N-term
3 4 1 2 5 N -term 3’ 4
A REPRESSOR: A MODEL SYSTEM 13 Specificity Determinants? TABLE I Generic Interactions? Protein-DNA Intractions Major groove interactions dNa backbone interactions Hydrogen bonding groups P Adenine 2 O-IP... GIn-33 N N-6... Gln-44 OEI O-2P..Tyr-22 OH N-7...Gn-4NE2 O-2P,. Lys-26 NZ Guanine 4 N-7., Ser-45 OG OIP and O-2P... Lys-19 NZ Guanine 6 OIP.. GIn-33 NG2 N-7...Asn-55ND2 OIP.. Asn-52 ND2 O-6... Lys-4 NZ Guanine 8 O-IP.. Gly-43N N-7... Thr-2 OGl D Hydrophobic interactions O-IP and O-2P... Asn-61 ND2 Thymine l C-5 M.. GIn-44 CG O- IP and O-2P... Asn-58 ND2 Thymine 3 (in consensus half-site) C-5M... Ile-54 CDI OIP.. Ala-56 N Gly-48 main chain (in nonconsensus half-site) Ser-45 CB and main chain Thymine 5 C-5M... Gly-46 CA Ser-45 CA and CB
Specificity Determinants? Generic Interactions? 5
Table 13. 2 Thermodynamic Effects of Mutations in the a Repressor on Operator Binding AG Relative to Wild-Type, kcal mol Mutant Wild-Type Interaction Operator△ G Nonoperator△G yr-22- Phe Backbone phosphate 1.6 GIn-33- Ser Backbone phosphate Asn-52-Asp Backbone phosphate 6.2 >2.8 Gly-43- Glu Backbone phosphate 6.2 0.5 GIn-44-Ser Hydrogen Bond to A(2)N7,-NH 3.7 0.2 GIn-44- Leu Hydrogen Bond to A(2)N7,NH >6.2 0.2 Ser-45- Leu Hydrogen Bond to G(4)N7 >6.2 0.1 Asn-55- Lys Hydrogen Bond to G(6)N7, Lys-4 Lys-4-GIn Hydrogen Bond to G(6)06, Asn-55 5.2 0.5 Ala-49- Val Hydrophobic T(3)-CH 4.6 0.2 Ala-49-+Asp Hydrophobic T(3)CH >6.2 0.1 6
6 >104 >103