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		PDBsum entry 1clf Go to PDB code: Electron transfer (iron-sulfur protein) PDB id 1clf Loading ... Contents Protein chain 55 a.a.* Ligands SF4 ×2 * Residue conservation analysis PDB id: 1clf Links PDBe RCSB MMDB JenaLib Proteopedia CATH SCOP PDBSWS ProSAT 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 PROCHECK Headers References Protein chain ? P00195 (FER_CLOPA) - Ferredoxin from Clostridium pasteurianum Seq:Struc: 56 a.a. 55 a.a. Key: PfamA domain Secondary structure CATH domain 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. Literature references that cite this PDB file's key reference PubMed id Reference 19146411 L.A.Abriata, G.N.Ledesma, R.Pierattelli, and A.J.Vila (2009). Electronic structure of the ground and excited states of the Cu(A) site by NMR spectroscopy. J Am Chem Soc,131, 1939-1946. 17457690 M.Heinnickel, and J.H.Golbeck (2007). Heliobacterial photosynthesis. Photosynth Res,92, 35-53. 17089149 R.Kutty, and G.N.Bennett (2007). Characterization of a novel ferredoxin with N-terminal extension from Clostridium acetobutylicum ATCC 824. Arch Microbiol,187, 161-169. 16596388 P.Giastas, N.Pinotsis, G.Efthymiou, M.Wilmanns, P.Kyritsis, J.M.Moulis, and I.M.Mavridis (2006). The structure of the 2[4Fe-4S] ferredoxin from Pseudomonas aeruginosa at 1.32-A resolution: comparison with other high-resolution structures of ferredoxins and contributing structural features to reduction potential values. J Biol Inorg Chem,11, 445-458. PDB code: 2fgo 16094696 I.Bertini, C.Luchinat, G.Parigi, and R.Pierattelli (2005). NMR spectroscopy of paramagnetic metalloproteins. Chembiochem,6, 1536-1549. 12626505 X.M.Gong, R.Agalarov, K.Brettel, and C.Carmeli (2003). Control of electron transport in photosystem I by the iron-sulfur cluster FX in response to intra- and intersubunit interactions. J Biol Chem,278, 19141-19150. 11463610 B.W.Beck, Q.Xie, and T.Ichiye (2001). Sequence determination of reduction potentials by cysteinyl hydrogen bonds and peptide pipoles in [4Fe-4S] ferredoxins. Biophys J,81, 601-613. 10200154 D.Bentrop, I.Bertini, R.Iacoviello, C.Luchinat, Y.Niikura, M.Piccioli, C.Presenti, and A.Rosato (1999). Structural and dynamical properties of a partially unfolded Fe4S4 protein: role of the cofactor in protein folding. Biochemistry,38, 4669-4680. 9521664 A.Díaz-Quintana, W.Leibl, H.Bottin, and P.Sétif (1998). Electron transfer in photosystem I reaction centers follows a linear pathway in which iron-sulfur cluster FB is the immediate electron donor to soluble ferredoxin. Biochemistry,37, 3429-3439. 9628728 A.Donaire, J.Salgado, and J.M.Moratal (1998). Determination of the magnetic axes of cobalt(II) and nickel(II) azurins from 1H NMR data: influence of the metal and axial ligands on the origin of magnetic anisotropy in blue copper proteins. Biochemistry,37, 8659-8673. 9537448 B.Scheiber, and H.Goldenberg (1998). The surface of rat hepatocytes can transfer iron from stable chelates to external acceptors. Hepatology,27, 1075-1080. 9718300 L.Banci, M.Benedetto, I.Bertini, R.Del Conte, M.Piccioli, and M.S.Viezzoli (1998). Solution structure of reduced monomeric Q133M2 copper, zinc superoxide dismutase (SOD). Why is SOD a dimeric enzyme?. Biochemistry,37, 11780-11791. PDB code: 1ba9 9657695 S.Aono, D.Bentrop, I.Bertini, A.Donaire, C.Luchinat, Y.Niikura, and A.Rosato (1998). Solution structure of the oxidized Fe7S8 ferredoxin from the thermophilic bacterium Bacillus schlegelii by 1H NMR spectroscopy. Biochemistry,37, 9812-9826. PDB codes: 1bc6 1bd6 9354632 D.Bentrop, I.Bertini, C.Luchinat, W.Nitschke, and U.Mühlenhoff (1997). Characterization of the unbound 2[Fe4S4]-ferredoxin-like photosystem I subunit PsaC from the Cyanobacterium synechococcus elongatus. Biochemistry,36, 13629-13637. 9294867 L.Banci, I.Bertini, G.G.Savellini, A.Romagnoli, P.Turano, M.A.Cremonini, C.Luchinat, and H.B.Gray (1997). Pseudocontact shifts as constraints for energy minimization and molecular dynamics calculations on solution structures of paramagnetic metalloproteins. Proteins,29, 68-76. 8617291 D.Bentrop, I.Bertini, C.Luchinat, J.Mendes, M.Piccioli, and M.Teixeira (1996). Paramagnetic NMR analysis of the seven-iron ferredoxin from the hyperthermoacidophilic archaeon Desulfurolobus ambivalens reveals structural similarity to other dicluster ferredoxins. Eur J Biochem,236, 92-99. 8917441 I.Bertini, M.M.Couture, A.Donaire, L.D.Eltis, I.C.Felli, C.Luchinat, M.Piccioli, and A.Rosato (1996). The solution structure refinement of the paramagnetic reduced high-potential iron-sulfur protein I from Ectothiorhodospira halophila by using stable isotope labeling and nuclear relaxation. Eur J Biochem,241, 440-452. 8841114 J.G.Huber, J.M.Moulis, and J.Gaillard (1996). Use of 1H longitudinal relaxation times in the solution structure of paramagnetic proteins. Application to [4Fe-4S] proteins. Biochemistry,35, 12705-12711. 8880900 J.M.Moulis, L.C.Sieker, K.S.Wilson, and Z.Dauter (1996). Crystal structure of the 2[4Fe-4S] ferredoxin from Chromatium vinosum: evolutionary and mechanistic inferences for [3/4Fe-4S] ferredoxins. Protein Sci,5, 1765-1775. PDB code: 1blu 8784186 P.L.Wang, A.Donaire, Z.H.Zhou, M.W.Adams, and G.N.La Mar (1996). Molecular model of the solution structure for the paramagnetic four-iron ferredoxin from the hyperthermophilic archaeon Thermococcus litoralis. Biochemistry,35, 11319-11328. The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.