QM/MM Study of the Conversion Mechanism of Lysine to Methylornithine Catalyzed By

Supplementary materials

QM/MM study of the conversion mechanism of lysine to methylornithine catalyzed by methylornithine synthase (PylB)

Wenyou Zhua, Yongjun Liu*a,b, Rui Zhangc

aKey Lab of Colloid and Interface Chemistry, Ministry of Education,, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China

bNorthwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, China

cSchool of Agriculture, Ludong University, Yantai, Shandong 264025, China

Figure S1 One typical structure derived from MD simulations withlysine was kept.

Table S1Calculated charges of heavy frontier atoms at the QM (B3LYP/6-31G(d,p))/MM (CHARMM) level of theory.

species / R / TS1 / IM1 / TS2 / IM2 / TS3 / IM3 / TS4 / IM4 / TS5 / IM5 / TS6 / IM6 / TS7 / P
Asp279C / -0.39 / -0.39 / -0.38 / -0.40 / -0.40 / -0.40 / -0.40 / -0.41 / -0.41 / -0.40 / -0.40 / -0.40 / -0.39 / -0.37 / -0.38
ADOC1’ / 0.07 / 0.07 / 0.07 / 0.07 / 0.07 / 0.07 / 0.07 / 0.07 / 0.07 / 0.07 / 0.07 / 0.07 / 0.07 / 0.07 / 0.07

The PDB coordinates of Figure 3(closecaptions only).

