Structure of the oxidized long‐chain flavodoxin from anabaena 7120 at 2 å resolution

Abstract

The structure of the long-chain flavodoxin from the photosynthetic cyanobacterium Anabaena 7120 has been determined at 2 A resolution by the molecular replacement method using the atomic coordinates of the long-chain flavodoxin from Anacystis nidulans. The structure of a third long-chain flavodoxin from Chondrus crispus has recently been reported. Crystals of oxidized A . 7120 flavodoxin belong to the monoclinic space group P2, with a = 48.0, b = 32.0, c = 51.6A, and 0 = 92", and one molecule in the asymmetric unit. The 2 A intensity data were collected with oscillation films at the CHESS synchrotron source and processed to yield 9,795 independent intensities with Rmerg of 0.07. Of these, 8,493 reflections had I > 2a and were used in the analysis. The model obtained by molecular replacement was initially refined by simulated annealing using the XPLOR program. Repeated refitting into omit maps and several rounds of conjugate gradient refinement led to an R-value of 0.185 for a model containing atoms for protein residues 2-169, flavin mononucleotide (FMN), and 104 solvent molecules. The FMN shows many interactions with the protein with the isoalloxazine ring, ribityl sugar, and the 5'-phosphate. The flavin ring has its pyrimidine end buried into the protein, and the functional dimethyl benzene edge is accessible to solvent. The FMN interactions in all three long-chain structures are similar except for the 04' of the ribityl chain, which interacts with the hydroxyl group of Thr 88 side chain in A. 7120, while with a water molecule in the other two. The phosphate group interacts with the atoms of the 9-15 loop as well as with NE1 of Trp 57. The N5 atom of flavin interacts with the amide NH of Ile 59 in A . 7120, whereas in A . nidulans it interacts with the amide NH of Val 59 in a similar manner. In C. crispus flavodoxin, N5 forms a hydrogen bond with the side chain hydroxyl group of the equivalent Thr 58. The hydrogen bond distances to the backbone NH groups in the first two flavodoxins are 3.6 A and 3.5 A , respectively, whereas in the third flavodoxin the distance is 3.1 A , close to the normal value. Even though the hydrogen bond distances are long in the first two cases, still they might have significant energy because their microenvironment in the protein is not accessible to solvent. In all three long-chain flavodoxins, a water molecule bridges the ends of the inserted loop in the os strand and minimally perturbs its hydrogen bonding with p4. Many of the water molecules in these proteins interact with the flavin binding loops. The conserved &core of the three long-chain and two short-chain flavodoxins superpose with root mean square deviations ranging from 0.48 A to 0.97 A .

Crystal Structure and Functional Characterization of Yeast YLR011wp, an Enzyme with NAD(P)H-FMN and Ferric Iron Reductase Activities

“…of 1.8 Å over 143 C␣ positions) (Protein Data Bank code 1NNI) and flavodoxins from the cyanobacterium Anabaena (14% sequence identity, r.m.s.d. of 1.9 Å over 118 C␣ positions) (19) and from Helicobacter pylori (17% sequence identity, r.m.s.d. of 1.9 Å over 117 C␣ positions) (6).…”

“…Although NAD and NADP are soluble cofactors used by dehydrogenases, FAD and FMN usually work as prosthetic groups in flavoproteins to which they are tightly bound. Flavodoxins are small monomeric flavoproteins (15)(16)(17)(18)(19)(20)(21)(22) kDa) that noncovalently bind a single FMN molecule, acting as a redox center (1). The flavodoxin scaffold contributes to the mechanism of electron transfer by stabilizing the FMN molecule in an environment that promotes the highly negative redox potential required for its biochemical activity.…”

Six new candidate members of the α/β twisted open‐sheet family detected by sequence similarity to flavodoxin

“…To evaluate the structural and functional relevance of the detected sequence similarities, we referred to 6 known structures of flavodoxins (Burnett et al, 1974;Smith et al, 1983;van Mierlo et al, 1990;Watt et al, 1991;Fukuyama et al, 1992;Rao et al, 1992). The common feature of the flavodoxin fold is a central 5-stranded parallel hydrophobic &sheet sandwiched between 2 pairs of amphipathic a-helices (Fig.…”

“…2). The fifth 0-strand is interrupted by 4 residues in 2 short-chain flavodoxins (Burnett et al, 1974;Watt et al, 1991) or by a long loop insertion in 3 long-chain flavodoxins (Smith et al, 1983;Fukuyama et al, 1992;Rao et al, 1992). A poorly conserved 310-helix is located between 02 and 03.…”

Anabaena Flavodoxin as an Electron Carrier from Photosystem I to Ferredoxin-NADP+ Reductase. Role of Flavodoxin Residues in Protein−Protein Interaction and Electron Transfer

“…In cyanobacteria and certain algae, Fld is synthesized instead of Fd when the organism is grown under low-iron conditions and replaces it in the transfer of one electron from PSI to FNR by shuttling between the semiquinone and hydroquinone states (15). Although the three-dimensional structure of Anabaena Fld is known (16), the structure of the FNR-Fld complex remains undetermined. Biochemical studies indicate that Fd and Fld interact with the same region on the FNR surface (5,17,18).…”