PDBsum entry 1fdb

Electron transport(iron-sulfur)

PDB id: 1fdb

Contents

Protein chain

106 a.a.

Ligands

SF4

F3S

Waters ×23

References listed in PDB file

Key reference

Title

Crystal structures of oxidized and reduced azotobacter vinelandii ferredoxin at ph 8 and 6.

Author

C.D.Stout.

Ref.

J Biol Chem, 1993, 268, 25920-25927.

PubMed id

8245025

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 percentage match of 94%.

Abstract

Crystal structures of Azotobacter vinelandii ferredoxin I (FdI) have been solved and refined at 2.2 to 1.9-A resolution at pH 8 and 6 for both the oxidized and dithionite-reduced proteins. Only the [3Fe-4S] cluster is reduced by dithionite. The four structures (denoted FdI8ox, FdI8red, FdI6ox, and FdI6red) have been compared to address three questions: the effect of reduction at pH 8, the effect of pH change on the structure, and the effect of reduction at pH 6. Comparison of the FdI8ox and FdI8red structures shows that Asp-15 changes conformation in a manner consistent with increased anionic repulsion between this residue and the reduced [3Fe-4S]0 cluster. By revealing an electrostatic interaction between Asp-15 and the [3Fe-4S] cluster, this result supports the conclusion in the accompanying paper (Shen, B., Martin, L. L., Butt, J. N., Armstrong, F. A., Stout, C. D., Jensen, G. M., Stephens, P. J., LaMar, G. N., Gorst, C. M., and Burgess, B. K. (1993) J. Biol. Chem. 268, 25928-25939) that Asp-15 participates in protonation of the reduced [3Fe-4S]0 cluster at acid pH. The [3Fe-4S]0 cluster in the FdI8red structure also displays a distinct shift within the protein as well as internal distortions when compared to the [3Fe-4S]+ cluster in the FdI8ox structure. Comparison of the FdI8ox and FdI6ox structures shows that pH change does not have any significant effect on the [3Fe-4S]+ cluster or surrounding residues. Comparison of the FdI6ox and FdI6red structures shows that reduction at pH 6 also does not have any significant effect on the [3Fe-4S] cluster or Asp-15. The absence of structural change supports the conclusion that at acid pH, the reduced [3Fe-4S] cluster is protonated, i.e. [3Fe-4S]0-H+ (Shen et al., 1993). The cluster is not shifted or distorted as in the FdI8red structure. Instead, the [3Fe-4S]o-H+ cluster FdI8red is structurally similar to the [3Fe-4S]+ cluster (FdI8ox, FdI6ox), which has the same net charge. An Asp-15-Lys-84 salt bridge is observed in all four structures, indicating that Asp-15 is ionized at pH 8 and 6. An ionized state for Asp-15 is also implied by a lack of conformational change in Lys-84; the side chain of this residue rearranges when Asp-15 is substituted with a neutral amino acid (Shen et al., 1993).(ABSTRACT TRUNCATED AT 400 WORDS)

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