The DNA Recognition Motif of GapR Has an Intrinsic DNA Binding Preference towards AT-rich DNA
Abstract
:1. Introduction
2. Results
2.1. Dimeric GapRΔC17 Has the Same Fold as the Dimer Units of Full-Length Tetramer GapR
2.2. GapRΔC17 Can Bind to DNA with a Preference towards AT-rich Sequences
2.3. GapRΔC17 Binds DNA at the Minor Groove through Electrostatic Interactions between Its Lysine/Arginine Network and DNA Phosphate Groups
3. Discussion
4. Materials and Methods
4.1. Protein Expression and Purification
4.2. Protein Crystallization
4.3. Crystallographic Structure Determination
4.4. Resonance Assignment of Backbone NH Signals of GapRΔC17
4.5. NMR Titration Experiments
4.6. MST Assay
4.7. Generation of Haddock Models of GapRΔC17 and DNA
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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GapRΔC17 (SeMet) | GapRΔC17 (Native) | |
---|---|---|
Data collection | ||
Space Group | I4,122 | I4,122 |
Cell dimensions | ||
a, b, c (Å) | 44.8, 44.8, 227.2 | 47.4, 47.4, 225.5 |
α, β, γ (º) | 90, 90, 90 | 90, 90, 90 |
Resolution (Å) | 56.8~3.0 | 47.72~2.08 |
Rmerge (%) | 11.6 (27.1) | 10.2 (53.3) |
I/σI | 29.28 (3.2) | 48.8 (1.93) |
Completeness (%) | 99 (94.6) | 98.06 (95.0) |
Redundancy | 22.4 (11.9) | 22.2 (12.7) |
Refinement | ||
Resolution (Å) | 47.72~2.08 | |
No. reflections | 8095 | |
Rwork/Rfree (%) | 25.1/26 | |
No. atoms | ||
Protein | 532 | |
B-factors | ||
Protein | 37.0 | |
R.m.s. deviations | ||
Bond lengths (Å) | 0.006 | |
Bond angles (º) | 0.742 | |
Ramachandran plot statistics | ||
Most favored (%) | 100 | |
Additional allowed (%) | 0.0 | |
Generously allowed (%) | 0.0 | |
Disallowed (%) | 0.0 |
GapRΔC17/6A | GapRΔC17/3GC | |
---|---|---|
Haddock score (kcal/mol) | −344 ± 27 | −335 ± 42 |
Cluster size | 39 | 31 |
RMSD (Å) | 4.2 ± 1.2 | 3.5 ± 2.1 |
Evdw (kcal/mol) | −43 ± 7 | −47 ± 9 |
Eelec (kcal/mol) | −735 ± 76 | −686 ± 98 |
Eair (kcal/mol) | 77 ± 43 | 109 ± 47 |
BSA (Å2) | 1695 ± 138 | 1641 ± 186 |
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Huang, Q.; Duan, B.; Qu, Z.; Fan, S.; Xia, B. The DNA Recognition Motif of GapR Has an Intrinsic DNA Binding Preference towards AT-rich DNA. Molecules 2021, 26, 5776. https://doi.org/10.3390/molecules26195776
Huang Q, Duan B, Qu Z, Fan S, Xia B. The DNA Recognition Motif of GapR Has an Intrinsic DNA Binding Preference towards AT-rich DNA. Molecules. 2021; 26(19):5776. https://doi.org/10.3390/molecules26195776
Chicago/Turabian StyleHuang, Qian, Bo Duan, Zhi Qu, Shilong Fan, and Bin Xia. 2021. "The DNA Recognition Motif of GapR Has an Intrinsic DNA Binding Preference towards AT-rich DNA" Molecules 26, no. 19: 5776. https://doi.org/10.3390/molecules26195776