@text KINEMAGE 2: The Major Conformational Changes in a Subunit of PFK. KINEMAGE 2 shows those segments near the allosteric site (residues 53-60 are not shown here). As in KINEMAGE 1, the polypeptide is represented by its Ca chain with R state Subunits 1 and 2 in redtint and pink, and T state Subunits 1 and 2 in bluetint and skyblue. KINEMAGE 2 comes up in the R state showing the phosphate group of F6P (hotpink) bound in the enzyme's active site in a hydrogen bonded salt bridge (dashed white lines) with the side chain of Arg 162 (cyan). An ADP (yellow; "ADP-allo") occupies the adjacent allosteric site. Click once on "ANIMATE" to switch to the T state. This replaces the ADP in the R state allosteric site with the inhibitor and PEP analog PGC (gold). F6P no longer occupies the active site but its position in the R state is indicated by the "ghost" F6P (gray; "F6P site"). What happens to the central polypeptide helical segment (residues 149-164) in the R to T transition? What does this do to the relative positions of the negatively charged Glu 161 and the positively charged Arg 162? Click on "F6P site". What influence would the presence of the carboxylate group of Glu 161 have on the phosphate group of F6P were it to bind in the active site? Does this explain, at least in part, why T state PFK has low affinity for F6P? Go to View2 for a closeup of the F6P-sidechain interactions. The atomic coordinates for R state PFK were obtained from 4PFK; those for T state PFK were obtained from Philip Evans, MRC Laboratory of Molecular Biology, Cambridge, U. K. @kinemage 2 @caption The allosteric site of phosphofructokinase (PFK) with residues 53-60 not shown. Residues of R-state Subunits 1 and 2 are pinktint and pink, whereas T state residues of Subunits 1 and 2 are bluetint and skyblue. In the R state, active site-bound F6P is hotpink and allosteric site-bound ADP is yellow. In the T state, allosteric site-bound 2-phosphoglycolate (PGC) is gold. The T state active site, which does not contain F6P, is marked by the position of R state-bound F6P (gray; "F6P site"). The side chains of Glu 161 and Arg 162 are red and cyan. @viewid {Allosteric site} @zoom 0.95 @zslab 284 @ztran 90 @center 3.029 22.541 -15.274 @matrix -0.79351 0.45801 0.40072 0.44705 -0.00806 0.89447 0.41290 0.88890 -0.19836 @2viewid {closeup} @2zoom 2.32 @2zslab 284 @2center 8.610 11.065 -20.899 @2matrix -0.66815 0.06825 0.74090 0.72516 0.28258 0.62792 -0.16651 0.95680 -0.23830 @perspective @group {R-state} animate @subgroup {Dimer} dominant @vectorlist {ca-ca} color= pinktint { ca ile 67 } P 7.041, 21.184, -5.782 { ca leu 68 } 9.425, 23.358, -7.921 { ca tyr 69 } 8.196, 21.713, -11.147 { ca thr 70 } 10.481, 20.729, -14.002 { ca ala 71 } 10.768, 21.640, -17.657 @vectorlist {ca-ca} color= pink { ca ala 149 } P -2.412, 4.539, -10.288 { ca ile 150 } -4.102, 7.918, -10.677 { ca asp 151 } -2.531, 9.121, -7.443 { ca lys 152 } 0.867, 8.334, -8.903 { ca ile 153 } 0.103, 9.748, -12.286 { ca arg 154 } -1.062, 12.978, -10.685 { ca asp 155 } 2.378, 13.446, -9.070 { ca thr 156 } 4.252, 13.094, -12.338 { ca ala 157 } 1.607, 15.035, -14.222 { ca thr 158 } 1.725, 18.020, -11.824 { ca ser 159 } 5.538, 17.961, -11.955 { ca his 160 } 5.703, 18.445, -15.757 { ca glu 161 } 2.302, 20.172, -16.135 { ca arg 162 } 0.951, 17.473, -18.507 { ca thr 163 } -2.262, 15.807, -19.566 { ca tyr 164 } -2.811, 12.119, -18.991 { ca val 165 } -5.222, 9.769, -20.696 @vectorlist {ca-ca} color= pink { ca arg 204 } P -13.783, 22.126, -20.654 { ca leu 205 } -10.042, 21.113, -20.592 { ca lys 206 } -8.872, 24.389, -22.115 { ca arg 207 } -10.998, 26.350, -19.638 { ca gly 208 } -9.456, 24.478, -16.657 { ca his 209 } -5.955, 25.046, -17.970 { ca glu 210 } -6.582, 28.782, -18.325 { ca arg 211 } -8.035, 28.874, -14.820 { ca gly 212 } -4.551, 27.679, -13.749 { ca lys 213 } -4.686, 23.891, -13.341 { ca lys 214 } -1.230, 22.326, -13.534 { ca his 215 } -2.125, 18.806, -14.720 { ca ser 216 } -5.170, 17.286, -16.440 { ca ile 217 } -6.405, 13.643, -15.925 @subgroup {Glu} dominant @balllist {glu-O} radius = 0.3 color=red { oe1 glu 161 } 2.991, 24.866, -14.681 { oe2 glu 161 } 2.973, 24.368, -16.763 @vectorlist {sc} color= red { ca glu 161 } P 2.302, 20.172, -16.135 { cb glu 161 } 2.479, 21.651, -16.380 { cg glu 161 } 3.029, 22.541, -15.274 { cd glu 161 } 2.998, 24.021, -15.560 { oe1 glu 161 } 2.991, 24.866, -14.681 { cd glu 161 } P 2.998, 24.021, -15.560 { oe2 glu 161 } 2.973, 24.368, -16.763 @subgroup {Arg} dominant @balllist {Arg-N} radius = 0.3 color=blue { ne arg 162 } 5.308, 15.274, -19.679 { nh1 arg 162 } 6.293, 13.262, -18.963 { nh2 arg 162 } 7.354, 14.608, -20.464 @vectorlist {sc} color= cyan { ca arg 162 } P 0.951, 17.473, -18.507 { cb arg 162 } 1.826, 16.200, -18.687 { cg arg 162 } 3.303, 16.367, -18.924 { cd arg 162 } 4.016, 15.074, -19.015 { ne arg 162 } 5.308, 15.274, -19.679 { cz arg 162 } 6.316, 14.398, -19.664 { nh1 arg 162 } 6.293, 13.262, -18.963 { cz arg 162 } P 6.316, 14.398, -19.664 { nh2 arg 162 } 7.354, 14.608, -20.464 @vectorlist {H bonds} color= white { o61 F6P} P U 8.628, 12.832, -21.329 { nh2 arg 162 } L U 7.733, 14.079, -20.721 { nh1 arg 162 } P U 6.800, 12.794, -19.078 { o63 F6P} L U 7.922, 11.759, -19.333 @subgroup {ADP-allo} dominant @vectorlist {ht} color= yellow { pb ADP-allo 1} P -8.236, 18.256, -8.053 { pb ADP-allo 1} -8.236, 18.256, -8.053 { o1b ADP-allo 1} -7.491, 17.886, -6.833 { pb ADP-allo 1} P -8.236, 18.256, -8.053 { o2b ADP-allo 1} -8.299, 17.230, -9.110 { pb ADP-allo 1} P -8.236, 18.256, -8.053 { o3b ADP-allo 1} -9.553, 18.831, -7.688 { pa ADP-allo 1} P -7.758, 20.451, -10.009 { o1a ADP-allo 1} -8.626, 21.615, -9.722 { pa ADP-allo 1} P -7.758, 20.451, -10.009 { o2a ADP-allo 1} -8.437, 