|
|
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal structure of "apo" form LpxK from Aquifex aeolicus in complex with ATP at 2.2 angstrom resolution== | | ==Crystal structure of "apo" form LpxK from Aquifex aeolicus in complex with ATP at 2.2 angstrom resolution== |
| - | <StructureSection load='4itm' size='340' side='right' caption='[[4itm]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='4itm' size='340' side='right'caption='[[4itm]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4itm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquae Aquae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ITM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ITM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4itm]] 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=4ITM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ITM FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4itm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4itm OCA], [https://pdbe.org/4itm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4itm RCSB], [https://www.ebi.ac.uk/pdbsum/4itm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4itm ProSAT]</span></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 AQUAE])</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=4itm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4itm OCA], [http://pdbe.org/4itm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4itm RCSB], [http://www.ebi.ac.uk/pdbsum/4itm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4itm ProSAT]</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 == |
| Line 25: |
Line 22: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aquae]] | + | [[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]]
| + | |
| - | [[Category: Ipid metabolism]]
| + | |
| - | [[Category: Kinase]]
| + | |
| - | [[Category: Lipid some]]
| + | |
| - | [[Category: Membrane]]
| + | |
| - | [[Category: Membrane protein]]
| + | |
| - | [[Category: P-loop]]
| + | |
| - | [[Category: P-loop containing nucleoside triphosphate hydrolase]]
| + | |
| - | [[Category: Transferase]]
| + | |
| 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
|
