang H, Perera L, Jork N, Zong G, Riley AM, Potter BVL, Jessen HJ, Shears SB. A structural expose of noncanonical molecular reactivity within the protein tyrosine phosphatase WPD loop. Nat Commun. 2022 Apr 25;13(1):2231. doi: 10.1038/s41467-022-29673-y. PMID:35468885 doi:http://dx.doi.org/10.1038/s41467-022-29673-y

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7mog"

Categories: Arabidopsis thaliana | Large Structures | Shears SB | Wang H

@@ Line 3: / Line 3: @@
 <StructureSection load='7mog' size='340' side='right'caption='[[7mog]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7mog]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MOG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MOG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7mog]] 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=7MOG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MOG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KDJ:(1,1-difluoro-2-oxo-2-{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]amino}ethyl)phosphonic+acid'>KDJ</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]] 1.8&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KDJ:(1,1-difluoro-2-oxo-2-{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]amino}ethyl)phosphonic+acid'>KDJ</scene></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=7mog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mog OCA], [https://pdbe.org/7mog PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mog RCSB], [https://www.ebi.ac.uk/pdbsum/7mog PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mog ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/DSP1_ARATH DSP1_ARATH]] Possesses phosphotyrosine phosphatase activity in vitro. Hydrolyzes para-nitrophenyl phosphate in vitro (PubMed:21409566, PubMed:18433060). Hydrolyzes O-methylfluorescein phosphate in vitro (PubMed:21409566). Hydrolyzes polyphosphate and ATP in vitro (PubMed:18433060). Dephosphorylates the phosphoinositides PI(3,4,5)P3, PI(3,5)P2, but not PI(3)P, PI(3,4)P2 or PI(4,5)P2 (PubMed:17976645).<ref>PMID:17976645</ref> <ref>PMID:18433060</ref> <ref>PMID:21409566</ref>
+[https://www.uniprot.org/uniprot/DSP1_ARATH DSP1_ARATH] Possesses phosphotyrosine phosphatase activity in vitro. Hydrolyzes para-nitrophenyl phosphate in vitro (PubMed:21409566, PubMed:18433060). Hydrolyzes O-methylfluorescein phosphate in vitro (PubMed:21409566). Hydrolyzes polyphosphate and ATP in vitro (PubMed:18433060). Dephosphorylates the phosphoinositides PI(3,4,5)P3, PI(3,5)P2, but not PI(3)P, PI(3,4)P2 or PI(4,5)P2 (PubMed:17976645).<ref>PMID:17976645</ref> <ref>PMID:18433060</ref> <ref>PMID:21409566</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 7mog" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Tyrosine phosphatase 3D structures|Tyrosine phosphatase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Protein-tyrosine-phosphatase]]
+[[Category: Shears SB]]
-[[Category: Shears, S B]]
+[[Category: Wang H]]
-[[Category: Wang, H]]
-[[Category: Catalytic water]]
-[[Category: Cell-signaling]]
-[[Category: Hydrolase]]
-[[Category: Inositol]]
-[[Category: Inositol pyrophosphate]]
-[[Category: Intermediate]]
-[[Category: Metaphosphate]]
-[[Category: Molecular dynamic simulation]]
-[[Category: Phosphatase]]
-[[Category: Phosphate]]
-[[Category: Reaction mechanism]]
-[[Category: Self-activation]]
-[[Category: Substrate recognition]]
-[[Category: Transferase]]

7mog

From Proteopedia

Current revision

Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) Cys150Ser in complex with 5-PCF2 Am-InsP5, an analogue of 5-InsP7

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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