PDBsum entry 1fdd

Electron transport(iron-sulfur)

PDB id: 1fdd

Contents

Protein chain

106 a.a.

Ligands

SF4

F3S

Waters ×23

References listed in PDB file

Key reference

Title

Azotobacter vinelandii ferredoxin i. Aspartate 15 facilitates proton transfer to the reduced [3fe-4s] cluster.

Authors

B.Shen, L.L.Martin, J.N.Butt, F.A.Armstrong, C.D.Stout, G.M.Jensen, P.J.Stephens, G.N.La mar, C.M.Gorst, B.K.Burgess.

Ref.

J Biol Chem, 1993, 268, 25928-25939.

PubMed id

8245026

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a perfect match.

Abstract

The [3Fe-4S]+/0 cluster of Azotobacter vinelandii ferredoxin I (AvFdI) has an unusually low and strongly pH-dependent reduction potential (E'0). The reduced cluster exists in two forms, depending upon pH, that exhibit substantially different magnetic circular dichroism (MCD) spectra. Recent studies have established that the MCD changes observed on decreasing the pH from 8.3 (alkaline form) to 6.0 (acid form) cannot be explained either by a change in spin state of the cluster (Stephens, P.J., Jensen, G.M., Devlin, F.J., Morgan, T.V., Stout, C. D., Martin, A.E., and Burgess, B.K. (1991) Biochemistry 30, 3200-3209) or by a major structural change (e.g. ligand exchange) (Stout, C.D. (1993) J. Biol. Chem. 268, 25920-25927). Here, we have examined the influence of aspartate 15 on the pH dependence of the spectroscopic and electrochemical properties of AvFdI by construction of a D15N mutant. Aspartate 15, which is salt-bridged to lysine 84 at the protein surface, is the closest ionizable residue to the [3Fe-4S] cluster. The results show that replacement of aspartate by asparagine results in an approximately 20-mV increase in E'0 for the [3Fe-4S]+/0 cluster at high pH concomitant with an approximately 0.8-pH unit decrease in the pK of the reduced form. The major pH dependence of E'0 is preserved as is the effect observed by MCD. These data eliminate the possibility that the MCD change is due to the presence of Asp-15 and support the conclusion that it originates in direct protonation of the [3Fe-4S]0 cluster, probably on a sulfide ion. Voltammetric studies show that interconversion between [3Fe-4S]+ and [3Fe-4S]0 at acidic pH involves rapid electron transfer followed by proton transfer (for reduction) and then proton transfer followed by electron transfer (for oxidation). Ionized aspartate 15 facilitates proton transfer. Thus, protonation and deprotonation are much slower for D15N relative to the native protein at pH > 5.5. Proton transfer reactions necessary for further reduction of the [3Fe-4S]0 cluster to the [3Fe-4S]- and [3Fe-4S]2- states are also retarded in D15N. The results suggest that the carboxylate-ammonium salt bridge afforded by Asp-15-Lys-84 conducts protons between the cluster and solvent H2O molecules. Overproduction of D15N FdI, but not native FdI, in A. vinelandii has a negative effect on the growth rate of the organism, suggesting that the rate of protonation or deprotonation of the [3Fe-4S]0 cluster may be important in vivo.

Secondary reference #1

Title

Crystallographic analysis of two site-Directed mutants of azotobacter vinelandii ferredoxin.

Authors

J.Soman, S.Iismaa, C.D.Stout.

Ref.

J Biol Chem, 1991, 266, 21558-21562.

PubMed id

1939185

Secondary reference #2

Title

Site-Directed mutagenesis of azotobacter vinelandii ferredoxin i: [fe-S] cluster-Driven protein rearrangement.

Authors

A.E.Martín, B.K.Burgess, C.D.Stout, V.L.Cash, D.R.Dean, G.M.Jensen, P.J.Stephens.

Ref.

Proc Natl Acad Sci U S A, 1990, 87, 598-602. [DOI no: 10.1073/pnas.87.2.598]

PubMed id

2153958

Secondary reference #3

Title

Refinement of the 7 fe ferredoxin from azotobacter vinelandii at 1.9 a resolution.

Author

C.D.Stout.

Ref.

J Mol Biol, 1989, 205, 545-555.

PubMed id

2926817

Secondary reference #4

Title

7-Iron ferredoxin revisited.

Author

C.D.Stout.

Ref.

J Biol Chem, 1988, 263, 9256-9260.

PubMed id

3379067

Secondary reference #5

Title

[4fe-4s]-Cluster-Depleted azotobacter vinelandii ferredoxin i: a new 3fe iron-Sulfur protein.

Authors

P.J.Stephens, T.V.Morgan, F.Devlin, J.E.Penner-Hahn, K.O.Hodgson, R.A.Scott, C.D.Stout, B.K.Burgess.

Ref.

Proc Natl Acad Sci U S A, 1985, 82, 5661-5665. [DOI no: 10.1073/pnas.82.17.5661]

PubMed id

2994040

Secondary reference #6

Title

Structure of azotobacter vinelandii 7fe ferredoxin. Amino acid sequence and electron density maps of residues.

Authors

J.B.Howard, T.W.Lorsbach, D.Ghosh, K.Melis, C.D.Stout.

Ref.

J Biol Chem, 1983, 258, 508-522.

PubMed id

6848518

Secondary reference #7

Title

Iron-Sulfur clusters and protein structure of azotobacter ferredoxin at 2.0 a resolution.

Authors

D.Ghosh, S.O'Donnell, W.Furey, A.H.Robbins, C.D.Stout.

Ref.

J Mol Biol, 1982, 158, 73. [DOI no: 10.1016/0022-2836(82)90451-X]

PubMed id

7120409

Figure 1.
FIG:. 1.5. Opposite view from Fig. 14 showing glutamate 18 and 0x0 in relation to Fr(2) of the [3Fe-3SI luster and adjacent water molecules within 45 A of 0x0. 0, 37 and 044,, are within 35 A of 0x0. Watrr oxygens in adition to 0x0 arr numbered from 109 to 451.

Figure 9.
FIG:. 9. (`o-ordintes of` [4Fr-4SJ(S,), cluster in t,hth tinal model

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #8

Title

Structure of a 7fe ferredoxin from azotobacter vinelandii.

Authors

D.Ghosh, W.Furey, S.O'Donnell, C.D.Stout.

Ref.

J Biol Chem, 1981, 256, 4185-4192.

PubMed id

7217079

Secondary reference #9

Title

Iron-Sulfur clusters in azotobacter ferredoxin at 2.5 a resolution.

Authors

C.D.Stout, D.Ghosh, V.Pattabhi, A.H.Robbins.

Ref.

J Biol Chem, 1980, 255, 1797-1800.

PubMed id

7354058

Secondary reference #10

Title

Structure of the iron-Sulfur clusters in azotobacter ferredoxin at 4.0 angstroms resolution

Author

C.D.Stout.

Ref.

am cryst assoc ,abstr papers, 1979, 6, 97.

Secondary reference #11

Title

Two crystal forms of azotobacter ferredoxin.

Author

C.D.Stout.

Ref.

J Biol Chem, 1979, 254, 3598-3599.

PubMed id

429371

Secondary reference #12

Title

Structure of the iron-Sulphur clusters in azotobacter ferredoxin at 4.0 a resolution.

Author

C.D.Stout.

Ref.

Nature, 1979, 279, 83-84.

PubMed id

450082