1JE8

Two-Component response regulator NarL/DNA Complex: DNA Bending Found in a High Affinity Site

Summary for 1JE8

• Entry DOI: 10.2210/pdb1je8/pdb
• Related: 1A04 1RNL
• Descriptor: 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3', Nitrate/Nitrite Response Regulator Protein NARL, SULFATE ION, ... (4 entities in total)
• Functional Keywords: protein-dna complex, two-component response regulator, helix-turn-helix, dna bending, transcription-dna complex, transcription/dna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 8
• Total formula weight: 64616.06

Authors

Maris, A.E.,Sawaya, M.R.,Kaczor-Grzeskowiak, M.,Jarvis, M.R.,Bearson, S.M.D.,Kopka, M.L.,Schroder, I.,Gunsalus, R.P.,Dickerson, R.E. (deposition date: 2001-06-15, release date: 2002-09-27, Last modification date: 2024-10-09)

Primary citation

Maris, A.E.,Sawaya, M.R.,Kaczor-Grzeskowiak, M.,Jarvis, M.R.,Bearson, S.M.,Kopka, M.L.,Schroder, I.,Gunsalus, R.P.,Dickerson, R.E.
Dimerization allows DNA target site recognition by the NarL response regulator.
Nat.Struct.Biol., 9:771-778, 2002

PubMed Abstract: Two-component signal transduction systems are modular phosphorelay regulatory pathways common in prokaryotes. In the co-crystal structure of the Escherichia coli NarL signal output domain bound to DNA, we observe how the NarL family of two-component response regulators can bind DNA. DNA recognition is accompanied by the formation of a new dimerization interface, which could occur only in the full-length protein via a large intramolecular domain rearrangement. The DNA is recognized by the concerted effects of solvation, van der Waals forces and inherent DNA deformability, rather than determined primarily by major groove hydrogen bonding. These subtle forces permit a small DNA-binding domain to perturb the DNA helix, leading to major DNA curvature and a transition from B- to A-form DNA at the binding site, where valine on the recognition helix interacts unexpectedly with the polar major groove floor.

PubMed: 12352954
DOI: 10.1038/nsb845

Experimental method

X-RAY DIFFRACTION (2.12 Å)