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. 2005 Jun 7;44(22):7998-8005.
doi: 10.1021/bi0502691.

Structure of a novel photoreceptor, the BLUF domain of AppA from Rhodobacter sphaeroides

Spencer Anderson  1 , Vladimira Dragnea, Shinji Masuda, Joel Ybe, Keith Moffat, Carl Bauer
Affiliations

Structure of a novel photoreceptor, the BLUF domain of AppA from Rhodobacter sphaeroides

Spencer Anderson et al. Biochemistry. .

Abstract

The flavin-binding BLUF domain of AppA represents a new class of blue light photoreceptors that are present in a number of bacterial and algal species. The dark state X-ray structure of this domain was determined at 2.3 A resolution. The domain demonstrates a new function for the common ferredoxin-like fold; two long alpha-helices flank the flavin, which is bound with its isoalloxazine ring perpendicular to a five-stranded beta-sheet. The hydrogen bond network and the overall protein topology of the BLUF domain (but not its sequence) bear some resemblance to LOV domains, a subset of PAS domains widely involved in signaling. Nearly all residues conserved in BLUF domains surround the flavin chromophore, many of which are involved in an intricate hydrogen bond network. Photoactivation may induce a rearrangement in this network via reorientation of the Gln63 side chain to form a new hydrogen bond to the flavin O4 position. This shift would also break a hydrogen bond to the Trp104 side chain, which may be critical in induction of global structural change in AppA.

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Figures

Figure 1
Figure 1
Protein fold and relative orientation of the A and B chain monomers of AppA forming the noncrystallographic dimer. The C-terminal helix and tail are not part of the BLUF domain. (A) Stereo ribbon diagram including models for the flavin cofactor and two detergent molecules. (B) The dimer in a slightly different orientation with the molecular surface color-coded according to electrostatic potential, red denoting negative and blue positive. The apparent hole between monomers is the location of the partially ordered detergent molecule shown in panel A.
Figure 2
Figure 2
Secondary structure of the AppA BLUF domain. Residues that are absolutely conserved in BLUF domains are highlighted in red, and those that are partly conserved with one alternate residue are highlighted in green (3). Arrows designate amino acids in the flavin-binding pocket and double lines those in the dimer interface. The C-terminal extra-domain region (Figure 1) is highlighted in gray.
Figure 3
Figure 3
Hydrogen bond network to the flavin. Hydrogen bonds are shown as dashed lines. (A) Hydrogen bond network with the presumed dark state orientation of Gln63. (B) Alternate hydrogen bond network with flipped orientation of Gln63.
Figure 4
Figure 4
Overall protein fold of flavin-binding blue light photoreceptors: (A) AppA BLUF domain in green, (B) phy3 LOV2 in blue (PDB entry 1G28), and (C) cryptochrome 1 Phr domain in purple (PDB entry 1U3C).
Figure 5
Figure 5
Overlay of hydrogen bond network to the flavin in AppA and phy3 LOV2 (PDB entry 1G28). The structures were aligned by superimposing the isoalloxazine rings. Hydrogen bonds are shown as dashed lines. AppA, yellow atoms with purple hydrogen bonds; LOV2, orange atoms with green hydrogen bonds.
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