Structural Analysis

RuBisCO is composed of 8 large subunits and 8 small subunits. The peptide of the large subunit has two domains; the N-terminal domain from residues 1 to 150 and the C-terminal domain from residues 151 to 475 in spinach RuBisCO. In the C-terminal domain, the C-terminal end of a p-sheet is connect to an a-helix with a loop. In total, 8 p-sheet-loop-a-helix structures are linked by 7 loops. Eight p-sheets construct a barrel structure which is covered by 8 a-helices. The amino acid residues involved in the binding of the substrate RuBP are located on the C-terminus sides of some p-sheets. Two large subunits form an L2 dimer, in which two dimers associate similarly to the number 69. The circular parts of the numbers 6 and 9 are the barrel structures of the C-terminal domain. The catalytic residues are from both the C-ter-minal domain of one large subunit and the N-terminal domain of the other subunit. Four L2 dimers construct an L8 core around the 4-fold axis. Two L2 dimers interact at several amino acid residues from both dimers. One of the interactions is formed by Arg-258 from one large subunit and Glu-259 from the other. The large space formed between two L2 dimers is occupied by a small subunit. Accordingly, four small subunits locate on one end of the L8 core and the remaining four on the other end. All amino acid residues from the small subunits are very far from the catalytic sites and have been deduced to participate, not in catalysis directly, but in supporting catalysis on the large subunits.

Figure 16.3 compares the primary structures of the small subunits of spinach,

Fig. 16.2. Evolution of structure and function of RuBisCO among photosynthetic organisms. Amino acid residues of the hysteresis sites are given by one-character designations.

Synechococcus and Galdieria.8 As has been noted for the phylogenetic tree of rbcL, the gene for the small subunits, rbcS, is divided into three groups. The most apparent difference among them is the lack of a loop composed of spinach residues 52 to 63 in the cyanobacterial and non-green algal small subunits. This loop is conserved in the sub-units of green algae and higher plants and located in the central solute channel formed in the L8 core in spinach RuBisCO.9 There are two types of small subunit in isolated spinach RuBisCO. One has histidine at residue 56. The imidazol residue of SHis-56 (the superscript S indicates that this residue is located on the small subunit) interacts with the oxygen atom of the caroxyl group of LGlu-259 (L indicates that this residue is from the large subunit) to influence interdimer communication

(Fig. 16.4). The other small subunit has leucine, which cannot have a similar interaction with the L8 core. Since the two types of small subunit occupy their positions one by one at one end of the core, and with 90°C rotation around the 4-fold axis at the other end, spinach RuBisCO may have a structure of (L2SI2)2(L2SII2)2, where S1 is the small subunit with histidine at residue 56 and Sn is the other type of subunit. The L2 dimers carrying SI might have different catalytic properties than those of the dimer with SII.

The small subunits of Galdieria RuBisCO do not have the loop from residues 52 to 63 (Fig. 16.3). Instead, the C-terminal end of the small subunit has a long extension, with two p-sheets. The E-amino group interacts with the main chain oxygen of L Glu-259, the carboxyl oxygen of which does spinach

Synechococcus

Galdieria

1 10 20 30 40 50 -MQVWPILGMKKYETLSYLPPLTTEQLLAEVNYLLVKNWIPCLEFEVKDGF SMKTLP--KERRFETFSYLPPLSDRQIAAQIEYMIEQGFHPLIEFNEHSNP --------VRITQGTFSFLPDLTDEQIKKQIDYMISKKLAIGTEYTNDIHP

spinach

Synechococcus

Galdieria

60 70 80 90 100

VYREHLKSPGYYDGRYWTMWKLPMFGCTDPAQVLNELEECKKAYPDAFIRI

E------------EFYWTMWKL PLFACAAPQQVLDEVRECRSEYGDCYIRV

R------------NAYWEIWGLPLFDVTDPAAVLFEINACRKARSNFYIKV

spinach

Synechococcus

Galdieria

110 120

IGFDNK- -RQVQCISFIAYKPAGY---------------------------

AGFDNI--KECQTSSFIVHRPGR----------------------------

VGFSSVRGIESTIISFIVNRPKHEPGFNLMRQEDKSRSIKYTIHSYESYKP

spinach

Synechococcus

Galdieria

EDERY

Fig. 16.3. Alignment of the primary structures of the small subunits of RuBisCOs of spinach, Synechococcus (cyanobacteria) and Galdieria (non-green alga). The loop conserved in plant and green algal small subunits is marked by a solid line, and the C-terminal extension specific to non-green algae by double lines.

not interact with LLys-258 from the large subunit of the neighboring L2 dimer, unlike spinach RuBisCO (Fig. 16.4). An ionic bond between the carbonyl oxygen of LGlu-259 and SLys-139 may block such a direct interaction between L2 dimers. Instead, the peptidyl nitrogen of SSer-135 interacts with the main chain carbonyl oxygen of LLys-258. Thus, all C-terminal extensions of the eight small sub-units in a Galdieria RuBisCO holoenzyme occupy the central solvent channel, as shown in Figure 16.5, in contrast to the case of the spinach enzyme. These extensions also make extensive interactions between the small sub-units in the channel.

In some bacteria and dinoflagellates, RuBisCO functions without the small sub-units. The Sr values of these RuBisCOs range from 10 to 20. It has been postulated that attainment of the small subunits may be the cause of the observed great increase in the Sr value. In fact, the Sr value of RuBisCO with small subunits of some bacteria is 2 to 3 times higher than the enzyme without the small subunits in the same organisms. Among RuBisCOs with the small subunits, there is a strong variation in the Sr value: 40 for the cyanobacterial enzyme to 240 for the red-algal enzyme. This great difference may be also related to the structure around the small subunits. Figure 16.5 depicts the structures of RuBisCOs of Synechococcus, spinach and Galdieria viewed from the end of the 4-fold axis passing through the center of four small subunits at one end.8 The small subunit of the cyanobacterium lacks both part of the loop conserved in the subunits of green algal and plant enzymes and the C-terminal end of the Galdieria enzyme. As a consequence of this lack, the central solvent channel of the Synechococcus enzyme is very wide. The other extreme is represnted by Galdieria RuBisCO, where the channel is almost completely buried by the C-terminal extension of the small subunits. The order of the occupation level of the space of the central solvent channel among the three RuBisCOs is very similar to that of the Sr value. It might be possible to postulate that not only the existence of the small subunits, but also the close interaction between the small subunits in the channel, is related to the increase in the Sr value of RuBisCO.

Fig. 16.4. Superimposition of the structures around LGlu-259 (E259) of spinach and Galdieria RuBisCOs. Amino acid residues of spinach RuBisCO are colored in blue and cyano and those of the Galdieria enzyme are depicted in pink and red. L and S are the subunit origin of the residues. Yellow dotted lines represent ionic and hydrogen bonds having distances of not more than 3.3 Â. Details of structural analysis are given in reference 8.

Fig. 16.4. Superimposition of the structures around LGlu-259 (E259) of spinach and Galdieria RuBisCOs. Amino acid residues of spinach RuBisCO are colored in blue and cyano and those of the Galdieria enzyme are depicted in pink and red. L and S are the subunit origin of the residues. Yellow dotted lines represent ionic and hydrogen bonds having distances of not more than 3.3 Â. Details of structural analysis are given in reference 8.

Organic Gardeners Composting

Organic Gardeners Composting

Have you always wanted to grow your own vegetables but didn't know what to do? Here are the best tips on how to become a true and envied organic gardner.

Get My Free Ebook


Post a comment