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| | ==INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM M. MUSCULUS IN COMPLEX WITH ATP and IP5== | | ==INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM M. MUSCULUS IN COMPLEX WITH ATP and IP5== |
| - | <StructureSection load='5mw8' size='340' side='right' caption='[[5mw8]], [[Resolution|resolution]] 2.40Å' scene=''> | + | <StructureSection load='5mw8' size='340' side='right'caption='[[5mw8]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5mw8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MW8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MW8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5mw8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MW8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MW8 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5MY:MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE'>5MY</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.4Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Ippk ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5MY:MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE'>5MY</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inositol-pentakisphosphate_2-kinase Inositol-pentakisphosphate 2-kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.158 2.7.1.158] </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=5mw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mw8 OCA], [https://pdbe.org/5mw8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mw8 RCSB], [https://www.ebi.ac.uk/pdbsum/5mw8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mw8 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=5mw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mw8 OCA], [http://pdbe.org/5mw8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mw8 RCSB], [http://www.ebi.ac.uk/pdbsum/5mw8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mw8 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/IPPK_MOUSE IPPK_MOUSE]] Phosphorylates Ins(1,3,4,5,6)P5 at position 2 to form Ins(1,2,3,4,5,6)P6 (InsP6 or phytate). InsP6 is involved in many processes such as mRNA export, non-homologous end-joining, endocytosis, ion channel regulation. It also protects cells from TNF-alpha-induced apoptosis.<ref>PMID:15939868</ref> | + | [https://www.uniprot.org/uniprot/IPPK_MOUSE IPPK_MOUSE] Phosphorylates Ins(1,3,4,5,6)P5 at position 2 to form Ins(1,2,3,4,5,6)P6 (InsP6 or phytate). InsP6 is involved in many processes such as mRNA export, non-homologous end-joining, endocytosis, ion channel regulation. It also protects cells from TNF-alpha-induced apoptosis.<ref>PMID:15939868</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Inositol-pentakisphosphate 2-kinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Lk3 transgenic mice]] | + | [[Category: Mus musculus]] |
| - | [[Category: Franco-Echevarria, E]] | + | [[Category: Franco-Echevarria E]] |
| - | [[Category: Gonzalez, B]] | + | [[Category: Gonzalez B]] |
| - | [[Category: Sanz-Aparicio, J]] | + | [[Category: Sanz-Aparicio J]] |
| - | [[Category: Inositol kinase]]
| + | |
| - | [[Category: Mammal ipk]]
| + | |
| - | [[Category: Protein structure]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
5mw8 is a 1 chain structure with sequence from Mus musculus. 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
IPPK_MOUSE Phosphorylates Ins(1,3,4,5,6)P5 at position 2 to form Ins(1,2,3,4,5,6)P6 (InsP6 or phytate). InsP6 is involved in many processes such as mRNA export, non-homologous end-joining, endocytosis, ion channel regulation. It also protects cells from TNF-alpha-induced apoptosis.[1]
Publication Abstract from PubMed
Inositol 1,3,4,5,6-pentakisphosphate 2-kinases (IP5 2-Ks) comprise a family of enzymes in charge of synthesizing inositol hexakisphosphate (IP6) in eukaryotic cells. This protein and its product IP6 present many roles in cells, participating in mRNA export, embryonic development, and apoptosis. We reported previously that the full-length IP5 2-K from Arabidopsis thaliana (At) is a zinc metallo-enzyme including two separated lobes (the N and C lobes). We have also shown conformational changes in IP5 2-K and have identified the residues involved in substrate recognition and catalysis. However, the specific features of mammalian IP5 2-Ks remain unknown. To this end, we report here the first structure for a murine IP5 2-K in complex with ATP/IP5 or IP6 Our structural findings indicated that the general folding in N and C lobes is conserved with AtIP5 2-K. A helical scaffold in the C lobe constitutes the inositol phosphate (IP)-binding site, which, along with the participation of the N lobe, endows high specificity to this protein. However, we also noted large structural differences between the orthologous from these two eukaryotic kingdoms. These differences include a novel zinc-binding site and regions unique to the mammalian IP5 2-K, as an unexpected basic patch on the protein surface. In conclusion, our findings have uncovered distinct features of a mammalian IP5 2-K and set the stage for investigations into protein-protein or protein-RNA interactions important for IP5 2-K function and activity.
The Crystal Structure of Mammalian Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase Reveals a New Zinc Binding Site and Key Features for Protein Function.,Franco-Echevarria E, Sanz-Aparicio J, Brearley CA, Gonzalez-Rubio JM, Gonzalez B J Biol Chem. 2017 Apr 27. pii: jbc.M117.780395. doi: 10.1074/jbc.M117.780395. PMID:28450399[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Verbsky J, Lavine K, Majerus PW. Disruption of the mouse inositol 1,3,4,5,6-pentakisphosphate 2-kinase gene, associated lethality, and tissue distribution of 2-kinase expression. Proc Natl Acad Sci U S A. 2005 Jun 14;102(24):8448-53. Epub 2005 Jun 6. PMID:15939868 doi:http://dx.doi.org/0503656102
- ↑ Franco-Echevarria E, Sanz-Aparicio J, Brearley CA, Gonzalez-Rubio JM, Gonzalez B. The Crystal Structure of Mammalian Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase Reveals a New Zinc Binding Site and Key Features for Protein Function. J Biol Chem. 2017 Apr 27. pii: jbc.M117.780395. doi: 10.1074/jbc.M117.780395. PMID:28450399 doi:http://dx.doi.org/10.1074/jbc.M117.780395
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