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| | ==Crystal structure of "compact P-loop" LpxK from Aquifex aeolicus in complex with chloride at 2.2 angstrom resolution== | | ==Crystal structure of "compact P-loop" LpxK from Aquifex aeolicus in complex with chloride at 2.2 angstrom resolution== |
| - | <StructureSection load='4itn' size='340' side='right' caption='[[4itn]], [[Resolution|resolution]] 2.19Å' scene=''> | + | <StructureSection load='4itn' size='340' side='right'caption='[[4itn]], [[Resolution|resolution]] 2.19Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4itn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus_vf5 Aquifex aeolicus vf5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ITN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ITN FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4itn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ITN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ITN 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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.1912Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ehw|4ehw]], [[4ehx|4ehx]], [[4ehy|4ehy]]</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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lpxK, aq_1656 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 Aquifex aeolicus VF5])</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=4itn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4itn OCA], [https://pdbe.org/4itn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4itn RCSB], [https://www.ebi.ac.uk/pdbsum/4itn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4itn 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/Tetraacyldisaccharide_4'-kinase Tetraacyldisaccharide 4'-kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.130 2.7.1.130] </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=4itn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4itn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4itn RCSB], [http://www.ebi.ac.uk/pdbsum/4itn PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/LPXK_AQUAE LPXK_AQUAE]] Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA) (By similarity). | + | [https://www.uniprot.org/uniprot/LPXK_AQUAE LPXK_AQUAE] Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA) (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4itn" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aquifex aeolicus vf5]] | + | [[Category: Aquifex aeolicus VF5]] |
| - | [[Category: Tetraacyldisaccharide 4'-kinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Emptage, R P]] | + | [[Category: Emptage RP]] |
| - | [[Category: IV, C W.Pemble]] | + | [[Category: Pemble IV CW]] |
| - | [[Category: Raetz, C R.H]] | + | [[Category: Raetz CRH]] |
| - | [[Category: York, J D]] | + | [[Category: York JD]] |
| - | [[Category: Zhou, P]] | + | [[Category: Zhou P]] |
| - | [[Category: Disaccharide-1-phosphate 4'-kinase]]
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| - | [[Category: Kinase]]
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| - | [[Category: Lipid some]]
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| - | [[Category: Lipid metabolism]]
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| - | [[Category: Membrane]]
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| - | [[Category: Membrane protein]]
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| - | [[Category: P-loop]]
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| - | [[Category: P-loop containing nucleoside triphosphate hydrolase]]
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| - | [[Category: Transferase]]
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| Structural highlights
Function
LPXK_AQUAE Transfers the gamma-phosphate of ATP to the 4'-position of a tetraacyldisaccharide 1-phosphate intermediate (termed DS-1-P) to form tetraacyldisaccharide 1,4'-bis-phosphate (lipid IVA) (By similarity).
Publication Abstract from PubMed
The sixth step in the lipid A biosynthetic pathway involves phosphorylation of the tetraacyldisaccharide-1-phosphate (DSMP) intermediate by the cytosol-facing inner membrane kinase LpxK, a member of the P-loop-containing nucleoside triphosphate (NTP) hydrolase superfamily. We report the kinetic characterization of LpxK from Aquifex aeolicus and the crystal structures of LpxK in complex with ATP in a precatalytic binding state, the ATP analogue AMP-PCP in the closed catalytically competent conformation, and a chloride anion revealing an inhibitory conformation of the nucleotide-binding P-loop. We demonstrate that LpxK activity in vitro requires the presence of a detergent micelle and formation of a ternary LpxK-ATP/Mg(2+)-DSMP complex. Using steady-state kinetics, we have identified crucial active site residues, leading to the proposal that the interaction of D99 with H261 acts to increase the pKa of the imidazole moiety, which in turn serves as the catalytic base to deprotonate the 4'-hydroxyl of the DSMP substrate. The fact that an analogous mechanism has not yet been observed for other P-loop kinases highlights LpxK as a distinct member of the P-loop kinase family, a notion that is also reflected through its localization at the membrane, lipid substrate, and overall structure.
Mechanistic Characterization of the Tetraacyldisaccharide-1-phosphate 4'-Kinase LpxK Involved in Lipid A Biosynthesis.,Emptage RP, Pemble CW 4th, York JD, Raetz CR, Zhou P Biochemistry. 2013 Apr 2;52(13):2280-90. doi: 10.1021/bi400097z. Epub 2013 Mar, 19. PMID:23464738[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Emptage RP, Pemble CW 4th, York JD, Raetz CR, Zhou P. Mechanistic Characterization of the Tetraacyldisaccharide-1-phosphate 4'-Kinase LpxK Involved in Lipid A Biosynthesis. Biochemistry. 2013 Apr 2;52(13):2280-90. doi: 10.1021/bi400097z. Epub 2013 Mar, 19. PMID:23464738 doi:http://dx.doi.org/10.1021/bi400097z
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