ATOM 829 N ASP A 112 43.128 47.256 6.928 1.00 12.91 N

ATOM 830 CA ASP A 112 43.264 46.122 5.947 1.00 12.22 C

ATOM 831 C ASP A 112 43.018 44.775 6.566 1.00 13.46 C

ATOM 832 O ASP A 112 43.818 44.395 7.461 1.00 16.62 O

ATOM 833 CB ASP A 112 44.640 46.232 5.276 1.00 14.25 C

ATOM 834 CG ASP A 112 44.956 45.149 4.309 1.00 17.72 C

ATOM 835 OD1 ASP A 112 44.115 44.259 3.989 1.00 20.02 O

ATOM 836 OD2 ASP A 112 46.125 45.156 3.779 1.00 19.74 O

TER

ATOM 1803 N ARG A 235 51.719 49.086 -5.478 1.00 12.35 N

ATOM 1804 CA ARG A 235 52.831 48.829 -4.559 1.00 12.87 C

ATOM 1805 C ARG A 235 53.923 47.976 -5.132 1.00 13.50 C

ATOM 1806 O ARG A 235 53.726 47.205 -6.101 1.00 13.58 O

ATOM 1807 CB ARG A 235 52.337 48.279 -3.240 1.00 19.15 C

ATOM 1808 CG ARG A 235 52.058 46.877 -3.244 1.00 18.98 C

ATOM 1809 CD ARG A 235 52.115 46.220 -1.816 1.00 18.15 C

ATOM 1810 NE ARG A 235 51.142 46.864 -0.906 1.00 16.20 N

ATOM 1811 CZ ARG A 235 51.231 46.814 0.420 1.00 17.55 C

ATOM 1812 NH1 ARG A 235 52.270 46.180 1.006 1.00 20.35 N

ATOM 1813 NH2 ARG A 235 50.324 47.441 1.148 1.00 18.28 N

TER

ATOM 2142 N SER A 277 55.516 50.198 3.352 1.00 14.54 N

ATOM 2143 CA SER A 277 55.205 49.085 4.262 1.00 13.15 C

ATOM 2144 C SER A 277 56.222 48.917 5.379 1.00 15.05 C

ATOM 2145 O SER A 277 57.428 48.855 5.119 1.00 20.12 O

ATOM 2146 CB SER A 277 55.139 47.756 3.472 1.00 16.20 C

ATOM 2147 OG SER A 277 54.941 46.661 4.389 1.00 15.33 O

TER

ATOM 2156 N ASP A 279 56.441 46.210 6.942 1.00 15.86 N

ATOM 2157 CA ASP A 279 56.700 44.770 7.020 1.00 15.19 C

ATOM 2158 C ASP A 279 58.099 44.365 6.483 1.00 15.92 C

ATOM 2159 O ASP A 279 58.592 43.269 6.791 1.00 16.47 O

ATOM 2160 CB ASP A 279 55.622 44.059 6.156 1.00 16.97 C

ATOM 2161 CG ASP A 279 55.291 42.651 6.598 1.00 18.54 C

ATOM 2162 OD1 ASP A 279 55.535 42.230 7.750 1.00 17.01 O

ATOM 2163 OD2 ASP A 279 54.635 41.980 5.738 1.00 21.41 O

TER

HETATM 2719 C5' SAM A 992 49.925 39.357 0.402 0.50 23.91 C

HETATM 2720 C4' SAM A 992 51.094 39.228 -0.558 1.00 22.74 C

HETATM 2721 O4' SAM A 992 52.123 39.514 0.584 1.00 19.41 O

HETATM 2722 C3' SAM A 992 51.512 38.543 -1.616 1.00 22.35 C

HETATM 2723 O3' SAM A 992 50.635 39.251 -2.503 1.00 18.65 O

HETATM 2724 C2' SAM A 992 52.860 39.276 -1.635 1.00 20.44 C

HETATM 2725 O2' SAM A 992 52.888 40.440 -2.524 1.00 21.87 O

HETATM 2726 C1' SAM A 992 53.304 39.660 -0.212 1.00 16.59 C

HETATM 2727 N9 SAM A 992 54.257 38.619 0.323 1.00 14.80 N

HETATM 2728 C8 SAM A 992 54.029 37.324 0.697 1.00 13.94 C

HETATM 2729 N7 SAM A 992 55.175 36.767 1.059 1.00 13.08 N

HETATM 2730 C5 SAM A 992 56.160 37.719 0.929 1.00 12.46 C

HETATM 2731 C6 SAM A 992 57.554 37.676 1.092 1.00 12.45 C

HETATM 2732 N6 SAM A 992 58.201 36.576 1.478 1.00 13.57 N

HETATM 2733 N1 SAM A 992 58.251 38.809 0.919 1.00 13.50 N

HETATM 2734 C2 SAM A 992 57.647 39.964 0.509 1.00 14.72 C

HETATM 2735 N3 SAM A 992 56.321 40.010 0.231 1.00 14.37 N

HETATM 2736 C4 SAM A 992 55.588 38.878 0.471 1.00 13.32 C

HETATM 2737 C MD0 A 993 51.560 45.326 4.129 1.00 18.66 C

HETATM 2738 N MD0 A 993 51.876 43.460 5.650 1.00 18.47 N

HETATM 2739 O MD0 A 993 50.855 46.314 3.838 1.00 18.89 O

HETATM 2740 CA MD0 A 993 50.922 44.143 4.782 1.00 15.61 C

HETATM 2741 CB MD0 A 993 50.374 43.157 3.706 1.00 15.20 C

HETATM 2742 CD MD0 A 993 48.267 42.911 2.225 1.00 16.16 C

HETATM 2743 NE MD0 A 993 47.206 43.673 1.579 1.00 17.91 N

HETATM 2744 CG MD0 A 993 49.218 43.866 2.942 1.00 15.00 C

HETATM 2745 CG2 MD0 A 993 51.441 42.663 2.696 1.00 17.28 C

HETATM 2746 OXT MD0 A 993 52.775 45.274 3.904 1.00 20.00 O

ATOM 1 N LYS C 420 52.061 43.429 5.472 1.00 25.19 N

ATOM 2 CA LYS C 420 51.636 43.505 4.051 1.00 24.58 C

ATOM 3 C LYS C 420 51.452 44.924 3.747 1.00 26.54 C

ATOM 4 O LYS C 420 52.462 45.693 3.820 1.00 27.30 O

ATOM 5 OXT LYS C 420 50.289 45.329 3.426 1.00 27.08 O

ATOM 6 CB LYS C 420 50.344 42.686 3.694 1.00 24.15 C

ATOM 7 CGLYS C 420 50.314 42.187 2.264 0.40 23.47 C

ATOM 8 CDLYS C 420 48.928 42.441 1.665 0.40 23.01 C

ATOM 9 CELYS C 420 47.946 43.147 2.599 0.40 23.70 C

ATOM 10 NZ LYS C 420 47.374 44.292 1.880 1.00 22.57 N

HETATM 2753 O HOH A 357 46.693 41.749 -0.656 1.00 19.55 O

HETATM 2758 O HOH A 362 47.983 47.049 3.793 1.00 22.73 O

END

The PDB coordinates of Figure 4 (closecaptions only).

