Pl. Wang et al., MOLECULAR-MODEL OF THE SOLUTION STRUCTURE FOR THE PARAMAGNETIC 4-IRONFERREDOXIN FROM THE HYPERTHERMOPHILIC ARCHAEON THERMOCOCCUS-LITORALIS, Biochemistry, 35(35), 1996, pp. 11319-11328
A molecular model for the three-dimensional solution structure of the
paramagnetic, four-iron ferredoxin (Fd) from the hyperthermophilic arc
haeon Thermococcus litoralis (TI) has been constructed on the basis of
the reported H-1 NMR spectral parameters [Donaire, A. (1996) J. Biomo
l. NMR 7, 35-47]. The conventional use of long mixing time NOESY cross
-peak intensity, backbone angles, and hydrogen-bonding constraints for
building the structure was augmented by short mixing time NOESY, stea
dy-state NOE, paramagnetic relaxation constraints, and the angular dep
endence of the ligated Cys H-beta contact shifts. Distance geometry wa
s used to generate various initial structures, and these structures we
re refined with the simulated annealing protocol. The family of struct
ures with inconsequential violations exhibited low RMS deviations for
the backbone except for a few residues in the immediate cluster vicini
ty and traces out a secondary structure very similar to those of the s
tructurally characterized single cubane cluster Fds. The ability to de
scribe the cluster environment depended on the use of numerous paramag
netic relaxation constraints which resulted in even the cluster loop r
esidues exhibiting well-defined orientations, with the exception of on
e residue (Ile11) whose H-1 signals have not been located. Comparison
of the structure of TI Fd to those of mesophilic ferredoxins reveals t
hat TI Fd possesses the same secondary structural elements, two beta-s
heets, two helices, and four turns, with the exception that the beta-s
heet involving the termini incorporates a third strand in TI Fd. Sever
al minor structural adjustments in TI Fd relative to other Fds, in add
ition to the third strand for beta-sheet, include the incorporation of
the termini into the beta-sheet, a likely salt bridge from the side c
hain of the third beta-strand to the N-terminus, and a more hydrophobi
c and compact interaction between the large beta-sheet and the long he
lix. It is likely that each of these modifications, among others not y
et well-defined (i.e., surface salt bridges), contributes to the extra
ordinary thermostability of TI Fd.