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| | <StructureSection load='2q47' size='340' side='right'caption='[[2q47]], [[Resolution|resolution]] 3.30Å' scene=''> | | <StructureSection load='2q47' size='340' side='right'caption='[[2q47]], [[Resolution|resolution]] 3.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2q47]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q47 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q47 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2q47]] 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=2Q47 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q47 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 3.3Å</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=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xri|1xri]]</div></td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At1g05000, T7A14.14 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q47 OCA], [https://pdbe.org/2q47 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q47 RCSB], [https://www.ebi.ac.uk/pdbsum/2q47 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q47 ProSAT]</span></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=2q47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q47 OCA], [https://pdbe.org/2q47 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q47 RCSB], [https://www.ebi.ac.uk/pdbsum/2q47 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q47 ProSAT]</span></td></tr> |
| | </table> | | </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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Protein-tyrosine-phosphatase]]
| + | [[Category: Kondrashov DA]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Levin EJ]] |
| - | [[Category: Kondrashov, D A]] | + | [[Category: Phillips Jr GN]] |
| - | [[Category: Levin, E J]] | + | [[Category: Wesenberg GE]] |
| - | [[Category: Phillips, G N]] | + | |
| - | [[Category: Wesenberg, G E]] | + | |
| - | [[Category: At1g05000]]
| + | |
| - | [[Category: Cesg]]
| + | |
| - | [[Category: Ensemble refinement]]
| + | |
| - | [[Category: Phosphoprotein phosphatase]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| - | [[Category: Refinement methodology development]]
| + | |
| - | [[Category: Unknown function]]
| + | |
| Structural highlights
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]
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
X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.
Ensemble refinement of protein crystal structures: validation and application.,Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr Structure. 2007 Sep;15(9):1040-52. PMID:17850744[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
- ↑ Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Ensemble refinement of protein crystal structures: validation and application. Structure. 2007 Sep;15(9):1040-52. PMID:17850744 doi:http://dx.doi.org/10.1016/j.str.2007.06.019
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