PDBsum entry 1clf

Electron transfer (iron-sulfur protein)

PDB id: 1clf

Contents

Protein chain

55 a.a. *

Ligands

SF4 ×2

* Residue conservation analysis

PDB id:

1clf

Name:

Electron transfer (iron-sulfur protein)

Title:

Clostridium pasteurianum ferredoxin

Structure:

Ferredoxin. Chain: a

Source:

Clostridium pasteurianum. Organism_taxid: 1501. Strain: winogradsky. Atcc: 6013

NMR struc:

16 models

Authors:

I.Bertini,A.Donaire,B.A.Feinberg,C.Luchinat,M.Piccioli,H.Yuan

Key ref:

I.Bertini et al. (1995). Solution structure of the oxidized 2[4Fe-4S] ferredoxin from Clostridium pasteurianum. Eur J Biochem, 232, 192-205. PubMed id: 7556151

Date:

21-Jun-95 Release date: 29-Jan-96

Protein chain

P00195  (FER_CLOPA) -  Ferredoxin from Clostridium pasteurianum

Seq: 56 a.a.

Struc: 55 a.a.

Eur J Biochem 232:192-205 (1995)

PubMed id: 7556151

Solution structure of the oxidized 2[4Fe-4S] ferredoxin from Clostridium pasteurianum.

I.Bertini, A.Donaire, B.A.Feinberg, C.Luchinat, M.Piccioli, H.Yuan.

ABSTRACT

Following the recently developed approach to the solution structure of paramagnetic high-potential iron-sulfur proteins, the three-dimensional structure in solution of the oxidized Clostridium pasteurianum ferredoxin has been solved by 1H-NMR. The X-ray structure is not available. The protein contains 55 amino acids and two [4Fe-4S] clusters. In the oxidized state, the clusters have S = 0 ground states, but are paramagnetic because of thermal population of excited states. Due to the somewhat small size of the protein and to the presence of two clusters, approximately 55% of the residues have at least one proton with a non-selective T1 smaller than 25 ms. The protein has thus been used as a test system to challenge the present paramagnetic NMR methodology both in achieving an extended assignment and in obtaining a suitable number of constraints. 79% of protein protons have been assigned. Analogy with other ferredoxins of known structure has been of help to speed up the final stages of the assignment, although we have shown that this independent information is not necessary. In addition to dipolar connectivities, partially detected through tailored experiments, 3JHN-H alpha, H-bond constraints and dihedral angle constraints on the Cys chi 2 angles have been generated by using a recently derived Karplus-type relationship for the hyperfine shifts of cysteine beta CH2 protons. In total, 456 constraints have been used in distance geometry calculations. The final quality of the structures is satisfactory, with root-mean-square deviation values of 66 pm and 108 pm for backbone and heavy atoms, respectively. The resulting structure is compared with that of Clostridium acidi urici ferredoxin [Duée, E. D., Fanchon, E., Vicat, J., Sieker, L. C., Meyer, J. & Moulis, J.-M. (1994) J. Mol. Biol. 243, 683-695]. The two proteins are very similar in the overall folding, secondary structure elements and side-chain orientations. The C alpha root-mean-square deviation values between the X-ray-determined C. acidi urici ferredoxin structure and the conformer with lowest energy of the C. pasteurianum ferredoxin family is 78 pm (residues 3-53). Discrepancies in residues 26-28 may arise from the disorder observed in the X-ray structure in that region.