ATOM 1642 N ASP 112 -9.297 4.226 -1.830 1.00 1.00 N

ATOM 1643 HN ASP 112 -8.531 4.577 -1.286 1.00 1.00 H

ATOM 1644 CA ASP 112 -8.969 3.054 -2.622 1.00 1.00 C

ATOM 1645 HA ASP 112 -9.680 2.952 -3.430 1.00 1.00 H

ATOM 1646 CB ASP 112 -7.548 3.248 -3.222 1.00 1.00 C

ATOM 1647 HB1 ASP 112 -7.514 4.257 -3.689 1.00 1.00 H

ATOM 1648 HB2 ASP 112 -6.783 3.216 -2.421 1.00 1.00 H

ATOM 1649 CG ASP 112 -7.157 2.256 -4.298 1.00 1.00 C

ATOM 1650 OD1 ASP 112 -7.803 1.195 -4.468 1.00 1.00 O

ATOM 1651 OD2 ASP 112 -6.135 2.543 -4.983 1.00 1.00 O

ATOM 1652 C ASP 112 -9.083 1.805 -1.745 1.00 1.00 C

ATOM 1653 O ASP 112 -8.246 1.540 -0.876 1.00 1.00 O

TER

ATOM 3574 N ARG 235 -1.650 6.913 -14.610 1.00 1.00 N

ATOM 3575 HN ARG 235 -2.065 6.038 -14.863 1.00 1.00 H

ATOM 3576 CA ARG 235 -0.401 6.869 -13.863 1.00 1.00 C

ATOM 3577 HA ARG 235 0.040 7.856 -13.829 1.00 1.00 H

ATOM 3578 CB ARG 235 -0.628 6.415 -12.396 1.00 1.00 C

ATOM 3579 HB1 ARG 235 0.347 6.281 -11.879 1.00 1.00 H

ATOM 3580 HB2 ARG 235 -1.159 7.223 -11.851 1.00 1.00 H

ATOM 3581 CG ARG 235 -1.474 5.138 -12.246 1.00 1.00 C

ATOM 3582 HG1 ARG 235 -2.550 5.370 -12.416 1.00 1.00 H

ATOM 3583 HG2 ARG 235 -1.166 4.421 -13.035 1.00 1.00 H

ATOM 3584 CD ARG 235 -1.304 4.419 -10.904 1.00 1.00 C

ATOM 3585 HD1 ARG 235 -1.818 3.432 -10.947 1.00 1.00 H

ATOM 3586 HD2 ARG 235 -0.221 4.250 -10.710 1.00 1.00 H

ATOM 3587 NE ARG 235 -1.937 5.223 -9.808 1.00 1.00 N

ATOM 3588 HE ARG 235 -2.917 5.485 -9.944 1.00 1.00 H

ATOM 3589 CZ ARG 235 -1.595 4.969 -8.539 1.00 1.00 C

ATOM 3590 NH1 ARG 235 -0.342 4.667 -8.212 1.00 1.00 N

ATOM 3591 HH1 ARG 235 -0.171 4.436 -7.242 1.00 1.00 H

ATOM 3592 HH1 ARG 235 0.387 4.994 -8.823 1.00 1.00 H

ATOM 3593 NH2 ARG 235 -2.491 4.986 -7.558 1.00 1.00 N

ATOM 3594 HH2 ARG 235 -2.313 4.313 -6.824 1.00 1.00 H

ATOM 3595 HH2 ARG 235 -3.456 5.160 -7.789 1.00 1.00 H

ATOM 3596 C ARG 235 0.662 5.992 -14.517 1.00 1.00 C

ATOM 3597 O ARG 235 0.418 5.198 -15.424 1.00 1.00 O

TER

ATOM 4281 N SER 277 2.291 8.802 -5.988 1.00 1.00 N

ATOM 4282 HN SER 277 2.893 8.525 -6.729 1.00 1.00 H

ATOM 4283 CA SER 277 2.011 7.800 -4.960 1.00 1.00 C

ATOM 4284 HA SER 277 0.995 7.927 -4.615 1.00 1.00 H

ATOM 4285 CB SER 277 2.124 6.359 -5.540 1.00 1.00 C

ATOM 4286 HB1 SER 277 1.421 6.279 -6.400 1.00 1.00 H

