Quite Interesting PDB Structures


Sunhats for plants
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How plants detect dangerous ultraviolet rays

Anyone who has ever suffered sunburn will know about the effects of too much ultraviolet (UV) radiation, in particular UV-B (from 280-315 nm in wavelength). Light in this region of the spectrum causes sunburn and DNA damage which may eventually lead to skin cancer. Humans are able to avoid excessive exposure to UV using a variety of tactics: applying sun block, wearing a sunhat or simply moving into the shade (or, more drastically, relocating to England).
UV-B-induced DNA damage is a problem for all organisms that are exposed to bright sunlight, including plants, which have no option but to stay out in the midday sunshine without even the option of putting on a hat. As Kermit the Frog observed, it’s not easy being green!
Because they can’t physically avoid UV-B, plants must detect high levels of UV-B light at a molecular level to protect against DNA damage and to repair any damage which may occur. The molecule responsible for detecting UV-B is a protein called UVR8. Structures of UVR8 (PDB 4d9s and 4dnw) from the model organism Arabidopsis thaliana have shed light on how this protein senses UV-B radiation and transduces that signal to activate photoprotective mechanisms.

A propeller with a new twist

UVR8 has a seven-bladed β-propeller fold (view-1) containing seven “regulator of chromosome condensation” (RCC1) Pfam sequence motifs that form the blades of the propeller.

Fig.1: Circular permutation of the β-propeller fold. β-strands forming the first blade of the propeller are shown as arrows and coloured blue if from the N-terminus of the protein and red if from the C-terminus. The other blades are shown as coloured circles.
Proteins in this family are ubiquitous in eukaryotes and are known to bind to chromatin. UVR8 belongs to the RCC1 Pfam family and it has 28% sequence identity to human RCC1 (PDB 1a12) and a Cα atom RMSD of 1.6Å for 318 equivalent residues. However, UVR8 is unique in that it is circularly permuted relative to other members of the family which have had their structure determined. In human RCC1, the first blade of the propeller is formed by β strands from both the N-terminus of the protein and the C-terminus, but in the case of UVR8, all blades are formed from contiguous regions of sequence (see Figure 1) (view-2).

Two propellers together

Blades five, six and seven of the propeller each have a conserved motif of Gly-Trp-Arg-His-Thr in a loop which is located near the centre of the propeller (view-3). Along with other positively charged residues, the central arginine in each motif contributes to a basic patch on the surface of the protein. In contrast, the first two blades of the propeller contain many acidic residues which form a negatively charged patch on the same surface of the protein (view-3).
These striking charged patches enable UVR8 to dimerise as they form complementary binding surfaces. The positive patch on one molecule of UVR8 interacts via a large number of salt bridges and hydrogen bonds with the negative patch on another molecule (view-4). Blades 3 and 4 also contribute to the interface, supplying a dozen hydrogen bonds between the two monomers. The dimer interaction is so strong that it is resistant to detergent denaturation.
The dimer may be very stable, but irradiation with UV-B light causes it to dissociate into its constituent monomers which localise to the nucleus. Once there, the monomeric protein interacts with the plant’s DNA via histones and also binds other proteins, including a key regulator of light response in plants called COP1. As a result, more than a hundred photoprotective genes are activated.

Indole chromophore

Unlike other light-sensing proteins with known structures, UVR8 does not bind a co-factor that acts as a chromophore; instead it uses some of its tryptophan residues for this. Tryptophan absorbs light from 280-300 nm, exactly the UV-B wavelengths which the plant needs to detect. UVR8 is particularly rich in tryptophan: it makes up 3% of its residues whereas the average occurrence in proteins is only 1%.

Fig.2: A π-cation interaction. The face of an aromatic ring such as a tryptophan is slightly negative due to the position of the electron cloud. This allows an electrostatic interaction with a positive residue such as arginine.
Several of these tryptophan residues are located in between the arginine residues in the basic patch on the dimerisation interface (view-5). Three of the tryptophans come from the Gly-Trp-Arg-His-Thr motif found in the fifth, sixth and seventh propeller blades and they form π-cation interactions with the adjacent arginines. A π-cation interaction (see Figure 2) is similar in strength to a hydrogen bond, but occurs between a positively charged residue and the negative π-electron cloud on the face of an aromatic group, in this case the tryptophan indole ring.

Are you sure there’s UV-B? Yes, I’m positive!

It is the tryptophans which form π-cation interactions in the basic patch that are responsible for UV-B detection. Their indole rings are close enough to be excitonically coupled (i.e., to share energy from a photon which any individual residue absorbs). When a photon is absorbed, the indole can become positively charged, possibly donating an electron to an adjacent arginine to neutralise it. This change in charge distribution has been proposed to disrupt the network of salt bridges and hydrogen bonds across the dimer interface and lead to dissociation of the UVR8 dimer. The monomer would then be able to signal to start the production of proteins required for photoprotection.

Back to a dimer when it gets dimmer

The precise structural rearrangement that occurs in the UVR8 monomer when photons are absorbed is not yet known as in the absence of UV-B, the monomers ‘relax’ back to the dimer state after a few hours. Growing crystals in the continuous presence of UV-B would be a challenge. Tryptophan 285 appears to be a key residue in the light-sensing process. Mutants where this residue has been replaced with a phenylalanine (PDB 4dnv) or an alanine (PDB 4dnu) are constitutive dimers even in the presence of UV-B radiation. In fact, the phenylalanine mutant is ‘tuned’ to the longer wavelength UV-C radiation and the dimer can be dissociated by light at 255 nm. Mutagenesis studies have shown that tryptophan 233 is also essential for sensing UV-B radiation.
So when you are soaking up the sun this summer, spare a thought for the plants that have to endure its rays all day long. Noel Coward should have sung that only mad dogs, Englishmen, and Arabidopsis go out in the midday sun. However, only the plant is prepared for it.

Further exploration

The accompanying mini-tutorial explains how PDBeFold can compare and superpose structures of proteins even if their sequences show circular permutation.