PDBsum entry 1de0

Oxidoreductase

PDB id: 1de0

Contents

Protein chains

289 a.a. *

Ligands

SF4

Waters ×224

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Modulating the midpoint potential of the [4fe-4s] cluster of the nitrogenase fe protein.

Authors

S.B.Jang, L.C.Seefeldt, J.W.Peters.

Ref.

Biochemistry, 2000, 39, 641-648. [DOI no: 10.1021/bi991694v]

PubMed id

10651628

Abstract

Protein-bound [FeS] clusters function widely in biological electron-transfer reactions, where their midpoint potentials control both the kinetics and thermodynamics of these reactions. The polarity of the protein environment around [FeS] clusters appears to contribute largely to modulating their midpoint potentials, with local protein dipoles and water dipoles largely defining the polarity. The function of the [4Fe-4S] cluster containing Fe protein in nitrogenase catalysis is, at least in part, to serve as the nucleotide-dependent electron donor to the MoFe protein which contains the sites for substrate binding and reduction. The ability of the Fe protein to function in this manner is dependent on its ability to adopt the appropriate conformation for productive interaction with the MoFe protein and on its ability to change redox potentials to provide the driving force required for electron transfer. Phenylalanine at position 135 is located near the [4Fe-4S] cluster of nitrogenase Fe protein and has been suggested by amino acid substitution studies to participate in defining both the midpoint potential and the nucleotide-induced changes in the [4Fe-4S] cluster. In the present study, the crystal structure of the Azotobacter vinelandii nitrogenase Fe protein variant having phenylalanine at position 135 substituted by tryptophan has been determined by X-ray diffraction methods and refined to 2.4 A resolution. A comparison of available Fe protein structures not only provides a structural basis for the more positive midpoint potential observed in the tryptophan substituted variant but also suggests a possible general mechanism by which the midpoint potential could be controlled by nucleotide interactions and nitrogenase complex formation.

Secondary reference #1

Title

Crystallographic structure of the nitrogenase iron protein from azotobacter vinelandii.

Authors

M.M.Georgiadis, H.Komiya, P.Chakrabarti, D.Woo, J.J.Kornuc, D.C.Rees.

Ref.

Science, 1992, 257, 1653-1659. [DOI no: 10.1126/science.1529353]

PubMed id

1529353

Secondary reference #2

Title

Conformational variability in structures of the nitrogenase iron proteins from azotobacter vinelandii and clostridium pasteurianum.

Authors

J.L.Schlessman, D.Woo, L.Joshua-Tor, J.B.Howard, D.C.Rees.

Ref.

J Mol Biol, 1998, 280, 669-685. [DOI no: 10.1006/jmbi.1998.1898]

PubMed id

9677296

Figure 4.
Figure 4. (a) A representation of one Fe-protein monomer colored according to rms deviation in C a position, follow- ing superposition of the four AV2 and CP2 subunits. Residues with high rms deviation, such as the C terminus, are indicated in red; regions of strong structural conservation, such as the b-sheet, are indicated in dark blue. (b) A rep- resentation of one Fe-protein monomer colored according to amino acid residue conservation, following alignment of 59 Fe-protein sequences. Residues in red, such as the C terminus, indicate the regions of greatest sequence variability; those in dark blue, such as the 4Fe:4S cluster ligands, P-loop, Switch I and Switch II residues, indicate regions of strongest sequence conservation. In both (a) and (b), the view is from the dimer interface, and Av2 residue numbers are included for reference.

Figure 6.
Figure 6. Structural variability in the subunit-subunit interactions near the 4Fe:4S clusters of CP2 and AV2. Subunit A of each protein is shown in red, and subunit B in green. The 4Fe:4S cluster atoms are colored as in Figure 2. Comp- lementary residues on the opposing subunits have been omitted for ease of viewing. (a) Three intersubunit hydrogen bonds are located near the 4Fe:4S cluster in CP2. (b) Crystal packing forces distort this region in AV2, with the loss of several of these intersubunit interactions. The C terminus of a neighboring molecule (shown in cyan) forms two hydrogen bonds with the 4Fe:4S region of subunit A in AV2 at residues Gly96 and Cys97. Despite this conformation- al alteration near the 4Fe:4S cluster in subunit A, the corresponding region in subunit B is undisturbed.

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

Secondary reference #3

Title

Structure of ADP X aif4(-)-Stabilized nitrogenase complex and its implications for signal transduction.

Authors

H.Schindelin, C.Kisker, J.L.Schlessman, J.B.Howard, D.C.Rees.

Ref.

Nature, 1997, 387, 370-376.

PubMed id

9163420