2OQQ

Crystal structure of HY5 leucine zipper homodimer from Arabidopsis thaliana

Summary for 2OQQ

• Entry DOI: 10.2210/pdb2oqq/pdb
• Descriptor: Transcription factor HY5 (2 entities in total)
• Functional Keywords: homodimer leucine zipper, transcription
• Biological source: Arabidopsis thaliana (thale cress)
• Total number of polymer chains: 2
• Total formula weight: 9929.01

Authors

Yoon, M.-K.,Kim, H.M.,Choi, G.,Lee, J.-O.,Choi, B.-S. (deposition date: 2007-02-01, release date: 2007-03-20, Last modification date: 2023-12-27)

Primary citation

Yoon, M.K.,Kim, H.M.,Choi, G.,Lee, J.O.,Choi, B.S.
Structural basis for the conformational integrity of the Arabidopsis thaliana HY5 leucine zipper homodimer.
J.Biol.Chem., 282:12989-13002, 2007

PubMed Abstract: The leucine zipper (LZ) domain of the HY5 transcription factor from Arabidopsis thaliana has unique primary structural properties, including major occupation by the Leu residues as well as two buried polar residues in the a positions and a localized distribution of charged and polar residues in the first three heptad repeats. In this study, we solved the crystal structure of the HY5 LZ domain and show that the peculiarities in the primary sequence yield unusual structural characteristics. For example, the HY5 LZ domain exhibits a bipartite charge distribution characterized by a highly negative electrostatic surface potential in its N-terminal half and a nearly neutral potential in its C-terminal half. The LZ N-terminal region also contains two consecutive putative trigger sites for dimerization of the coiled coils. In addition, two buried asparagines at a positions 19 and 33 in the HY5 LZ domain display distinct modes of polar interaction. Whereas Asn(19) shows a conformational flip-flop, Asn(33) is engaged in a permanent hydrogen bond network. CD spectropolarimetry and analytical ultracentrifugation experiments performed with versions of the HY5 LZ domain containing mutations in the a positions yielded further evidence that position a amino acid residues are crucial for achieving an oligomeric state and maintaining stability. However, a low correlation between position a amino acid preference, core packing geometry, and rotamer conformations suggests that the oligomeric state of the LZ domain is not governed entirely by known structural properties. Taken together, our results suggest structural factors conferring conformational integrity of the HY5 LZ homodimer that are more complicated than proposed previously.

PubMed: 17261584
DOI: 10.1074/jbc.M611465200

Experimental method

X-RAY DIFFRACTION (2 Å)