Editing ABC transporter (section)

== Structure ==
[[Image:btucd.jpg|thumb|Structure of an ABC importer: BtuCD with binding protein ({{PDB|2qi9}})]]
[[Image:Abc-sav.jpg|thumb|Structure of an ABC exporter: Sav1866 with bound nucleotide ({{PDB|2onj}})]]

All ABC transport proteins share a structural organization consisting of four core domains.<ref>{{cite journal | vauthors = Shuman HA | year = 1982 | title = Active transport of maltose in Escherichia coli K12. Role of the periplasmic maltose-binding protein and evidence for a substrate recognition site in the cytoplasmic membrane | journal = J. Biol. Chem. | volume = 257 | issue = 10| pages = 5455–61 | doi = 10.1016/S0021-9258(19)83799-7 |pmid=7040366  | doi-access = free }}</ref>  These domains consist of two trans-membrane (T) domains and two cytosolic (A) domains.  The two T domains alternate between an inward and outward facing orientation, and the alternation is powered by the hydrolysis of adenosine triphosphate or [[Adenosine triphosphate|ATP]]. ATP binds to the A subunits and it is then hydrolyzed to power the alternation, but the exact process by which this happens is not known.   The four domains can be present in four separate [[polypeptides]], which occur mostly in bacteria, or present in one or two multi-domain [[polypeptides]].<ref name="Lodish_2012"/> When the polypeptides are one domain, they can be referred to as a full domain, and when they are two multi-domains they can be referred to as a half domain.<ref name="Dean_2001"/>  The T domains are each built of typically 10 membrane spanning alpha helices, through which the transported substance can cross through the [[plasma membrane]].  Also, the structure of the T domains determines the specificity of each ABC protein.  In the inward facing conformation, the binding site on the A domain is open directly to the surrounding aqueous solutions.  This allows hydrophilic molecules to enter the binding site directly from the inner leaflet of the [[phospholipid bilayer]].  In addition, a gap in the protein is accessible directly from the hydrophobic core of the inner leaflet of the membrane bilayer.  This allows hydrophobic molecules to enter the binding site directly from the inner leaflet of the [[phospholipid bilayer]].  After the ATP powered move to the outward facing conformation, molecules are released from the binding site and allowed to escape into the exoplasmic leaflet or directly into the [[extracellular medium]].<ref name="Lodish_2012"/>

The common feature of all ABC transporters is that they consist of two distinct domains, the ''transmembrane domain (TMD)'' and the ''[[ATP-binding domain of ABC transporters|nucleotide-binding domain (NBD)]]''. The TMD, also known as membrane-spanning domain (MSD) or integral membrane (IM) domain, consists of [[alpha helices]], embedded in the membrane bilayer. It recognizes a variety of substrates and undergoes conformational changes to transport the substrate across the membrane. The sequence and architecture of TMDs is variable, reflecting the chemical diversity of substrates that can be translocated. The NBD or ATP-binding cassette (ABC) domain, on the other hand, is located in the cytoplasm and has a highly conserved sequence. The NBD is the site for ATP binding.<ref name=rees>{{cite journal | vauthors = Rees DC, Johnson E, Lewinson O | title = ABC transporters: the power to change | journal = Nature Reviews Molecular Cell Biology | volume = 10 | issue = 3 | pages = 218–27 | date = Mar 2009 | pmid = 19234479 | pmc = 2830722 | doi = 10.1038/nrm2646 }}</ref> In most exporters, the [[N-terminal]] transmembrane domain and the C-terminal ABC domains are fused as a single polypeptide chain, arranged as TMD-NBD-TMD-NBD. An example is the ''E. coli'' hemolysin exporter HlyB. Importers have an inverted organization, that is, NBD-TMD-NBD-TMD, where the ABC domain is N-terminal whereas the TMD is C-terminal, such as in the ''E. coli'' MacB protein responsible for [[macrolide]] resistance.<ref name=davidson/><ref name=goffeau/>

