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Albany 2001

category image Biomolecular
Stereodynamics
SUNY at Albany
June 19-23, 2001

Crystal Structure Of The NarL Effector Domain-DNA Complex

The crystal structure of the NarL C-terminal domain (NarLc) in complex with DNA has been solved to 2.1 Å resolution. NarL is a two-domain DNA-binding response regulator of E. coli nitrate/nitrite anaerobic respiration pathways, whose DNA binding is controlled by a two-component signal transduction system. Two-component signaling systems typically consist of a membrane-spanning transmitter which autophosphorylates upon stimulation, and a cytosolic receiver, which is then activated by receiving the phosphorylation signal. Phosphorylation of the receiver domain causes structural changes allowing signal output, such as DNA binding.

When the structure of the full-length NarL protein was solved several years ago in our lab, it was clear that major structural changes must occur in order for the phosphorylated protein to bind DNA. Because NarL phosphorylation was short-lived, we chose to perform initial structural studies using only the C-terminal DNA binding domain, and to model the structural changes occurring upon phosphorylation. This is the first crystal structure of a two-component response regulator in complex with DNA..

The helix-turn-helix NarLc protein binds as an antiparallel dimer to a 20mer oligonucleotide containing two tail-to-tail recognition sequences. Contacts in adjacent DNA major grooves cause major DNA curvature of approximately 42 degrees. Although the curvature occurs over the entire helix, how the bend is accomplished differs throughout the helix. Protein oligomerization, protein-DNA contacts, and the deformability of particular DNA steps all contribute to the DNA bending. This type of major curvature is also found in eukaryotic transcription factors such as the homeodomain proteins, and probably provides an additional level of transcription control. For example, the NarL protein can bind at multiple DNA promoter sites and in different arrangements. DNA curvature and the source of sequence specificity are discussed.

Ann E. Maris(1), Michael Sawaya(2), Maria Grzeskowiak(2), Mike Jarvis(3),
Mary L. Kopka(2),Robert Gunsalus(3), Richard E. Dickerson(2)

(1)Biochemistry & Molecular Biology, (2)Molecular Biology Institute,
(3)Microbiology & Molecular Genetics,
University of California, Los Angeles, CA 90095,
email: maris@mbi.ucla.edu , fax: (310) 267-1957, ph:. (310) 206-8278