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		PDBsum entry 1ff2 Go to PDB code: Electron transport PDB id 1ff2 Loading ... Contents Protein chain 106 a.a.* Ligands SF4 F3S Waters ×48 * Residue conservation analysis PDB id: 1ff2 Links PDBe RCSB MMDB JenaLib Proteopedia CATH SCOP PDBSWS PDBePISA CSA ProSAT Name: Electron transport Title: Crystal structure of the c42d mutant of azotobacter vinelandii 7fe ferredoxin (fdi) Structure: Ferredoxin i. Chain: a. Synonym: fdi, ferredoxin [3fe-4s][4fe-4s]. Engineered: yes. Mutation: yes Source: Azotobacter vinelandii. Organism_taxid: 354. Expressed in: escherichia coli. Expression_system_taxid: 562 Resolution: 2.30Å R-factor: 0.217 R-free: 0.269 Authors: C.D.Stout,B.K.Burgess Key ref: Y.S.Jung et al. (2000). Structure of C42D Azotobacter vinelandii FdI. A Cys-X-X-Asp-X-X-Cys motif ligates an air-stable [4Fe-4S]2+/+ cluster.J Biol Chem,275, 36974-36983.PubMed id: 10961993 DOI: 10.1074/jbc.M004947200 Date: 24-Jul-00 Release date: 21-Aug-00 PROCHECK Headers References Protein chain ? P00214 (FER1_AZOVI) - Ferredoxin-1 from Azotobacter vinelandii Seq:Struc: 107 a.a. 106 a.a.* Key: PfamA domain Secondary structure CATH domain * PDB and UniProt seqs differ at 1 residue position (black cross) DOI no: 10.1074/jbc.M004947200 J Biol Chem 275:36974-36983 (2000) PubMed id: 10961993 Structure of C42D Azotobacter vinelandii FdI. A Cys-X-X-Asp-X-X-Cys motif ligates an air-stable [4Fe-4S]2+/+ cluster. Y.S.Jung, C.A.Bonagura, G.J.Tilley, H.S.Gao-Sheridan, F.A.Armstrong, C.D.Stout, B.K.Burgess. ABSTRACT All naturally occurring ferredoxins that have Cys-X-X-Asp-X-X-Cys motifs contain [4Fe-4S](2+/+) clusters that can be easily and reversibly converted to [3Fe-4S](+/0) clusters. In contrast, ferredoxins with unmodified Cys-X-X-Cys-X-X-Cys motifs assemble [4Fe-4S](2+/+) clusters that cannot be easily interconverted with [3Fe-4S](+/0) clusters. In this study we changed the central cysteine of the Cys(39)-X-X-Cys(42)-X-X-Cys(45) of Azotobacter vinelandii FdI, which coordinates its [4Fe-4S](2+/+) cluster, into an aspartate. UV-visible, EPR, and CD spectroscopies, metal analysis, and x-ray crystallography show that, like native FdI, aerobically purified C42D FdI is a seven-iron protein retaining its [4Fe-4S](2+/+) cluster with monodentate aspartate ligation to one iron. Unlike known clusters of this type the reduced [4Fe-4S](+) cluster of C42D FdI exhibits only an S = 1/2 EPR with no higher spin signals detected. The cluster shows only a minor change in reduction potential relative to the native protein. All attempts to convert the cluster to a 3Fe cluster using conventional methods of oxygen or ferricyanide oxidation or thiol exchange were not successful. The cluster conversion was ultimately accomplished using a new electrochemical method. Hydrophobic and electrostatic interaction and the lack of Gly residues adjacent to the Asp ligand explain the remarkable stability of this cluster. Selected figure(s) Figure 1. Fig. 1. Structures of [3Fe-4S] and [4Fe-4S] clusters. S, inorganic sulfide; S (cys), cysteine. Figure 8. Fig. 8. X-ray crystal structure of [4Fe-4S] cluster regions in C42D FdI. The view is similar to that in Fig. 5. Atoms are colored as follows: Fe, orange; S, yellow; O, red; N, blue; C, gray. A, all atoms of residues 19-22 and 40-45, and the [4Fe-4S] cluster, are shown. Dotted lines indicate short hydrophobic contacts of Asp42 with amino acid residues Pro21, Ile^40, and Leu44, and hydrogen bonds between O 1 of Asp42 and Pro21 and between O 2 of Asp42 and the amide of Leu44. B, same view as in A with all atoms of residues 19-22 and 40-45, and the cluster, rendered as spheres with radii corresponding to van der Waals radii. Short contacts between oxygen atoms of the Asp42 side chain include 3.31 Å to C 1 of Ile^40 and 3.33 Å to C of Leu44. The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000,275, 36974-36983) copyright 2000. Figures were selected by an automated process. Literature references that cite this PDB file's key reference PubMed id Reference 15163408 E.Gross, D.B.Kastner, C.A.Kaiser, and D.Fass (2004). Structure of Ero1p, source of disulfide bonds for oxidative protein folding in the cell. Cell,117, 601-610. PDB codes: 1rp4 1rq1 14996793 J.A.Lewis, A.R.Horswill, B.E.Schwem, and J.C.Escalante-Semerena (2004). The Tricarballylate utilization (tcuRABC) genes of Salmonella enterica serovar Typhimurium LT2. J Bacteriol,186, 1629-1637. 15181002 S.Agarwalla, R.M.Stroud, and B.J.Gaffney (2004). Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies. J Biol Chem,279, 34123-34129. 11900536 T.E.Messick, N.H.Chmiel, M.P.Golinelli, M.R.Langer, L.Joshua-Tor, and S.S.David (2002). Noncysteinyl coordination to the [4Fe-4S]2+ cluster of the DNA repair adenine glycosylase MutY introduced via site-directed mutagenesis. Structural characterization of an unusual histidinyl-coordinated cluster. Biochemistry,41, 3931-3942. PDB code: 1kqj 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 codes are shown on the right.