The structural architecture of ABC transporters consists minimally of two TMDs and two NBDs. Four individual polypeptide chains including two TMD and two NBD subunits, may combine to form a ''full transporter'' such as in the ''E. coli'' BtuCD<ref name=btucd>{{cite journal | vauthors = Locher KP, Lee AT, Rees DC | title = The E. coli BtuCD structure: a framework for ABC transporter architecture and mechanism | journal = Science | volume = 296 | issue = 5570 | pages = 1091–8 | date = May 2002 | pmid = 12004122 | doi = 10.1126/science.1071142 | url = https://authors.library.caltech.edu/51806/7/suppdata.pdf | bibcode = 2002Sci...296.1091L | s2cid = 906489 }}</ref><ref>{{cite journal | vauthors = Hvorup RN, Goetz BA, Niederer M, Hollenstein K, Perozo E, Locher KP | title = Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF | journal = Science | volume = 317 | issue = 5843 | pages = 1387–90 | date = Sep 2007 | pmid = 17673622 | doi = 10.1126/science.1145950 | bibcode = 2007Sci...317.1387H | s2cid = 37232959 }}</ref> importer involved in the uptake of [[vitamin B12|vitamin B<sub>12</sub>]]. Most exporters, such as in the multidrug exporter Sav1866<ref name=sav1866>{{cite journal | vauthors = Dawson RJ, Locher KP | title = Structure of a bacterial multidrug ABC transporter | journal = Nature | volume = 443 | issue = 7108 | pages = 180–5 | date = Sep 2006 | pmid = 16943773 | doi = 10.1038/nature05155 | bibcode = 2006Natur.443..180D | s2cid = 27132450 }}</ref> from ''Staphylococcus aureus'', are made up of a [[homodimer]] consisting of two ''half transporters'' or [[monomers]] of a TMD fused to a nucleotide-binding domain (NBD). A full transporter is often required to gain functionality. Some ABC transporters have additional elements that contribute to the regulatory function of this class of proteins. In particular, importers have a high-affinity ''binding protein (BP)'' that specifically associates with the substrate in the periplasm for delivery to the appropriate ABC transporter. Exporters do not have the binding protein but have an ''intracellular domain (ICD)'' that joins the membrane-spanning helices and the ABC domain. The ICD is believed to be responsible for communication between the TMD and NBD.<ref name=rees/>

=== Transmembrane domain (TMD) ===
Most transporters have transmembrane domains that consist of a total of 12 α-helices with 6 α-helices per monomer. Since TMDs are structurally diverse, some transporters have varying number of helices (between six and eleven). The TM domains are categorized into three distinct sets of folds: ''type I ABC importer'', ''type II ABC importer'' and ''ABC exporter'' folds. The classification of importer folds is based on detailed characterization of the sequences.<ref name=rees/>

The type I ABC importer fold was originally observed in the ModB TM subunit of the [[molybdate]] transporter.<ref name=modb>{{cite journal | vauthors = Hollenstein K, Frei DC, Locher KP | title = Structure of an ABC transporter in complex with its binding protein | journal = Nature | volume = 446 | issue = 7132 | pages = 213–6 | date = Mar 2007 | pmid = 17322901 | doi = 10.1038/nature05626 | bibcode = 2007Natur.446..213H | s2cid = 4417002 }}</ref> This diagnostic fold can also be found in the MalF and MalG TM subunits of MalFGK<sub>2</sub><ref name=malkoldham>{{cite journal | vauthors = Oldham ML, Khare D, Quiocho FA, Davidson AL, Chen J | title = Crystal structure of a catalytic intermediate of the maltose transporter | journal = Nature | volume = 450 | issue = 7169 | pages = 515–21 | date = Nov 2007 | pmid = 18033289 | doi = 10.1038/nature06264 | bibcode = 2007Natur.450..515O | s2cid = 4384771 }}</ref> and the Met transporter MetI.<ref name="pmid18621668">{{cite journal | vauthors = Kadaba NS, Kaiser JT, Johnson E, Lee A, Rees DC | title = The high-affinity E. coli methionine ABC transporter: structure and allosteric regulation | journal = Science | volume = 321 | issue = 5886 | pages = 250–3 | date = Jul 2008 | pmid = 18621668 | pmc = 2527972 | doi = 10.1126/science.1157987 | bibcode = 2008Sci...321..250K }}</ref> In the MetI transporter, a minimal set of 5 transmembrane helices constitute this fold while an additional helix is present for both ModB and MalG. The common organization of the fold is the "up-down" topology of the TM2-5 helices that lines the translocation pathway and the TM1 helix wrapped around the outer, membrane-facing surface and contacts the other TM helices.

