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gray in Figure 1.3a through d) is a member of the nuclear transport factor II (NTF2; Pfam 02136)
superfamily, a group of
folds that form a i ve-stranded beta-sheet with a deep hydrophobic
pocket. In addition to nuclear transport factors, other proteins containing this domain include
enzymes such as the NTF2-like delta5-3-ketosteroid isomerases and other light-responsive signaling
proteins, discussed below.
In
Thermosynechococcus elongatus
, the two domains of the OCP occur as separate but adja-
cent genes (and appear to be coordinately controlled) (Kucho et al. 2004), suggesting that in the
evolutionary history of the OCP, a gene fusion occurred (Figure 1.1). Likewise, in
Crocosphaera
watsonii
, there is no full-length OCP gene; single copies of the genes for the N- and C-termini are
present, but they are in different parts of the chromosome. Other organisms contain, in addition
to a full-length OCP gene, separate genes for the domains and/or various combinations of shorter
paralogs, as shown in Table 1.1. Several cyanobacterial genomes have multiple copies of genes for
the N-terminal domain and a single copy of the gene for the C-terminal domain (Table 1.1), located
in disparate parts of the genome. This suggests that in some organisms, full-length OCPs may be
assembled from smaller proteins. These putative modular full-length OCPs, containing a unique
C-terminus combined with different N-terminal domains, is reminiscent of the modular assem-
bly of light oxygen voltage (LOV) domain-containing proteins. Among the different kingdoms of
life, LOV domain serves as an input light-sensing domain connected to very diverse functional
groups (Briggs 2007). By analogy, this suggests that in the OCP, the conserved C-terminal NTF2
domain could serve as the input through which the signal is propagated to the different N-terminal
modules.
In addition, in some organisms, multiple paralogs for only the N-terminal domain are scattered
throughout the genome. There are several lines of evidence to suggest that these are playing a func-
tional role: In
Nostoc punctiforme
several of the N-terminal paralogs are known to be expressed,
Table 1.1 (Anderson et al. 2006). Krogmann and his colleagues (Holt and Krogmann 1981, Wu
and Krogmann 1997, Knutson 1998) have isolated what appears to be a functional homolog of the
N-terminal domain of the OCP. This protein appears red; the absorbance maximum is at 505 nm
instead of 495 nm as in the OCP. This red carotenoid protein (RCP) from cell extracts of several
cyanobacterial species including
Synechocystis
PCC6803 was assumed to be a proteolytic fragment
of the OCP. A 16 kDa RCP can be generated by proteolysis
in vitro
(Kerfeld, unpublished). Based
on the structure of the OCP, removal of the NTF2 domain would render the carotenoid exposed
to solvent in the 16 kDa RCP; more likely, the structure of the RCP differs in conformation and/
or oligomerization state from the N-terminal domain of the OCP. For example, in the 16 kDa RCP
the carotenoid could be shielded by oligomerization; the 16 kDa RCP isolated from cells appeared
to be a dimer (Holt and Krogmann 1981). In addition or alternatively, a substantial rearrangement
of the tertiary structure may be involved. Domains composed entirely of alpha-helices are thought
to be able to reorganize relatively readily (Minary and Levitt 2008). Another intriguing clue, sug-
gestive of a conformational change, comes from the observation that exposing the OCP to low pH
causes its spectrum to resemble that of the 16 kDa RCP. This low pH induced form of the RCP has a
different secondary structure proi le as measured by circular dichroism (Kerfeld 2004a,b).
α
/
β
1.4 THE STRUCTURE OF THE OCP IN THE CONTEXT OF FUNCTION
The structure of the OCP from the cyanobacterium
A. maxima
was reported in 2003 (Kerfeld
et al. 2003) before its function had been established. The recent revelations about the OCP's func-
tion make a reconsideration of the structure timely. In addition, there are available structure-func-
tion data for other light responsive proteins. Blue-green light (400-550 nm), which can trigger
OCP-mediated photoprotection is an important environmental signal; blue-light receptors are wide-
spread among the prokaryotes and eukaryotes—blue-light photoreceptors such as l avin binding
phototropins that contain LOV domains are known in bacteria, plants (Briggs 2006), and algae
(Crosson and Moffat 2001, Takahashi et al. 2007) while photoactive yellow protein (PYP) mediates
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