Editing ABC transporter (section)

=== MsbA ===
MsbA (3.A.1.106.1) is a multi-drug resistant (MDR) ABC transporter and possibly a lipid [[flippase]]. It is an [[ATPase]] that transports [[lipid A]], the hydrophobic moiety of [[lipopolysaccharide]] (LPS), a glucosamine-based saccharolipid that makes up the outer monolayer of the outer membranes of most gram-negative bacteria. Lipid A is an [[endotoxin]] and so loss of MsbA from the cell membrane or [[mutations]] that disrupt transport results in the accumulation of lipid A in the inner cell membrane resulting to cell death. It is a close bacterial homolog of P-glycoprotein (Pgp) by protein sequence homology and has overlapping substrate specificities with the MDR-ABC transporter LmrA from ''Lactococcus lactis''.<ref name=msbareuter2003>{{cite journal | vauthors = Reuter G, Janvilisri T, Venter H, Shahi S, Balakrishnan L, van Veen HW | title = The ATP binding cassette multidrug transporter LmrA and lipid transporter MsbA have overlapping substrate specificities | journal = The Journal of Biological Chemistry | volume = 278 | issue = 37 | pages = 35193–8 | date = Sep 2003 | pmid = 12842882 | doi = 10.1074/jbc.M306226200 | doi-access = free }}</ref> MsbA from ''E. coli'' is 36% identical to the NH<sub>2</sub>-terminal half of human MDR1, suggesting a common mechanism for transport of amphiphatic and hydrophobic substrates. The MsbA gene encodes a half transporter that contains a transmembrane domain (TMD) fused with a nucleotide-binding domain (NBD). It is assembled as a homodimer with a total molecular mass of 129.2 kD. MsbA contains 6 TMDs on the periplasmic side, an NBD located on the cytoplasmic side of the cell membrane, and an intracellular domain (ICD), bridging the TMD and NBD. This conserved helix extending from the TMD segments into or near the active site of the NBD is largely responsible for crosstalk between TMD and NBD. In particular, ICD1 serves as a conserved pivot about which the NBD can rotate, therefore allowing the NBD to disassociate and dimerize during ATP binding and hydrolysis.<ref name=davidson/><ref name=davidsonchen/><ref name=pohl/><ref name=rees/><ref name=msbareyes2006/><ref name=oldham2008/><ref name=msbachang2003/><ref name="pmid17362200">{{cite journal | vauthors = Raetz CR, Reynolds CM, Trent MS, Bishop RE | title = Lipid A modification systems in gram-negative bacteria | journal = Annual Review of Biochemistry | volume = 76 | pages = 295–329 | year = 2007 | pmid = 17362200 | pmc = 2569861 | doi = 10.1146/annurev.biochem.76.010307.145803 }}</ref> 
[[Image:Msba.jpg|thumb|Structures of MsbA depicting the three conformational states: open apo ({{PDB|3b5w}}), closed apo ({{PDB|3b5x}}), and nucleotide-bound ({{PDB|3b60}})]]

Previously published (and now retracted) X-ray structures of MsbA were inconsistent with the bacterial homolog Sav1866.<ref name=msbachang2001>{{cite journal | vauthors = Chang G, Roth CB | title = Structure of MsbA from E. coli: a homolog of the multidrug resistance ATP binding cassette (ABC) transporters | journal = Science | volume = 293 | issue = 5536 | pages = 1793–800 | date = Sep 2001 | pmid = 11546864 | doi = 10.1126/science.293.5536.1793 | bibcode = 2001Sci...293.1793C }}{{Retracted|doi=10.1126/science.314.5807.1875b|pmid=17185584|intentional=yes}} {{Retracted paper|doi=10.1126/science.314.5807.1875b|intentional=yes}}</ref><ref name=msbareyes2005>{{cite journal | vauthors = Reyes CL, Chang G | title = Structure of the ABC transporter MsbA in complex with ADP.vanadate and lipopolysaccharide | journal = Science | volume = 308 | issue = 5724 | pages = 1028–31 | date = May 2005 | pmid = 15890884 | doi = 10.1126/science.1107733 | bibcode = 2005Sci...308.1028R | s2cid = 37250061 }}{{Retracted|doi=10.1126/science.314.5807.1875b|pmid=17185584|intentional=yes}}{{Retracted paper|doi=10.1126/science.314.5807.1875b |intentional=yes}}</ref> The structures were reexamined and found to have an error in the assignment of the hand resulting to incorrect models of MsbA. Recently, the errors have been rectified and new structures have been reported.<ref name=msbaward/> The resting state of ''E. coli'' MsbA exhibits an inverted "V" shape with a chamber accessible to the interior of the transporter suggesting an ''open, inward-facing conformation''. The dimer contacts are concentrated between the extracellular loops and while the NBDs are ≈50Å apart, the subunits are facing each other. The distance between the residues in the site of the dimer interface have been verified by [[cross-link]]ing experiments<ref name="pmid15222771">{{cite journal | vauthors = Buchaklian AH, Funk AL, Klug CS | title = Resting state conformation of the MsbA homodimer as studied by site-directed spin labeling | journal = Biochemistry | volume = 43 | issue = 26 | pages = 8600–6 | date = Jul 2004 | pmid = 15222771 | doi = 10.1021/bi0497751 }}</ref> and [[EPR spectroscopy]] studies.