ATOM 4287 HB2 SER 277 3.155 6.191 -5.925 1.00 1.00 H

ATOM 4288 OG SER 277 1.810 5.341 -4.585 1.00 1.00 O

ATOM 4289 HG1 SER 277 1.102 4.789 -4.984 1.00 1.00 H

ATOM 4290 C SER 277 2.929 7.904 -3.749 1.00 1.00 C

ATOM 4291 O SER 277 4.128 8.146 -3.877 1.00 1.00 O

TER

ATOM 4311 N ASP 279 3.478 5.175 -2.006 1.00 1.00 N

ATOM 4312 HN ASP 279 3.148 5.451 -2.912 1.00 1.00 H

ATOM 4313 CA ASP 279 3.878 3.792 -1.838 1.00 1.00 C

ATOM 4314 HA ASP 279 4.428 3.667 -0.911 1.00 1.00 H

ATOM 4315 CB ASP 279 2.624 2.893 -1.828 1.00 1.00 C

ATOM 4316 HB1 ASP 279 1.993 3.344 -1.052 1.00 1.00 H

ATOM 4317 HB2 ASP 279 2.112 3.088 -2.767 1.00 1.00 H

ATOM 4318 CG ASP 279 2.707 1.387 -1.515 1.00 1.00 C

ATOM 4319 OD1 ASP 279 3.339 1.009 -0.486 1.00 1.00 O

ATOM 4320 OD2 ASP 279 2.040 0.630 -2.276 1.00 1.00 O

ATOM 4321 C ASP 279 4.856 3.430 -2.934 1.00 1.00 C

ATOM 4322 O ASP 279 4.760 2.412 -3.622 1.00 1.00 O

TER 5414 SFE 991

HETATM 5415 HN1 LAI 420 1.922 1.255 -5.024 1.00 1.00 H

HETATM 5416 HN2 LAI 420 1.288 1.259 -3.494 1.00 1.00 H

HETATM 5417 N LAI 420 1.107 1.647 -4.501 1.00 1.00 N

HETATM 5418 HN3 LAI 420 1.223 2.669 -4.528 1.00 1.00 H

HETATM 5419 CA LAI 420 -0.205 1.386 -5.179 1.00 1.00 C

HETATM 5420 HA LAI 420 0.036 0.867 -6.113 1.00 1.00 H

HETATM 5421 CB LAI 420 -1.176 0.498 -4.387 1.00 1.00 C

HETATM 5422 HB1 LAI 420 -0.641 -0.033 -3.596 1.00 1.00 H

HETATM 5423 HB2 LAI 420 -1.910 1.136 -3.888 1.00 1.00 H

HETATM 5424 CG LAI 420 -1.847 -0.501 -5.349 1.00 1.00 C

HETATM 5425 HG1 LAI 420 -1.966 -0.019 -6.327 1.00 1.00 H

HETATM 5426 HG2 LAI 420 -1.159 -1.334 -5.533 1.00 1.00 H

HETATM 5427 CD LAI 420 -3.210 -1.042 -4.915 1.00 1.00 C

HETATM 5428 HD1 LAI 420 -3.553 -1.790 -5.641 1.00 1.00 H

HETATM 5429 HD2 LAI 420 -3.136 -1.560 -3.951 1.00 1.00 H

HETATM 5430 CE LAI 420 -4.288 0.024 -4.763 1.00 1.00 C

HETATM 5431 HE1 LAI 420 -5.261 -0.420 -4.560 1.00 1.00 H

HETATM 5432 HE2 LAI 420 -4.074 0.716 -3.945 1.00 1.00 H

HETATM 5433 NZ LAI 420 -4.459 0.886 -5.988 1.00 1.00 N

HETATM 5434 HZ1 LAI 420 -5.248 1.559 -5.753 1.00 1.00 H

HETATM 5435 HZ2 LAI 420 -3.613 1.444 -6.187 1.00 1.00 H

HETATM 5436 HZ3 LAI 420 -4.719 0.321 -6.823 1.00 1.00 H

HETATM 5437 C LAI 420 -0.823 2.747 -5.613 1.00 1.00 C

HETATM 5438 OD1 LAI 420 -0.018 3.720 -5.695 1.00 1.00 O