19.676, -11.093 { pb ADP-allo 1} P -8.236, 18.256, -8.053 { o3a ADP-allo 1} -7.520, 19.557, -8.695 { pa ADP-allo 1} P -7.758, 20.451, -10.009 { o5* ADP-allo 1} -6.284, 20.747, -10.477 { c5* ADP-allo 1} -5.266, 19.862, -11.015 { c4* ADP-allo 1} -3.943, 20.275, -10.394 { o4* ADP-allo 1} -3.781, 21.723, -10.572 { c4* ADP-allo 1} P -3.943, 20.275, -10.394 { c3* ADP-allo 1} -3.777, 20.025, -8.889 { o3* ADP-allo 1} -2.446, 19.902, -8.459 { c3* ADP-allo 1} P -3.777, 20.025, -8.889 { c2* ADP-allo 1} -4.317, 21.354, -8.315 { o2* ADP-allo 1} -3.992, 21.521, -6.952 { o4* ADP-allo 1} P -3.781, 21.723, -10.572 { c1* ADP-allo 1} -3.659, 22.346, -9.290 { n9 ADP-allo 1} -4.314, 23.659, -9.352 { c8 ADP-allo 1} -5.627, 23.876, -9.684 { n7 ADP-allo 1} -5.993, 25.142, -9.674 { c5 ADP-allo 1} P -4.845, 25.795, -9.301 { c6 ADP-allo 1} -4.614, 27.180, -9.109 { n6 ADP-allo 1} -5.563, 28.100, -9.278 { c6 ADP-allo 1} P -4.614, 27.180, -9.109 { n1 ADP-allo 1} -3.359, 27.517, -8.732 { c2 ADP-allo 1} -2.415, 26.525, -8.574 { n3 ADP-allo 1} -2.533, 25.237, -8.724 { n9 ADP-allo 1} P -4.314, 23.659, -9.352 { c4 ADP-allo 1} -3.800, 24.913, -9.096 { pa ADP-allo 1} P -7.758, 20.451, -10.009 { o3a ADP-allo 1} -7.520, 19.557, -8.695 { c2* ADP-allo 1} P -4.317, 21.354, -8.315 { c1* ADP-allo 1} -3.659, 22.346, -9.290 { n7 ADP-allo 1} P -5.993, 25.142, -9.674 { c5 ADP-allo 1} -4.845, 25.795, -9.301 { c4 ADP-allo 1} -3.800, 24.913, -9.096 { n3 ADP-allo 1} P -2.533, 25.237, -8.724 { c4 ADP-allo 1} -3.800, 24.913, -9.096 @balllist color= yellow radius= 0.2 {Mg ADP-allo 1} -8.936, 17.383, -10.956 @subgroup {F6P} dominant @balllist {} radius=0.3 color=red { o1 F6P 1} P 13.626, 9.201, -16.841 { o2 F6P 1} 10.391, 7.537, -17.045 { o3 F6P 1} 12.364, 5.618, -17.960 { o4 F6P 1} 11.951, 6.378, -20.896 { o5 F6P 1} 11.283, 9.091, -18.590 { o6 F6P 1} 9.864, 10.053, -21.018 { o61 F6P 1} 9.007, 12.303, -21.586 { o62 F6P 1} 7.448, 10.426, -21.553 { o63 F6P 1} 8.429, 11.291, -19.448 @balllist {} radius=0.3 color=gold { p6 F6P 1} P 8.610, 11.065, -20.899 @vectorlist {ht} color= hotpink { o1 F6P 1} P 13.626, 9.201, -16.841 { o1 F6P 1} 13.626, 9.201, -16.841 { c1 F6P 1} 12.362, 8.703, -16.439 { c2 F6P 1} 11.618, 8.043, -17.622 { o2 F6P 1} 10.391, 7.537, -17.045 { c2 F6P 1} P 11.618, 8.043, -17.622 { c3 F6P 1} 12.298, 6.949, -18.475 { o3 F6P 1} 12.364, 5.618, -17.960 { c3 F6P 1} P 12.298, 6.949, -18.475 { c4 F6P 1} 11.382, 6.919, -19.704 { o4 F6P 1} 11.951, 6.378, -20.896 { c4 F6P 1} P 11.382, 6.919, -19.704 { c5 F6P 1} 11.131, 8.424, -19.887 { c2 F6P 1} P 11.618, 8.043, -17.622 { o5 F6P 1} 11.283, 9.091, -18.590 { c5 F6P 1} P 11.131, 8.424, -19.887 { c6 F6P 1} 9.752, 8.729, -20.473 { o6 F6P 1} 9.864, 10.053, -21.018 { p6 F6P 1} 8.610, 11.065, -20.899 { o61 F6P 1} 9.007, 12.303, -21.586 { p6 F6P 1} P 8.610, 11.065, -20.899 { o62 F6P 1} 7.448, 10.426, -21.553 { p6 F6P 1} P 