Table 1.
Structural relationships between λ-exonuclease and type II restriction enzymes
| PvuII (15, 16) | EcoRV (17) | EcoRI (18) | BamHI (19) | Cfr10I (20) | |
|---|---|---|---|---|---|
| Structurally equivalent residues | 78 | 90 | 51 | 63 | 74 |
| Deviation between Cα atoms, Å | 2.7 | 4.5 | 3.5 | 4.1 | 3.0 |
| Chemically identical residues | 12 | 10 | 2 | 8 | 6 |
| Corresponding active-site residues | |||||
| λ-exonuclease: Glu-85 | Glu-55 | Glu-45 | Asp-59 | Glu-77 | Glu-71 |
| λ-exonuclease: Asp-119 | Asp-58 | Asp-74 | Asp-91 | Asp-94 | Asp-134 |
| λ-exonuclease: Glu-129 | Glu-68 | Asp-90 | Clu-111 | Glu-111 | Glu-204 |
| λ-exonuclease: Lys-131 | Lys-70 | Lys-92 | Lys-113 | Glu-11 | Lys-190 |
| Structurally equivalent residues | |||||
| λ-exonuclease: αE | 83–98, 33–48 | 74–97, 34–57 | 79–97, 33–51 | 80–97, 56–73 | 74–96, 60–82 |
| λ-exonuclease: βa | 99–103, 49–53 | 98–106, 61–69 | 98–109, 53–64 | 100–103, 74–77 | 98–103, 89–94 |
| λ-exonuclease: βc | — | — | 111–117, 83–89 | — | 113–118, 128–133 |
| λ-exonuclease: βd | 121–124, 58–61 | 116–124, 71–79 | 119–124, 94–99 | 117–124, 92–99 | 119–123, 134–138 |
| λ-exonuclease: βe | 125–135, 66–76 | 125–132, 86–93 | 125–131, 104–110 | 125–133, 107–115 | 124–133, 183–192 |
| λ-exonuclease: loop | — | 134–137, 94–97 | — | — | — |
| λ-exonuclease: αG | — | — | — | 149–165, 118–134 | 148–166, 195–213 |
| λ-exonuclease: loop | 163–166, 91–94 | 165–168, 125–128 | — | 166–169, 135–138 | — |
| λ-exonuclease: βf | 167–177, 96–106 | 169–176, 130–137 | — | 170–174, 139–143 | 168–175, 227–234 |
| λ-exonuclease: βg | 183–191, 109–117 | 183–189, 167–173 | — | — | — |
| λ-exonuclease: αH | 192–207, 120–135 | 192–202, 209–219 | — | — | — |
| λ-exonuclease: αH | — | 205–210, 220–225 | — | — | — |
Each of the proteins listed was compared with λ-exonuclease using the Dali database server (22). The table gives the number of equivalent residues, the rms deviation, and the number of structurally equivalent residues that are chemically identical in the pairwise comparison of λ-exonuclease with each enzyme. The segments of structure that correspond are identified, with the residues from λ-exonuclease given first, followed by the structurally equivalent residues in the restriction enzyme. In addition to the overall regions of similarity, the server identified residues 154–157 in λ-exonuclease and residues 80–83 in PvuII and residues 153–156 in λ-exonuclease and residues 106–109 in EcoRV as equivalent. However, by visual inspection, it was clear that these short segments are not part of the overall correspondence, and they therefore were deleted from the analysis. Similar short segments were identified by Dali in the pairwise comparison of λ-exonuclease with EcoRI, BamHI, and Cfr10I and also were omitted.