|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Orthorhombic crystal form of pir1 dual specificity phosphatase core== | | ==Orthorhombic crystal form of pir1 dual specificity phosphatase core== |
| - | <StructureSection load='4nyh' size='340' side='right' caption='[[4nyh]], [[Resolution|resolution]] 1.20Å' scene=''> | + | <StructureSection load='4nyh' size='340' side='right'caption='[[4nyh]], [[Resolution|resolution]] 1.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4nyh]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NYH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NYH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4nyh]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NYH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NYH FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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]] 1.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4mbb|4mbb]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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">DUSP11, PIR1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4nyh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nyh OCA], [https://pdbe.org/4nyh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nyh RCSB], [https://www.ebi.ac.uk/pdbsum/4nyh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nyh 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=4nyh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nyh OCA], [http://pdbe.org/4nyh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nyh RCSB], [http://www.ebi.ac.uk/pdbsum/4nyh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nyh ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DUS11_HUMAN DUS11_HUMAN]] Possesses RNA 5'-triphosphatase and diphosphatase activities, but displays a poor protein-tyrosine phosphatase activity. Binds to RNA. May participate in nuclear mRNA metabolism.<ref>PMID:9685386</ref> | + | [https://www.uniprot.org/uniprot/DUS11_HUMAN DUS11_HUMAN] Possesses RNA 5'-triphosphatase and diphosphatase activities, but displays a poor protein-tyrosine phosphatase activity. Binds to RNA. May participate in nuclear mRNA metabolism.<ref>PMID:9685386</ref> |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | PIR1 is an atypical dual-specificity phosphatase (DSP) that dephosphorylates RNA with a higher specificity than phosphoproteins. Here we report the atomic structure of a catalytically inactive mutant (C152S) of the human PIR1 phosphatase core (PIR1-core, residues 29-205), refined at 1.20 A resolution. PIR1-core shares structural similarities with DSPs related to Vaccinia virus VH1 and with RNA 5'-phosphatases such as the baculovirus RNA triphosphatase and the human mRNA capping enzyme. The PIR1 active site cleft is wider and deeper than that of VH1 and contains two bound ions: a phosphate trapped above the catalytic cysteine C152 exemplifies the binding mode expected for the gamma-phosphate of RNA, and approximately 6 A away, a chloride ion coordinates the general base R158. Two residues in the PIR1 phosphate-binding loop (P-loop), a histidine (H154) downstream of C152 and an asparagine (N157) preceding R158, make close contacts with the active site phosphate, and their nonaliphatic side chains are essential for phosphatase activity in vitro. These residues are conserved in all RNA 5'-phosphatases that, analogous to PIR1, lack a "general acid" residue. Thus, a deep active site crevice, two active site ions, and conserved P-loop residues stabilizing the gamma-phosphate of RNA are defining features of atypical DSPs that specialize in dephosphorylating 5'-RNA.
| + | |
| | | | |
| - | Structure of Human PIR1, an Atypical Dual-Specificity Phosphatase.,Sankhala RS, Lokareddy RK, Cingolani G Biochemistry. 2014 Feb 11;53(5):862-71. doi: 10.1021/bi401240x. Epub 2014 Jan 31. PMID:24447265<ref>PMID:24447265</ref>
| + | ==See Also== |
| - | | + | *[[Dual specificity phosphatase 3D structures|Dual specificity phosphatase 3D structures]] |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 4nyh" style="background-color:#fffaf0;"></div>
| + | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Cingolani, G]] | + | [[Category: Large Structures]] |
| - | [[Category: Lokareddy, R K]] | + | [[Category: Cingolani G]] |
| - | [[Category: Sankhala, R S]] | + | [[Category: Lokareddy RK]] |
| - | [[Category: Dephosphorylation]] | + | [[Category: Sankhala RS]] |
| - | [[Category: Dual specificity phosphatase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Nucleus]]
| + | |
| - | [[Category: P-loop]]
| + | |
| - | [[Category: Protein tyrosine phosphatase]]
| + | |
| - | [[Category: Rna-rnp complex-1]]
| + | |