The type II ABC importer fold is observed in the twenty TM helix-domain of BtuCD<ref name=btucd/> and in Hi1471,<ref name=hi1471>{{cite journal | vauthors = Pinkett HW, Lee AT, Lum P, Locher KP, Rees DC | title = An inward-facing conformation of a putative metal-chelate-type ABC transporter | journal = Science | volume = 315 | issue = 5810 | pages = 373–7 | date = Jan 2007 | pmid = 17158291 | doi = 10.1126/science.1133488 | s2cid = 10531462 | url = https://authors.library.caltech.edu/51627/7/Pinkett-SOM.pdf }}</ref> a homologous transporter from ''Haemophilus influenzae''. In BtuCD, the packing of the helices is complex. The noticeable pattern is that the TM2 helix is positioned through the center of the subunit where it is surrounded in close proximity by the other helices. Meanwhile, the TM5 and TM10 helices are positioned in the TMD interface. The membrane spanning region of ABC exporters is organized into two "wings" that are composed of helices TM1 and TM2 from one subunit and TM3-6 of the other, in a domain-swapped arrangement. A prominent pattern is that helices TM1-3 are related to TM4-6 by an approximate twofold rotation around an axis in the plane of the membrane.<ref name=rees/>

The exporter fold is originally observed in the Sav1866 structure. It contains 12 TM helices, 6 per monomer.<ref name=rees/>

=== Nucleotide-binding domain (NBD) ===
[[Image:Abc domain.jpg|thumb|left|Structure of the NBD of ABC transporters with bound nucleotide ({{PDB|2onj}}). Linear representation of protein sequence above shows the relative positions of the conserved amino acid motifs in the structure (colors match with 3D structure)]]

The ABC domain consists of two domains, the ''catalytic core domain'' similar to [[RecA]]-like motor [[ATPases]] and a smaller, structurally diverse ''α-helical subdomain'' that is unique to ABC transporters. The larger domain typically consists of two β-sheets and six α helices, where the catalytic ''[[Walker motifs|Walker A motif]]'' (GXXGXGKS/T where X is any amino acid) or ''P-loop'' and ''Walker B motif'' (ΦΦΦΦD, of which Φ is a hydrophobic residue) is situated. The helical domain consists of three or four helices and the ''ABC signature motif'', also known as ''LSGGQ motif'', linker peptide or C motif. The ABC domain also has a glutamine residue residing in a flexible loop called ''Q loop'', lid or γ-phosphate switch, that connects the TMD and ABC. The Q loop is presumed to be involved in the interaction of the NBD and TMD, particularly in the coupling of nucleotide [[hydrolysis]] to the conformational changes of the TMD during substrate translocation. The ''H motif'' or switch region contains a highly conserved [[histidine]] residue that is also important in the interaction of the ABC domain with ATP. The name ATP-binding cassette is derived from the diagnostic arrangement of the folds or motifs of this class of proteins upon formation of the ATP sandwich and ATP hydrolysis.<ref name=davidson/><ref name=davidsonchen/><ref name=rees/>