HETATM 5439 OD2 LAI 420 -2.046 2.775 -5.909 1.00 1.00 O

HETATM 5459 C5' ADO 669 -2.000 -1.917 -8.362 1.00 1.00 C

HETATM 5460 H5' ADO 669 -2.770 -1.275 -8.774 1.00 1.00 H

HETATM 5461 H5' ADO 669 -2.279 -2.549 -7.533 1.00 1.00 H

HETATM 5462 C4' ADO 669 -0.631 -1.927 -8.914 1.00 1.00 C

HETATM 5463 H4' ADO 669 -0.467 -1.027 -9.528 1.00 1.00 H

HETATM 5464 O4' ADO 669 0.389 -2.009 -7.893 1.00 1.00 O

HETATM 5465 C1' ADO 669 1.617 -2.221 -8.610 1.00 1.00 C

HETATM 5466 H1' ADO 669 2.064 -1.264 -8.901 1.00 1.00 H

HETATM 5467 N9 ADO 669 2.611 -2.908 -7.763 1.00 1.00 N

HETATM 5468 C5 ADO 669 4.488 -3.498 -6.767 1.00 1.00 C

HETATM 5469 N7 ADO 669 3.601 -4.551 -6.585 1.00 1.00 N

HETATM 5470 C8 ADO 669 2.517 -4.166 -7.216 1.00 1.00 C

HETATM 5471 H8 ADO 669 1.604 -4.760 -7.307 1.00 1.00 H

HETATM 5472 N1 ADO 669 6.457 -2.193 -6.838 1.00 1.00 N

HETATM 5473 C2 ADO 669 5.724 -1.246 -7.423 1.00 1.00 C

HETATM 5474 H2 ADO 669 6.257 -0.318 -7.652 1.00 1.00 H

HETATM 5475 N3 ADO 669 4.432 -1.270 -7.763 1.00 1.00 N

HETATM 5476 C4 ADO 669 3.882 -2.461 -7.456 1.00 1.00 C

HETATM 5477 C6 ADO 669 5.864 -3.362 -6.487 1.00 1.00 C

HETATM 5478 N6 ADO 669 6.616 -4.351 -5.965 1.00 1.00 N

HETATM 5479 H61 ADO 669 7.614 -4.215 -5.958 1.00 1.00 H

HETATM 5480 H62 ADO 669 6.307 -5.301 -6.007 1.00 1.00 H

HETATM 5481 C2' ADO 669 1.267 -2.955 -9.940 1.00 1.00 C

HETATM 5482 H2' ADO 669 1.768 -3.927 -10.063 1.00 1.00 H

HETATM 5483 O2' ADO 669 1.594 -2.115 -11.027 1.00 1.00 O

HETATM 5484 H2' ADO 669 0.816 -2.025 -11.609 1.00 1.00 H

HETATM 5485 C3' ADO 669 -0.265 -3.138 -9.802 1.00 1.00 C

HETATM 5486 H3' ADO 669 -0.475 -4.057 -9.233 1.00 1.00 H

HETATM 5487 O3' ADO 669 -0.964 -3.102 -11.021 1.00 1.00 O

HETATM 5488 H3' ADO 669 -0.740 -3.933 -11.518 1.00 1.00 H

HETATM 5507 OH2 TIP3 7 -5.328 -0.891 -7.933 1.00 1.00 O

HETATM 5508 H1 TIP3 7 -5.739 -1.086 -8.793 1.00 1.00 H

HETATM 5509 H2 TIP3 7 -6.124 -0.952 -7.356 1.00 1.00 H

HETATM 5522 OH2 TIP3 12 -4.037 4.010 -4.399 1.00 1.00 O

HETATM 5523 H1 TIP3 12 -4.845 3.501 -4.654 1.00 1.00 H

HETATM 5524 H2 TIP3 12 -3.336 3.551 -4.894 1.00 1.00 H

HETATM10745 OH2 TIP3 1753 3.465 0.785 -5.534 1.00 1.00 O

HETATM10746 H1 TIP3 1753 4.134 1.192 -4.950 1.00 1.00 H

HETATM10747 H2 TIP3 1753 3.986 0.229 -6.132 1.00 1.00 H

END