8DMM

Structure of the vanadate-trapped MsbA bound to KDL

Summary for 8DMM

• Entry DOI: 10.2210/pdb8dmm/pdb
• Related: 8DHY
• EMDB information: 27544 27545
• Descriptor: ATP-binding transport protein MsbA, ADP ORTHOVANADATE, (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid (3 entities in total)
• Functional Keywords: abc transporter, transport protein
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 134652.69

Authors

Liu, C.,Lyu, J.,Laganowsky, A.D.,Zhao, M. (deposition date: 2022-07-08, release date: 2022-12-14, Last modification date: 2024-06-12)

Primary citation

Lyu, J.,Liu, C.,Zhang, T.,Schrecke, S.,Elam, N.P.,Packianathan, C.,Hochberg, G.K.A.,Russell, D.,Zhao, M.,Laganowsky, A.
Structural basis for lipid and copper regulation of the ABC transporter MsbA.
Nat Commun, 13:7291-7291, 2022

PubMed Abstract: A critical step in lipopolysaccharide (LPS) biogenesis involves flipping lipooligosaccharide, an LPS precursor, from the cytoplasmic to the periplasmic leaflet of the inner membrane, an operation carried out by the ATP-binding cassette transporter MsbA. Although LPS binding to the inner cavity of MsbA is well established, the selectivity of MsbA-lipid interactions at other site(s) remains poorly understood. Here we use native mass spectrometry (MS) to characterize MsbA-lipid interactions and guide structural studies. We show the transporter co-purifies with copper(II) and metal binding modulates protein-lipid interactions. A 2.15 Å resolution structure of an N-terminal region of MsbA in complex with copper(II) is presented, revealing a structure reminiscent of the GHK peptide, a high-affinity copper(II) chelator. Our results demonstrate conformation-dependent lipid binding affinities, particularly for the LPS-precursor, 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)-lipid A (KDL). We report a 3.6 Å-resolution structure of MsbA trapped in an open, outward-facing conformation with adenosine 5'-diphosphate and vanadate, revealing a distinct KDL binding site, wherein the lipid forms extensive interactions with the transporter. Additional studies provide evidence that the exterior KDL binding site is conserved and a positive allosteric modulator of ATPase activity, serving as a feedforward activation mechanism to couple transporter activity with LPS biosynthesis.

PubMed: 36435815
DOI: 10.1038/s41467-022-34905-2

Experimental method

ELECTRON MICROSCOPY (3.47 Å)