=== ATP binding and hydrolysis ===
Dimer formation of the two ABC domains of transporters requires ATP binding.<ref name=moody>{{cite journal | vauthors = Moody JE, Millen L, Binns D, Hunt JF, Thomas PJ | title = Cooperative, ATP-dependent association of the nucleotide binding cassettes during the catalytic cycle of ATP-binding cassette transporters | journal = The Journal of Biological Chemistry | volume = 277 | issue = 24 | pages = 21111–4 | date = Jun 2002 | pmid = 11964392 | pmc = 3516282 | doi = 10.1074/jbc.C200228200 | doi-access = free }}</ref> It is generally observed that the ATP bound state is associated with the most extensive interface between ABC domains, whereas the structures of nucleotide-free transporters exhibit conformations with greater separations between the ABC domains.<ref name=rees/> Structures of the ATP-bound state of isolated NBDs have been reported for importers including HisP,<ref name="pmid9872322">{{cite journal | vauthors = Hung LW, Wang IX, Nikaido K, Liu PQ, Ames GF, Kim SH | title = Crystal structure of the ATP-binding subunit of an ABC transporter | journal = Nature | volume = 396 | issue = 6712 | pages = 703–7 | date = Dec 1998 | pmid = 9872322 | doi = 10.1038/25393 | bibcode = 1998Natur.396..703H | s2cid = 204996524 }}</ref> GlcV,<ref name=verdon>{{cite journal | vauthors = Verdon G, Albers SV, Dijkstra BW, Driessen AJ, Thunnissen AM | title = Crystal structures of the ATPase subunit of the glucose ABC transporter from Sulfolobus solfataricus: nucleotide-free and nucleotide-bound conformations | journal = Journal of Molecular Biology | volume = 330 | issue = 2 | pages = 343–58 | date = Jul 2003 | pmid = 12823973 | doi = 10.1016/S0022-2836(03)00575-8 }}</ref> MJ1267,<ref name=mj1267>{{cite journal | vauthors = Karpowich N, Martsinkevich O, Millen L, Yuan YR, Dai PL, MacVey K, Thomas PJ, Hunt JF | title = Crystal structures of the MJ1267 ATP binding cassette reveal an induced-fit effect at the ATPase active site of an ABC transporter | journal = Structure | volume = 9 | issue = 7 | pages = 571–86 | date = Jul 2001 | pmid = 11470432 | doi = 10.1016/S0969-2126(01)00617-7 | doi-access = free }}</ref> ''E. coli'' MalK (E.c.MalK),<ref name=malkchen>{{cite journal | vauthors = Chen J, Lu G, Lin J, Davidson AL, Quiocho FA | title = A tweezers-like motion of the ATP-binding cassette dimer in an ABC transport cycle | journal = Molecular Cell | volume = 12 | issue = 3 | pages = 651–61 | date = Sep 2003 | pmid = 14527411 | doi = 10.1016/j.molcel.2003.08.004 | doi-access = free }}</ref> ''T. litoralis'' MalK (TlMalK),<ref name=malkdiederichs>{{cite journal | vauthors = Diederichs K, Diez J, Greller G, Müller C, Breed J, Schnell C, Vonrhein C, Boos W, Welte W | title = Crystal structure of MalK, the ATPase subunit of the trehalose/maltose ABC transporter of the archaeon Thermococcus litoralis | journal = The EMBO Journal | volume = 19 | issue = 22 | pages = 5951–61 | date = Nov 2000 | pmid = 11080142 | pmc = 305842 | doi = 10.1093/emboj/19.22.5951 }}</ref> and exporters such as TAP,<ref name=gaudet>{{cite journal | vauthors = Gaudet R, Wiley DC | title = Structure of the ABC ATPase domain of human TAP1, the transporter associated with antigen processing | journal = The EMBO Journal | volume = 20 | issue = 17 | pages = 4964–72 | date = Sep 2001 | pmid = 11532960 | pmc = 125601 | doi = 10.1093/emboj/20.17.4964 }}</ref> HlyB,<ref name="pmid12823972">{{cite journal | vauthors = Schmitt L, Benabdelhak H, Blight MA, Holland IB, Stubbs MT | title = Crystal structure of the nucleotide-binding domain of the ABC-transporter haemolysin B: identification of a variable region within ABC helical domains | journal = Journal of Molecular Biology | volume = 330 | issue = 2 | pages = 333–42 | date = Jul 2003 | pmid = 12823972 | doi = 10.1016/S0022-2836(03)00592-8 }}</ref> MJ0796,<ref name=mj0796yuan>{{cite journal | vauthors = Yuan YR, Blecker S, Martsinkevich O, Millen L, Thomas PJ, Hunt JF | title = The crystal structure of the MJ0796 ATP-binding cassette. Implications for the structural consequences of ATP hydrolysis in the active site of an ABC transporter | journal = The Journal of Biological Chemistry | volume = 276 | issue = 34 | pages = 32313–21 | date = Aug 2001 | pmid = 11402022 | doi = 10.1074/jbc.M100758200 | doi-access = free }}</ref><ref name=mj0796smith>{{cite journal | vauthors = Smith PC, Karpowich N, Millen L, Moody JE, Rosen J, Thomas PJ, Hunt JF | title = ATP binding to the motor domain from an ABC transporter drives formation of a nucleotide sandwich dimer | journal = Molecular Cell | volume = 10 | issue = 1 | pages = 139–49 | date = Jul 2002 | pmid = 12150914 | pmc = 3516284 | doi = 10.1016/S1097-2765(02)00576-2 }}</ref> Sav1866,<ref name=sav1866/> and MsbA.<ref name=msbaward>{{cite journal | vauthors = Ward A, Reyes CL, Yu J, Roth CB, Chang G | title = Flexibility in the ABC transporter MsbA: Alternating access with a twist | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 48 | pages = 19005–10 | date = Nov 2007 | pmid = 18024585 | pmc = 2141898 | doi = 10.1073/pnas.0709388104 | bibcode = 2007PNAS..10419005W | doi-access = free }}</ref> In these transporters, ATP is bound to the ABC domain. Two molecules of ATP are positioned at the interface of the dimer, sandwiched between the Walker A motif of one subunit and the LSGGQ motif of the other.<ref name=rees/> This was first observed in Rad50<ref name=hopfner>{{cite journal | vauthors = Hopfner KP, Karcher A, Shin DS, Craig L, Arthur LM, Carney JP, Tainer JA | title = Structural biology of Rad50 ATPase: ATP-driven conformational control in DNA double-strand break repair and the ABC-ATPase superfamily | journal = Cell | volume = 101 | issue = 7 | pages = 789–800 | date = Jun 2000 | pmid = 10892749 | doi = 10.1016/S0092-8674(00)80890-9 | s2cid = 18850076 | doi-access = free }}</ref> and reported in structures of MJ0796, the NBD subunit of the LolD transporter from ''Methanococcus jannaschii''<ref name=mj0796smith/> and E.c.MalK of a maltose transporter.<ref name=malkchen/> These structures were also consistent with results from biochemical studies revealing that ATP is in close contact with residues in the P-loop and LSGGQ motif during [[catalysis]].<ref name="pmid12093921">{{cite journal | vauthors = Fetsch EE, Davidson AL | title = Vanadate-catalyzed photocleavage of the signature motif of an ATP-binding cassette (ABC) transporter | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 99 | issue = 15 | pages = 9685–90 | date = Jul 2002 | pmid = 12093921 | pmc = 124977 | doi = 10.1073/pnas.152204499 | doi-access = free }}</ref>