<ref name=dong>{{cite journal | vauthors = Dong J, Yang G, McHaourab HS | title = Structural basis of energy transduction in the transport cycle of MsbA | journal = Science | volume = 308 | issue = 5724 | pages = 1023–8 | date = May 2005 | pmid = 15890883 | doi = 10.1126/science.1106592 | bibcode = 2005Sci...308.1023D | s2cid = 1308350 }}</ref> The relatively large chamber allows it to accommodate large head groups such as that present in lipid A. Significant conformational changes are required to move the large sugar head groups across the membrane. The difference between the two nucleotide-free (apo) structures is the ≈30° pivot of TM4/TM5 helices relative to the TM3/TM6 helices. In the closed apo state (from ''V. cholerae'' MsbA), the NBDs are aligned and although closer, have not formed an ATP sandwich, and the P loops of opposing monomers are positioned next to one another. In comparison to the open conformation, the dimer interface of the TMDs in the ''closed, inward-facing conformation'' has extensive contacts. For both apo conformations of MsbA, the chamber opening is facing inward. The structure of MsbA-AMP-PNP (5'-adenylyl-β-γ-imidodiphosphate), obtained from ''S. typhimurium'', is similar to Sav1866. The NBDs in this ''nucleotide-bound, outward-facing conformation'', come together to form a canonical ATP dimer sandwich, that is, the nucleotide is situated in between the P-loop and LSGGQ motif. The conformational transition from MsbA-closed-apo to MsbA-AMP-PNP involves two steps, which are more likely concerted: a ≈10° pivot of TM4/TM5 helices towards TM3/TM6, bringing the NBDs closer but not into alignment followed by tilting of TM4/TM5 helices ≈20° out of plane. The twisting motion results in the separation of TM3/TM6 helices away from TM1/TM2 leading to a change from an inward- to an outward- facing conformation. Thus, changes in both the orientation and spacing of the NBDs dramatically rearrange the packing of transmembrane helices and effectively switch access to the chamber from the inner to the outer leaflet of the membrane.<ref name=msbaward/> The structures determined for MsbA is basis for the tilting model of transport.<ref name=pohl/> The structures described also highlight the dynamic nature of ABC exporters as also suggested by [[fluorescence]] and EPR studies.<ref name=oldham2008/><ref name=dong/><ref>{{cite journal | vauthors = Borbat PP, Surendhran K, Bortolus M, Zou P, Freed JH, Mchaourab HS | title = Conformational motion of the ABC transporter MsbA induced by ATP hydrolysis | journal = PLOS Biology | volume = 5 | issue = 10 | pages = e271 | date = Oct 2007 | pmid = 17927448 | pmc = 2001213 | doi = 10.1371/journal.pbio.0050271 | doi-access = free }}</ref> Recent work has resulted in the discovery of MsbA inhibitors.<ref>{{cite journal |last1=Zhang |first1=Ge |last2=Baidin |first2=Vadim |last3=Pahil |first3=Karanbir S. |last4=Moison |first4=Eileen |last5=Tomasek |first5=David |last6=Ramadoss |first6=Nitya S. |last7=Chatterjee |first7=Arnab K. |last8=McNamara |first8=Case W. |last9=Young |first9=Travis S. |last10=Schultz |first10=Peter G. |last11=Meredith |first11=Timothy C. |last12=Kahne |first12=Daniel |title=Cell-based screen for discovering lipopolysaccharide biogenesis inhibitors |journal=Proceedings of the National Academy of Sciences |volume=115 |issue=26 |date=7 May 2018 |pages=6834–6839 |doi=10.1073/pnas.1804670115 |pmid=29735709 |pmc=6042065 |bibcode=2018PNAS..115.6834Z |doi-access=free }}</ref><ref>{{cite journal |last1=Ho |first1=Hoangdung |last2=Miu |first2=Anh |last3=Alexander |first3=Mary Kate |last4=Garcia |first4=Natalie K. |last5=Oh |first5=Angela |last6=Zilberleyb |first6=Inna |last7=Reichelt |first7=Mike |last8=Austin |first8=Cary D. |last9=Tam |first9=Christine |last10=Shriver |first10=Stephanie |last11=Hu |first11=Huiyong |last12=Labadie |first12=Sharada S. |last13=Liang |first13=Jun |last14=Wang |first14=Lan |last15=Wang |first15=Jian |last16=Lu |first16=Yan |last17=Purkey |first17=Hans E. |last18=Quinn |first18=John |last19=Franke |first19=Yvonne |last20=Clark |first20=Kevin |last21=Beresini |first21=Maureen H. |last22=Tan |first22=Man-Wah |last23=Sellers |first23=Benjamin D. |last24=Maurer |first24=Till |last25=Koehler |first25=Michael F. T. |last26=Wecksler |first26=Aaron T. |last27=Kiefer |first27=James R. |last28=Verma |first28=Vishal |last29=Xu |first29=Yiming |last30=Nishiyama |first30=Mireille |last31=Payandeh |first31=Jian |last32=Koth |first32=Christopher M. |title=Structural basis for dual-mode inhibition of the ABC transporter MsbA |journal=Nature |date=May 2018 |volume=557 |issue=7704 |pages=196–201 |doi=10.1038/s41586-018-0083-5 |pmid=29720648 |bibcode=2018Natur.557..196H |s2cid=13660653 }}</ref>