Table 3.
Structural characteristics of 2′-deoxyribosyltransferases of known 3D structure.
| DpNDT | EfPDT | LmPDT | TbNDT | LlNDT | LhPDT | BpNDT | |
|---|---|---|---|---|---|---|---|
|
| |||||||
| PDB entry | 7062 | 7M5H | 6QAI | 2F62 | 1F8X | 1S2D | 6EVS |
|
| |||||||
| No. aa/subunita (n° aa/ assembly) | 137(548) | 158(632) | 156(312) | 153(306) | 157 (942) | 167(1002) | 142(828) |
| Hydrophobic residuesb (%) | 55 (40.1) | 71 (45.0) | 76 (48.7) | 68 (44.4) | 63 (40.1) | 72 (43.1) | 75 (52.8) |
| Polar residuesc (%) | 42 (30.7) | 49 (31.0) | 43 (27.6) | 43 (28.1) | 51 (32.5) | 49 (29.3) | 39 (27.5) |
| Charged residuesd (%) | 40 (29.2) | 38 (24.0) | 37 (23.7) | 42 (27.5) | 43 (27.4) | 46 (27.6) | 28 (19.7) |
| Lys/Asp (%/%) | 7.3/8.3 | 5.0/8.2 | 4.5Z7.7 | 7.2/7.8 | 8.3/8.9 | 6.6/7.8 | 6.3/7.0 |
| Cys residues (disulfide bonds) | 6(2) | 0(0) | 2(0) | 3(0) | 0(0) | 2(0) | 0(0) |
| ILVe (%) | 24.6 | 27 | 19.9 | 18.9 | 20.4 | 13.8 | 15.4 |
| No. H-bonds per residue in assemblyf | 2.20 | 3.20 | 1.79 | 2.04 | 2.21 | 2.11 | 1,99 |
| PIg | 4.56 | 4.51 | 4.81 | 5.23 | 4.65 | 4.93 | 4.70 |
| No. SSf,h H-bonds per residue in assembly | 0.48 | 0.43 | 0.23 | 0.30 | 0.40 | 0.47 | 0.31 |
| No. SMi H-bonds per residue in assembly | 0.43 | 0.47 | 0.32 | 0.52 | 0.50 | 0.49 | 0.39 |
| No. MMj H-bonds per residue in assembly | 1.29 | 2.30 | 1.24 | 1.22 | 1.31 | 1.15 | 1.29 |
| No. ion pairs intrasubunitf 6 Å (4 Å) | 19(10) | 13(7) | 7(2) | 13 (12) | 19(12) | 15 (7) | 11(5) |
| No. 2-member networks 6 A (4 A) | 10(4) | 3 (3) | 2(2) | 3(12) | 4(2) | 6(7) | 3(3) |
| No. 3-member networks 6 Å (4 Å) | 0(3) | 2(2) | 1 (0) | 2(0) | 3(1) | 1(0) | 2(1) |
| No. 4-member networks 6 Å (4 Å) | 0(0) | 2(0) | 1 (0) | 2(0) | 0(1) | 0(0) | 1 (0) |
| No. >= 5-member networks 6 Å (4 Å) | 1(0) | 0(0) | 0(0) | 0(0) | 2(1) | 1(0) | 0(0) |
| No. ion pairs intersubunitf 6 Å (4 Å) | 9(5) | 22(4) | 4(1) | 6(4) | 15(15) | 12(6) | 18(3) |
| No. 2-member networks 6 Å (4 Å) | 3(5) | 12(4) | 2(2) | 2(0) | 15(15) | 8(6) | 12(3) |
| No. 3-member networks 6 Å (4 Å) | 3(0) | 2(0) | 1(0) | 2(2) | 0(0) | 2(0) | 3(0) |
| No. 4-member networks 6 Å (4 Å) | 0(0) | 2(0) | 0(0) | 0(0) | 0(0) | 0(0) | 0(0) |
| No. >=5-member networks 6 Å (4 Å) | 0(0) | 0(0) | 0(0) | 0(0) | 0(0) | 0(0) | 0(0) |
| T,„ (°C) | 58.5 | 54.4 | 55 | 69 | — | — | 49 |
| Accessible surface arcak (ASA) of assembly (Å2) | 22,930 | 23,957 | 13,100 | 14,909 | 33,120 | 35,094 | 31,112 |
| Buried area of assemblyl (Å2) (%) | 9,890(43) | 16,648(44) | 4,585(40) | 4,941(40) | 17,265(49) | 22,904(51) | 15,809(48) |
| ⊠ASAnp (Å2) | 43,415 | 54,697 | 25,842 | 26,003 | 84,476 | 82,744 | 76,966 |
| ⊠ASAp, (Å2) | 21,790 | 28,351 | 11,203 | 11,968 | 41,296 | 40.575 | 31,547 |
| ⊠CpT (kJ K−1 mol−1) | 57.98 | 67.13 | 36.43 | 35.90 | 114.03 | 111.54 | 110.49 |
| ⊠H60 (kJ mol−1) | 1,328 | 2,385 | 559 | 653 | 2,440 | 2,406 | 1,425 |
| ⊠HTm (kJ mol−1) | 1,270 | 1,646 | 377 | 976 | — | — | 209.6 |