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| | ==myo-inositol 3-kinase bound with its products (ADP and 1D-myo-inositol 3-phosphate)== | | ==myo-inositol 3-kinase bound with its products (ADP and 1D-myo-inositol 3-phosphate)== |
| - | <StructureSection load='4xf6' size='340' side='right' caption='[[4xf6]], [[Resolution|resolution]] 2.08Å' scene=''> | + | <StructureSection load='4xf6' size='340' side='right'caption='[[4xf6]], [[Resolution|resolution]] 2.08Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4xf6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XF6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XF6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4xf6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XF6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XF6 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=INS:1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE'>INS</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=LIP:L-MYO-INOSITOL-1-PHOSPHATE'>LIP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.08Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xf7|4xf7]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=INS:1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE'>INS</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=LIP:L-MYO-INOSITOL-1-PHOSPHATE'>LIP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TK2285 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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=4xf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xf6 OCA], [https://pdbe.org/4xf6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xf6 RCSB], [https://www.ebi.ac.uk/pdbsum/4xf6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xf6 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inositol_3-kinase Inositol 3-kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.64 2.7.1.64] </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=4xf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xf6 OCA], [http://pdbe.org/4xf6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xf6 RCSB], [http://www.ebi.ac.uk/pdbsum/4xf6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xf6 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q5JDA3_THEKO Q5JDA3_THEKO] |
| | <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 3-kinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Fujihashi, M]] | + | [[Category: Thermococcus kodakarensis KOD1]] |
| - | [[Category: Miki, K]] | + | [[Category: Fujihashi M]] |
| - | [[Category: Nagata, R]] | + | [[Category: Miki K]] |
| - | [[Category: Product complex]] | + | [[Category: Nagata R]] |
| - | [[Category: Ribokinase]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
4xf6 is a 2 chain structure with sequence from Thermococcus kodakarensis KOD1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.08Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
Q5JDA3_THEKO
Publication Abstract from PubMed
The TK2285 protein from Thermococcus kodakarensis was recently characterized as an enzyme catalyzing the phosphorylation of myo-inositol. Only two myo-inositol kinases have been identified so far, the TK2285 protein and Lpa3 from Zea mays, both of which belong to the ribokinase family. In either case, which of the six hydroxyl groups of myo-inositol is phosphorylated is still unknown. In addition, little is known about the myo-inositol binding mechanism of these enzymes. In this work, we determined two crystal structures: those of the TK2285 protein complexed with the substrates (ATP analogue and myo-inositol) or the reaction products formed by the enzyme. Analysis of the ternary substrates-complex structure and site-directed mutagenesis showed that five residues were involved in the interaction with myo-inositol. Structural comparison with other ribokinase family enzymes indicated that two of the five residues, Q136 and R140, are characteristic of myo-inositol kinase. The crystal structure of the ternary products-complex, which was prepared by incubating the TK2285 protein with myo-inositol and ATP, holds 1d-myo-inositol 3-phosphate (Ins(3)P) in the active site. NMR and HPLC analyses with a chiral column also indicated that the TK2285 reaction product was Ins(3)P. The results obtained here showed that the TK2285 protein specifically catalyzes the phosphorylation of the 3-OH of myo-inositol. We thus designated TK2285 as myo-inositol 3-kinase (MI3K). The precise identification of the reaction product should provide a sound basis to further explore inositol metabolism in Archaea.
Crystal Structure and Product Analysis of an Archaeal myo-Inositol Kinase Reveal Substrate Recognition Mode and 3-OH Phosphorylation.,Nagata R, Fujihashi M, Sato T, Atomi H, Miki K Biochemistry. 2015 May 29. PMID:25972008[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Nagata R, Fujihashi M, Sato T, Atomi H, Miki K. Crystal Structure and Product Analysis of an Archaeal myo-Inositol Kinase Reveal Substrate Recognition Mode and 3-OH Phosphorylation. Biochemistry. 2015 May 29. PMID:25972008 doi:http://dx.doi.org/10.1021/acs.biochem.5b00296
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