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		PDBsum entry 1b0v Go to PDB code: Electron transport PDB id 1b0v Loading ... Contents Protein chains 106 a.a.* Ligands SF4 ×4 F3S ×4 * Residue conservation analysis PDB id: 1b0v Links PDBe RCSB MMDB JenaLib Proteopedia CATH SCOP PDBSWS PDBePISA CSA ProSAT Name: Electron transport Title: I40n mutant of azotobacter vinelandii fdi Structure: Protein (ferredoxin). Chain: a, b, c, d. Engineered: yes. Mutation: yes Source: Azotobacter vinelandii. Organism_taxid: 354. Strain: jg100. Expressed in: azotobacter vinelandii. Expression_system_taxid: 354 Resolution: 2.80Å R-factor: 0.209 Authors: V.Sridhar,G.S.Prasad,C.D.Stout,K.Chen,B.K.Burgess Key ref: K.Chen et al. (1999). Alteration of the reduction potential of the [4Fe-4S](2+/+) cluster of Azotobacter vinelandii ferredoxin I.J Biol Chem,274, 36479-36487.PubMed id: 10593945 DOI: 10.1074/jbc.274.51.36479 Date: 12-Nov-98 Release date: 19-Jan-00 PROCHECK Headers References Protein chains ? 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.274.51.36479 J Biol Chem 274:36479-36487 (1999) PubMed id: 10593945 Alteration of the reduction potential of the [4Fe-4S](2+/+) cluster of Azotobacter vinelandii ferredoxin I. K.Chen, G.J.Tilley, V.Sridhar, G.S.Prasad, C.D.Stout, F.A.Armstrong, B.K.Burgess. ABSTRACT The [4Fe-4S](2+/+) cluster of Azotobacter vinelandii ferredoxin I (FdI) has an unusually low reduction potential (E(0')) relative to other structurally similar ferredoxins. Previous attempts to raise that E(0') by modification of surface charged residues were unsuccessful. In this study mutants were designed to alter the E(0') by substitution of polar residues for nonpolar residues near the cluster and by modification of backbone amides. Three FdI variants, P21G, I40N, and I40Q, were purified and characterized, and electrochemical E(0') measurements show that all had altered E(0') relative to native FdI. For P21G FdI and I40Q FdI, the E(0') increased by +42 and +53 mV, respectively validating the importance of dipole orientation in control of E(0'). Protein Dipole Langevin Dipole calculations based on models for those variants accurately predicted the direction of the change in E(0') while overestimating the magnitude. For I40N FdI, initial calculations based on the model predicted a +168 mV change in E(0') while a -33 mV change was observed. The x-ray structure of that variant, which was determined to 2.8 A, revealed a number of changes in backbone and side chain dipole orientation and in solvent accessibility, that were not predicted by the model and that were likely to influence E(0'). Subsequent Protein Dipole Langevin Dipole calculations (using the actual I40N x-ray structures) did quite accurately predict the observed change in E(0'). Selected figure(s) Figure 1. Fig. 1. Structural representation of the amino acid residues of interest in this study, Asn, Gln, Ile, Pro, and Gly with the orientation of the dipoles shown by the arrows. Figure 2. Fig. 2. Stereo representation of the relative positions of the residues of interest in this study, Ile^40, Ile^34, and Pro21, relative to the [4Fe-4S]2+/+ cluster of FdI taken from the 1.35-Å oxidized structure, which includes hydrogen atoms in the refinement (34). The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999,274, 36479-36487) copyright 1999. Figures were selected by an automated process. Literature references that cite this PDB file's key reference PubMed id Reference 19820092 Y.L.Chiang, Y.C.Hsieh, J.Y.Fang, E.H.Liu, Y.C.Huang, P.Chuankhayan, J.Jeyakanthan, M.Y.Liu, S.I.Chan, and C.J.Chen (2009). Crystal structure of Adenylylsulfate reductase from Desulfovibrio gigas suggests a potential self-regulation mechanism involving the C terminus of the beta-subunit. J Bacteriol,191, 7597-7608. PDB code: 3gyx 18729093 M.S.Koay, M.L.Antonkine, W.Gärtner, and W.Lubitz (2008). Modelling low-potential [Fe4S4] clusters in proteins. Chem Biodivers,5, 1571-1587. 18643707 R.Chakrabarti, H.Rabitz, S.L.Springs, and G.L.McLendon (2008). Mutagenic evidence for the optimal control of evolutionary dynamics. Phys Rev Lett,100, 258103. 17385891 M.S.Rogers, E.M.Tyler, N.Akyumani, C.R.Kurtis, R.K.Spooner, S.E.Deacon, S.Tamber, S.J.Firbank, K.Mahmoud, P.F.Knowles, S.E.Phillips, M.J.McPherson, and D.M.Dooley (2007). The stacking tryptophan of galactose oxidase: a second-coordination sphere residue that has profound effects on tyrosyl radical behavior and enzyme catalysis. Biochemistry,46, 4606-4618. PDB codes: 2eib 2eic 2eid 2eie 16133205 G.Battistuzzi, M.Bellei, M.Borsari, G.Di Rocco, A.Ranieri, and M.Sola (2005). Axial ligation and polypeptide matrix effects on the reduction potential of heme proteins probed on their cyanide adducts. J Biol Inorg Chem,10, 643-651. 11842205 G.Fritz, A.Roth, A.Schiffer, T.Büchert, G.Bourenkov, H.D.Bartunik, H.Huber, K.O.Stetter, P.M.Kroneck, and U.Ermler (2002). Structure of adenylylsulfate reductase from the hyperthermophilic Archaeoglobus fulgidus at 1.6-A resolution. Proc Natl Acad Sci U S A,99, 1836-1841. PDB codes: 1jnr 1jnz 11875515 K.Chen, C.A.Bonagura, G.J.Tilley, J.P.McEvoy, Y.S.Jung, F.A.Armstrong, C.D.Stout, and B.K.Burgess (2002). Crystal structures of ferredoxin variants exhibiting large changes in [Fe-S] reduction potential. Nat Struct Biol,9, 188-192. PDB codes: 1f5b 1f5c 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.