NDLI: Repetitive use of a phosphate-binding module in DNA polymerase β, Oct-1 POU domain and phage repressors

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Cellular and Molecular Life Sciences : Volume 55, Issue 2, February 1999

Cellular and Molecular Life Sciences : Volume 55, Issue 1, January 1999

Cellular and Molecular Life Sciences : Volume 54

Cellular and Molecular Life Sciences : Volume 53

Repetitive use of a phosphate-binding module in DNA polymerase β, Oct-1 POU domain and phage repressors

Content Provider	Springer Nature Link
Author	Yura, K. Shionyu, M. Kawatani, K. Gō, M.
Copyright Year	1999
Abstract	Motifs for sequence specific-protein-DNA interactions, such as helix-turn-helix, zinc finger and leucine zipper, are now better understood as a result of extensive studies of three-dimensional (3D) structures of transcription factors. On the other hand, little attention has been paid to motifs for sequence nonspecific binding, namely DNA-phosphate binding. To address the question whether different transcription factors and DNA manipulation enzymes, that is enzymes that work on DNA, share a similar mode of phosphate binding, we surveyed interactions between DNA and protein module, a structural unit of a globular protein. We analyzed the modular organization of DNA polymerase β and found that residues making contact with DNA phosphates were localized to five modules. Structural comparison of these phosphate-binding modules against others in transcription factors and DNA manipulation enzymes revealed that DNA polymerase β, the Oct-1 POU domain, 434 Cro and the Arc repressor have a phosphate-binding module with 3D structures similar to one another. This newly detected module, the phosphate-binding helix-turn-helix (pbHTH) module, named for its function and 3D structure, interacts with DNA by (i) making hydrogen bonds between a DNA phosphodiester oxygen and an amino hydrogen of the main chain located at the N-terminus of a C-terminal α-helix, and (ii) making electrostatic interactions between DNA phosphates and side chains of lysine or arginine. Finding structurally and functionally similar phosphate-binding units in different transcription factors and DNA manipulation enzymes suggests that shuffling of modules is not limited to the DNA base-recognition motif. Phosphate-binding modules are apparently also shuffled in DNA-binding proteins.
Starting Page	472
Ending Page	486
Page Count	15
File Format	PDF
ISSN	1420682X
Journal	Cellular and Molecular Life Sciences
Volume Number	55
Issue Number	3
e-ISSN	14209071
Language	English
Publisher	Birkhäuser Verlag
Publisher Date	1999-03-01
Publisher Place	Basel
Access Restriction	Subscribed
Content Type	Text
Resource Type	Article
Subject	Cell Biology Molecular Biology Molecular Medicine Pharmacology Cellular and Molecular Neuroscience

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