4ITN

Crystal structure of "compact P-loop" LpxK from Aquifex aeolicus in complex with chloride at 2.2 angstrom resolution

Summary for 4ITN

• Entry DOI: 10.2210/pdb4itn/pdb
• Related: 4EHW 4EHX 4EHY
• Descriptor: Tetraacyldisaccharide 4'-kinase, GLYCEROL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... (5 entities in total)
• Functional Keywords: membrane protein, kinase, lipid a, p-loop, p-loop containing nucleoside triphosphate hydrolase, disaccharide-1-phosphate 4'-kinase, membrane, transferase, lipid metabolism, tetraacyldisaccharide 4'-kinase
• Biological source: Aquifex aeolicus
• Total number of polymer chains: 1
• Total formula weight: 37239.86

Authors

Emptage, R.P.,Pemble IV, C.W.,York, J.D.,Raetz, C.R.H.,Zhou, P. (deposition date: 2013-01-18, release date: 2013-04-03, Last modification date: 2023-09-20)

Primary citation

Emptage, R.P.,Pemble, C.W.,York, J.D.,Raetz, C.R.,Zhou, P.
Mechanistic Characterization of the Tetraacyldisaccharide-1-phosphate 4'-Kinase LpxK Involved in Lipid A Biosynthesis.
Biochemistry, 52:2280-2290, 2013

PubMed Abstract: 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.

PubMed: 23464738
DOI: 10.1021/bi400097z

Experimental method

X-RAY DIFFRACTION (2.1912 Å)