|
Flores et al. 10.1073/pnas.0407455102. |
Table 3. Forward (F) and reverse (R) primer sequences used for PCR amplifications to determine N- and C-terminal sequences of R. pachyptila globin chains
|
Chain |
N-terminal |
C-terminal |
|
A1 |
R1:5'-CTTCTCCGGAACACGAAAAGAAC-3' |
F1:5'-CCATCGACCCCGTTAACTTCGT-3' |
|
|
|
F2:5'-GTTCCGTAAGGCACTCATCGC-3' |
|
B2 |
F1:5'-ATGGGNCTNGTNGCNGGNGGNCTNG-3' |
R1:5'-CTANGCNGGNAGNGGYTCNGTC-3' |
|
|
|
F1:5'-CATCAGGCGAGTTATGTGTC-3' |
Table 4. Alignment of the globin polypeptide chain nomenclature in R. pachyptila and L. terrestris based on the C1 crystal structure
|
Ref. |
Chain names |
Organism |
|||
|
1 |
B1a or b |
A1 |
B2 |
A2 |
R. pachyptila |
|
2 |
c, a |
f |
e |
b |
R. pachyptila |
|
3 |
c |
b |
a |
d |
L. terrestris |
In ref. 1, L. Terrestris globin chain d is aligned with R. pachyptila globin chain A1, and L. terrestris globin chain b is aligned with R. pachyptila globin chain A2. These are reversed here due to the structural equivalence of the subunit positions in the dodecamers of L. terrestris and R. pachyptila hemoglobins.
1. Bailly, X., Jollivet, D., Vanin, S., Deutsch, J., Zal, F., Lallier, F. & Toulmond, A. (2002) Mol. Biol. Evol. 19, 1421-1433.
2. Zal, F., Lallier, F. H., Green, B. N., Vinogradov, S. N. & Toulmond, A. (1996) J. Biol. Chem. 271, 8875-8881.
3. Fushitani, K., Matsuura, M. S. & Riggs, A. F. (1998) J. Biol. Chem. 263, 6502-6517.
Fig. 5. Comparison of the two distinct EF dimer assemblies in the R. pachyptila C1 Hb with one in L. terrestris HBL Hb. In each case, the trace of the backbone of the E and F helices is shown along with the heme groups and side chains E7 (distal His), E10 (Arg), F3 (His), F7 (Gln), and F8 (proximal His). Dotted lines show likely hydrogen bonds (< 3.3 Å) involving heme propionates. Note the high structural conservation of the EF dimer interface of these annelid hemoglobins, including interactions with the heme groups and the packing between Arg E10 and His F3' (primes designate partner subunit).
Fig. 6. Stereo image of the heme pockets for subunits A1 and B1. Included is the heme, oxygen ligand, proximal histidine (F8), distal histidine (E7), B10 (Trp or Phe), and E10 Arg. Van der Waals representations are included for the oxygen ligand and side chains for B7 and B10 to show the crowded nature of the oxygen-binding pocket. Note also how close the key dimer interface residue E10 Arg is to the oxygen-binding pocket, suggesting a possible coupling between binding of ligands and interface structure.