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| | ==Crystal Structure of Isopentenyl Phosphate Kinase from M. jannaschii in complex with IPP beta-S== | | ==Crystal Structure of Isopentenyl Phosphate Kinase from M. jannaschii in complex with IPP beta-S== |
| - | <StructureSection load='3k56' size='340' side='right' caption='[[3k56]], [[Resolution|resolution]] 2.34Å' scene=''> | + | <StructureSection load='3k56' size='340' side='right'caption='[[3k56]], [[Resolution|resolution]] 2.34Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3k56]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K56 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3k56]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K56 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IS3:ISOPENTENYL+DIPHOSPHATE+BETA-S'>IS3</scene>, <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]] 2.34Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3k4o|3k4o]], [[3k4y|3k4y]], [[3k52|3k52]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IS3:ISOPENTENYL+DIPHOSPHATE+BETA-S'>IS3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MJ0044 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3k56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k56 OCA], [https://pdbe.org/3k56 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k56 RCSB], [https://www.ebi.ac.uk/pdbsum/3k56 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k56 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=3k56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k56 OCA], [http://pdbe.org/3k56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3k56 RCSB], [http://www.ebi.ac.uk/pdbsum/3k56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3k56 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/IPK_METJA IPK_METJA]] Catalyzes the formation of isopentenyl diphosphate (IPP), the building block of all isoprenoids. Has no activity with farnesyl phosphate.<ref>PMID:16621811</ref> <ref>PMID:20392112</ref> | + | [https://www.uniprot.org/uniprot/IPK_METJA IPK_METJA] Catalyzes the formation of isopentenyl diphosphate (IPP), the building block of all isoprenoids. Has no activity with farnesyl phosphate.<ref>PMID:16621811</ref> <ref>PMID:20392112</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k5/3k56_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k5/3k56_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 43067]] | + | [[Category: Large Structures]] |
| - | [[Category: Dellas, N]]
| + | |
| - | [[Category: Noel, J P]]
| + | |
| - | [[Category: Archaea]]
| + | |
| - | [[Category: Atp gamma-]]
| + | |
| - | [[Category: Atp-binding]]
| + | |
| - | [[Category: Isopentenyl diphosphate]]
| + | |
| - | [[Category: Isopentenyl monophosphate]]
| + | |
| - | [[Category: Isoprenoid biosynthesis]]
| + | |
| | [[Category: Methanocaldococcus jannaschii]] | | [[Category: Methanocaldococcus jannaschii]] |
| - | [[Category: Mevalonate pathway]] | + | [[Category: Dellas N]] |
| - | [[Category: Small molecule kinase]] | + | [[Category: Noel JP]] |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
IPK_METJA Catalyzes the formation of isopentenyl diphosphate (IPP), the building block of all isoprenoids. Has no activity with farnesyl phosphate.[1] [2]
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
The biosynthesis of isopentenyl diphosphate (IPP) from either the mevalonate (MVA) or the 1-deoxy-d-xylulose-5-phosphate (DXP) pathway provides the key metabolite for primary and secondary isoprenoid biosynthesis. Isoprenoid metabolism plays crucial roles in membrane stability, steroid biosynthesis, vitamin production, protein localization, defense and communication, photoprotection, sugar transport and glycoprotein biosynthesis. Recently, an alternative branch of the MVA pathway was discovered in the archaeon Methanocaldococcus jannaschii involving a small molecule kinase, isopentenyl phosphate kinase (IPK). IPK belongs to the amino acid kinase (AAK) superfamily. In vitro, IPK phosphorylates isopentenyl monophosphate (IP) in an ATP and Mg2+-dependent reaction producing IPP. Here, we describe crystal structures of IPK from M. jannaschii refined to nominal resolutions of 2.0-2.8 A. Notably, an active site histidine residue (His60) forms a hydrogen bond with the terminal phosphate of both substrate and product. This His residue serves as a marker for a subset of the AAK family that catalyze phosphorylation of phosphate or phosphonate functional groups; the larger family includes carboxyl-directed kinases, which lack this active site residue. Using steady-state kinetic analysis of H60A, H60N and H60Q mutants, the protonated form of the Nepsilon2 nitrogen of His60 was shown to be essential for catalysis, most likely through hydrogen bond stabilization of the transition state accompanying transphosphorylation. Moreover, the structures served as the starting point for the engineering of IPK mutants capable of the chemoenzymatic synthesis of longer chain isoprenoid diphosphates from monophosphate precursors.
Mutation of Archaeal Isopentenyl Phosphate Kinase Highlights Mechanism and Guides Phosphorylation of Additional Isoprenoid Monophosphates.,Dellas N, Noel JP ACS Chem Biol. 2010 Apr 14. PMID:20392112[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Grochowski LL, Xu H, White RH. Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate. J Bacteriol. 2006 May;188(9):3192-8. PMID:16621811 doi:http://dx.doi.org/10.1128/JB.188.9.3192-3198.2006
- ↑ Dellas N, Noel JP. Mutation of Archaeal Isopentenyl Phosphate Kinase Highlights Mechanism and Guides Phosphorylation of Additional Isoprenoid Monophosphates. ACS Chem Biol. 2010 Apr 14. PMID:20392112 doi:10.1021/cb1000313
- ↑ Dellas N, Noel JP. Mutation of Archaeal Isopentenyl Phosphate Kinase Highlights Mechanism and Guides Phosphorylation of Additional Isoprenoid Monophosphates. ACS Chem Biol. 2010 Apr 14. PMID:20392112 doi:10.1021/cb1000313
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