PDBsum entry 2oqq

Transcription

PDB id: 2oqq

Contents

Protein chains

42 a.a. *

Waters ×102

* Residue conservation analysis

PDB id:

2oqq

Name:

Transcription

Title:

Crystal structure of hy5 leucine zipper homodimer from arabidopsis thaliana

Structure:

Transcription factor hy5. Chain: a, b. Fragment: hy5 leucine zipper. Synonym: protein long hypocol5, atbzip56. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

2.00Å R-factor: 0.243 R-free: 0.296

Authors:

M.-K.Yoon,H.M.Kim,G.Choi,J.-O.Lee,B.-S.Choi

Key ref:

M.K.Yoon et al. (2007). Structural basis for the conformational integrity of the Arabidopsis thaliana HY5 leucine zipper homodimer. J Biol Chem, 282, 12989-13002. PubMed id: 17261584 DOI: 10.1074/jbc.M611465200

Date:

01-Feb-07 Release date: 20-Mar-07

Protein chains

O24646  (HY5_ARATH) -  Transcription factor HY5 from Arabidopsis thaliana

Seq: 168 a.a.

Struc: 42 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1074/jbc.M611465200

J Biol Chem 282:12989-13002 (2007)

PubMed id: 17261584

Structural basis for the conformational integrity of the Arabidopsis thaliana HY5 leucine zipper homodimer.

M.K.Yoon, H.M.Kim, G.Choi, J.O.Lee, B.S.Choi.

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.

Selected figure(s)

Figure 2.
FIGURE 2. Electrostatic interactions of the HY5 LZ homodimer. A, helical wheel diagrams of the HY5 LZ homodimer. The view is from the N terminus. Heptad positions are labeled a-g. Solid and dashed gray lines indicate electrostatic attractions between oppositely charged residues and hydrogen bonds, respectively. Boxed amino acid residues are within the putative trigger sites. The intrahelical hydrogen bond between Leu^8 and Glu^9 in strand B was omitted for simplicity. B, front (upper) and back (lower) views of electrostatic surface potential representations of the HY5 LZ dimer. All positively charged residues and some negatively charged residues that interact with positive charges are labeled. Surface potentials were calculated using GRASP (59).

Figure 5.
FIGURE 5. Buried polar interactions of position a asparagine residues in the HY5 LZ domain. A, the electron densities (2F[o] - F[c]) contoured at 1.5 of Asn^19 (left) and Asn^33 (right) from each helix strand are shown. Hydrogen bonds formed between the side chains of asparagines from each monomer are indicated by dashed green lines. B, shown is the extensive hydrogen bond network of Asn^33 in the HY5 LZ domain. Interstrand and non-helical intrastrand hydrogen bonds are formed in and around Asn^33. Hydrogen bonds are indicated by dashed green lines. Distances are expressed in angstroms. Ribbon diagrams of the residues from strands A and B are shown in orange and purple, respectively. C, the hexad structure of Asn^33, which consists of Glu^32-Asn^33-Arg^37/Glu^32'-Asn^33'-Arg^37' (upper), is contrasted with the corresponding regions that contain Lys^18-Asn^19-Glu^23/Lys^18'-Asn^19'-Glu^23' (lower). The hexad structure of Asn^33 is tightly packed, whereas that of Asn^19 is loosely packed. Polar, negatively charged, and positively charged residues are colored yellow, red, and blue, respectively. The figure was prepared with the program Swiss-PdbViewer (39).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 12989-13002) copyright 2007.

Figures were selected by an automated process.