8.610, 11.065, -20.899 { o63 F6P 1} 8.429, 11.291, -19.448 { c5 F6P 1} P 11.131, 8.424, -19.887 { o5 F6P 1} 11.283, 9.091, -18.590 @subgroup {R labels} nobutton off master= {Labels} @labellist {Glu 161} color= red nobutton { Glu 161 } 2.973, 24.368, -16.763 @labellist {Arg 162} color= cyan nobutton { Arg 162 } 7.354, 14.608, -20.440 @labellist {F6P} color= hotpink nobutton { F6P} 10.391, 7.537, -17.045 @labellist {R site} color= yellow nobutton { ADP-allo} -2.415, 26.525, -8.574 @group {T-state} animate @subgroup {Dimer} dominant @vectorlist {ca-ca} color= bluetint { ca ile a 67 } P 7.047, 21.460, -4.432 { ca leu a 68 } 9.332, 23.778, -6.435 { ca tyr a 69 } 8.244, 22.182, -9.711 { ca thr a 70 } 10.494, 21.309, -12.617 { ca ala a 71 } 10.393, 22.783, -16.101 @vectorlist {ca-ca} color= sky { ca ala b 149 } P -2.119, 4.413, -9.985 { ca ile b 150 } -3.939, 7.744, -10.542 { ca asp b 151 } -2.617, 9.105, -7.296 { ca lys b 152 } 0.927, 8.103, -8.414 { ca ile b 153 } 0.472, 10.096, -11.737 { ca arg b 154 } -0.985, 13.004, -9.687 { ca asp b 155 } 2.550, 13.614, -8.171 { ca thr b 156 } 4.297, 14.117, -11.618 { ca ala b 157 } 4.719, 17.983, -11.251 { ca thr b 158 } 6.055, 18.926, -14.759 { ca ser b 159 } 3.896, 21.395, -16.805 { ca his b 160 } 5.121, 19.885, -20.140 { ca glu b 161 } 3.606, 16.591, -19.196 { ca arg b 162 } 0.126, 17.255, -17.838 { ca thr b 163 } -2.037, 14.927, -20.010 { ca tyr b 164 } -2.471, 11.394, -18.837 { ca val b 165 } -4.705, 8.778, -20.295 @vectorlist {ca-ca} color= sky { ca arg b 204 } P -12.360, 20.720, -21.753 { ca leu b 205 } -8.615, 19.998, -21.842 { ca lys b 206 } -8.013, 23.404, -23.417 { ca arg b 207 } -10.246, 25.057, -20.791 { ca gly b 208 } -8.614, 23.239, -17.811 { ca his b 209 } -5.231, 24.199, -19.222 { ca glu b 210 } -6.298, 27.878, -19.483 { ca arg b 211 } -7.146, 28.085, -15.821 { ca gly b 212 } -3.880, 26.423, -14.976 { ca lys b 213 } -5.175, 23.055, -13.768 { ca lys b 214 } -2.187, 20.927, -12.709 { ca his b 215 } -3.288, 17.788, -14.548 { ca ser b 216 } -5.749, 16.682, -17.176 { ca ile b 217 } -6.328, 12.954, -16.437 @subgroup {Glu} dominant @balllist {} color=red radius = 0.3 { oe2 glu b 161 } 7.084, 13.586, -19.983 { oe1 glu b 161 } 7.568, 15.034, -18.408 @vectorlist {sc} color= red { cd glu b 161 } P 6.898, 14.637, -19.351 { oe2 glu b 161 } 7.084, 13.586, -19.983 { cd glu b 161 } P 6.898, 14.637, -19.351 { oe1 glu b 161 } 7.568, 15.034, -18.408 { cg glu b 161 } P 5.712, 15.372, -19.886 { cd glu b 161 } 6.898, 14.637, -19.351 { cb glu b 161 } P 4.562, 15.461, -18.858 { cg glu b 161 } 5.712, 15.372, -19.886 { ca glu b 161 } P 3.606, 16.591, -19.196 { cb glu b 161 } 4.562, 15.461, -18.858 @subgroup {Arg} dominant @balllist {} color=blue radius = 0.3 { nh2 arg b 162 } -3.160, 22.968, -17.566 { nh1 arg b 162 } -0.976, 23.575, -17.082 { ne arg b 162 } P -1.634, 21.356, -17.790 @vectorlist {sc} color= cyan { cz arg b 162 } P -1.865, 22.643, -17.432 { nh2 arg b 162 } -3.160, 22.968, -17.566 { cz arg b 162 } P -1.865, 22.643, -17.432 { nh1 arg b 162 } -0.976, 23.575, -17.082 { ne arg b 162 } P -1.634, 21.356, -17.790 { cz arg b 162 } -1.865, 22.643, -17.432 { cd arg b 162 } P -0.219, 20.977, -17.935 { ne arg b 162 } -1.634, 21.356, -17.790 { cg arg b 162 } P -0.111, 19.701, -18.746 { cd arg b 162 } -0.219, 20.977, -17.935 { cb arg b 162 } P -0.418, 18.658, -17.671 { cg arg b 162 } -0.111, 19.701, -18.746 { ca arg b 162 } P 0.126, 17.255, -17.838 { cb arg b 162 } -0.418, 18.658, -17.671 @subgroup {PGC} dominant @vectorlist {ht} color= gold { p1 h} P -8.144, 18.294, -9.260 { p1 PGC 2} -8.144, 18.294, -9.260 { o1 PGC 2} -9.638, 18.244, -9.023 { p1 PGC 2} P -8.144, 18.294, -9.260 { o2 PGC 2} -7.788, 17.399, -10.411 { p1 PGC 2} P -8.144, 18.294, -9.260 { o3 PGC 2} -7.444, 17.803, -7.991 { p1 PGC 2} P -8.144, 18.294, -9.260 { o4 PGC 2} -7.757, 19.848, -9.528 { c1 PGC 2} -6.772, 20.129, -10.537 { c2 PGC 2} -6.304, 21.553, -10.168 { o5 PGC 2} -7.174, 22.481, -9.675 { c2 PGC 2} P -6.304, 21.553, -10.168 { o6 PGC 2} -4.984, 21.847, -10.238 @subgroup {F6P site} dominant off @balllist {} color=red radius=0.1 { o61 F6P 1} 9.007, 12.303, -21.586 { o62 F6P 1} 7.448, 10.426, -21.553 { o63 F6P 1} 8.429, 11.291, -19.448 @balllist {} color=gold radius=0.1 { p6 F6P 1} P 8.610, 11.065, -20.899 @vectorlist {ht} color= gray { o1 F6P 1} P 13.626, 9.201, -16.841 { o1 F6P 1} 13.626, 9.201, -16.841 { c1 F6P 1} 12.362, 8.703, -16.439 { c2 F6P 1} 11.618, 8.043, -17.622 { o2 F6P 1} 10.391, 7.537, -17.045 { c2 F6P 1} P 11.618, 8.043, -17.622 { c3 F6P 1} 12.298, 6.949, -18.475 { o3 F6P 1} 12.364, 5.618, -17.960 { c3 F6P 1} P 12.298, 6.949, -18.475 { c4 F6P 1} 11.382, 6.919, -19.704 { o4 F6P 1} 11.951, 6.378, -20.896 { c4 F6P 1} P 11.382, 6.919, -19.704 { c5 F6P 1} 11.131, 8.424, -19.887 { c2 F6P 1} P 11.618, 8.043, -17.622 { o5 F6P 1} 11.283, 9.091, -18.590 { c5 F6P 1} P 11.131, 8.424, -19.887 { c6 F6P 1} 9.752, 8.729, -20.473 { o6 F6P 1} 9.864, 10.053, -21.018 { p6 F6P 1} 8.610, 11.065, -20.899 { o61 F6P 1} 9.007, 12.303, -21.586 { p6 F6P 1} P 8.610, 11.065, -20.899 { o62 F6P 1} 7.448, 10.426, -21.553 { p6 F6P 1} P 8.610, 11.065, -20.899 { o63 F6P 1} 8.429, 11.291, -19.448 { c5 F6P 1} P 11.131, 8.424, -19.887 { o5 F6P 1} 11.283, 9.091, -18.590 @subgroup {T labels} nobutton off master= {Labels} @labellist {Glu 161} color= red nobutton { Glu 161 } P 5.712, 15.372, -19.886 @labellist {Arg 162} color= cyan nobutton { Arg 162 } P -1.634, 21.356, -17.790 @labellist {F6P site} color= gray nobutton { F6P site} P 10.391, 7.537, -17.045 @labellist {T site} color= gold nobutton { PGC} P -7.174, 22.481, -9.675 1 Exercise 13. Phosphofructokinase Allosterism 42 Exercise 14. Glycogen Phosphorylase 46 Exercise 14. Glycogen Phosphorylase