Editing ABC transporter (section)

=== 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/>