Nucleotide binding is required to ensure the electrostatic and/or structural integrity of the active site and contribute to the formation of an active NBD dimer.<ref name=msbareyes2006>{{cite journal | vauthors = Reyes CL, Ward A, Yu J, Chang G | title = The structures of MsbA: Insight into ABC transporter-mediated multidrug efflux | journal = FEBS Letters | volume = 580 | issue = 4 | pages = 1042–8 | date = Feb 2006 | pmid = 16337944 | doi = 10.1016/j.febslet.2005.11.033 | bibcode = 2006FEBSL.580.1042R | s2cid = 34114828 }}</ref> Binding of ATP is stabilized by the following interactions: (1) ring-stacking interaction of a conserved aromatic residue preceding the Walker A motif and the adenosine ring of ATP,<ref>{{cite journal | vauthors = Ambudkar SV, Kim IW, Xia D, Sauna ZE | title = The A-loop, a novel conserved aromatic acid subdomain upstream of the Walker A motif in ABC transporters, is critical for ATP binding | journal = FEBS Letters | volume = 580 | issue = 4 | pages = 1049–55 | date = Feb 2006 | pmid = 16412422 | doi = 10.1016/j.febslet.2005.12.051 | s2cid = 20550226 | doi-access = free | bibcode = 2006FEBSL.580.1049A }}</ref><ref name=geourjon>{{cite journal | vauthors = Geourjon C, Orelle C, Steinfels E, Blanchet C, Deléage G, Di Pietro A, Jault JM | title = A common mechanism for ATP hydrolysis in ABC transporter and helicase superfamilies | journal = Trends in Biochemical Sciences | volume = 26 | issue = 9 | pages = 539–44 | date = Sep 2001 | pmid = 11551790 | doi = 10.1016/S0968-0004(01)01907-7 }}</ref> (2) hydrogen-bonds between a conserved [[lysine]] residue in the Walker A motif and the oxygen atoms of the β- and γ-phosphates of ATP and coordination of these phosphates and some residues in the Walker A motif with Mg<sup>2+</sup> ion,<ref name=verdon/><ref name=gaudet/> and (3) γ-phosphate coordination with side chain of [[serine]] and backbone [[amide]] groups of [[glycine]] residues in the LSGGQ motif.<ref name="pmid15511523">{{cite journal | vauthors = Ye J, Osborne AR, Groll M, Rapoport TA | title = RecA-like motor ATPases--lessons from structures | journal = Biochimica et Biophysica Acta (BBA) - Bioenergetics | volume = 1659 | issue = 1 | pages = 1–18 | date = Nov 2004 | pmid = 15511523 | doi = 10.1016/j.bbabio.2004.06.003 | doi-access = free }}</ref> In addition, a residue that suggests the tight coupling of ATP binding and dimerization, is the conserved histidine in the H-loop. This histidine contacts residues across the dimer interface in the Walker A motif and the D loop, a conserved sequence following the Walker B motif.<ref name=malkchen/><ref name=mj0796smith/><ref name=hopfner/><ref name=zaitseva>{{cite journal | vauthors = Zaitseva J, Jenewein S, Jumpertz T, Holland IB, Schmitt L | title = H662 is the linchpin of ATP hydrolysis in the nucleotide-binding domain of the ABC transporter HlyB | journal = The EMBO Journal | volume = 24 | issue = 11 | pages = 1901–10 | date = Jun 2005 | pmid = 15889153 | pmc = 1142601 | doi = 10.1038/sj.emboj.7600657 }}</ref>

The enzymatic hydrolysis of ATP requires proper binding of the phosphates and positioning of the γ-phosphate to the attacking water.<ref name=rees/> In the nucleotide binding site, the oxygen atoms of the β- and γ-phosphates of ATP are stabilized by residues in the Walker A motif<ref name="pmid8710841">{{cite journal | vauthors = Maegley KA, Admiraal SJ, Herschlag D | title = Ras-catalyzed hydrolysis of GTP: a new perspective from model studies | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 93 | issue = 16 | pages = 8160–6 | date = Aug 1996 | pmid = 8710841 | pmc = 38640 | doi = 10.1073/pnas.93.16.8160 | bibcode = 1996PNAS...93.8160M | doi-access = free }}</ref><ref name="pmid9562560">{{cite journal | vauthors = Matte A, Tari LW, Delbaere LT | title = How do kinases transfer phosphoryl groups? | journal = Structure | volume = 6 | issue = 4 | pages = 413–9 | date = Apr 1998 | pmid = 9562560 | doi = 10.1016/S0969-2126(98)00043-4 | doi-access = free }}</ref> and coordinate with Mg<sup>2+</sup>.<ref name=rees/> This Mg<sup>2+</sup> ion also coordinates with the terminal [[aspartate]] residue in the Walker B motif through the attacking H<sub>2</sub>O.<ref name=verdon/><ref name=mj1267/><ref name=mj0796yuan/> A general base, which may be the [[glutamate]] residue adjacent to the Walker B motif,<ref name=moody/><ref name=mj0796smith/><ref name=geourjon/> [[glutamine]] in the Q-loop,<ref name=hi1471/><ref name=malkdiederichs/><ref name=mj0796smith/> or a histidine in the switch region that forms a hydrogen bond with the γ-phosphate of ATP, is found to catalyze the rate of ATP hydrolysis by promoting the attacking H<sub>2</sub>O.<ref name=malkchen/><ref name=malkdiederichs/><ref name=mj0796smith/><ref name=zaitseva/> The precise molecular mechanism of ATP hydrolysis is still controversial.<ref name=davidson/>