PDBsum entry 1f5c

Electron transport

PDB id: 1f5c

Contents

Protein chain

106 a.a. *

Ligands

SO4

F3S

SF4

Waters ×165

* Residue conservation analysis

PDB id:

1f5c

Name:

Electron transport

Title:

Crystal structure of f25h ferredoxin 1 mutant from azotobacter vinelandii at 1.75 angstrom resolution

Structure:

Ferredoxin 1. Chain: a. Synonym: fdi. Engineered: yes. Mutation: yes

Source:

Azotobacter vinelandii. Organism_taxid: 354. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.75Å R-factor: 0.204 R-free: 0.227

Authors:

K.Chen,C.A.Bonagura,G.J.Tilley,Y.S.Jung,F.A.Armstrong,C.D.Stout, B.K.Burgess

Key ref:

K.Chen et al. (2002). Crystal structures of ferredoxin variants exhibiting large changes in [Fe-S] reduction potential. Nat Struct Biol, 9, 188-192. PubMed id: 11875515 DOI: 10.1038/nsb751

Date:

13-Jun-00 Release date: 28-Jun-00

Protein chain

P00214  (FER1_AZOVI) -  Ferredoxin-1 from Azotobacter vinelandii

Seq: 107 a.a.

Struc: 106 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1038/nsb751

Nat Struct Biol 9:188-192 (2002)

PubMed id: 11875515

Crystal structures of ferredoxin variants exhibiting large changes in [Fe-S] reduction potential.

K.Chen, C.A.Bonagura, G.J.Tilley, J.P.McEvoy, Y.S.Jung, F.A.Armstrong, C.D.Stout, B.K.Burgess.

ABSTRACT

clusters is a longstanding fundamental problem in bioinorganic chemistry. Two site-directed variants of Azotobacter vinelandii ferredoxin I (FdI) that show cluster E0' (100--200 mV versus standard hydrogen electrode (SHE)) have been characterized. High resolution X-ray structures of F2H and F25H variants in their oxidized forms, and circular dichroism (CD) and electron paramagnetic resonance (EPR) of the reduced forms indicate that the overall structure is not affected by the mutations and reveal that there is no increase in solvent accessibility nor any reorientation of backbone amide dipoles or NH--S bonds. The structures, combined with detailed investigation of the variation of E0' with pH and temperature, show that the largest increases in E0' result from the introduction of positive charge due to protonation of the introduced His residues. The smaller (50--100 mV) increases observed for the neutral form are proposed to occur by directing a Hdelta+--Ndelta- dipole toward the reduced form of the cluster.

Selected figure(s)

Figure 1.
Figure 1. Crystal structures of FdI mutants showing His 2 and His 25 contacts, solvent accessibility and electron density. Stereo diagrams showing contacts <4 Å from His N atoms to [Fe−S] clusters and hydrogen bonds (green dotted lines). Hydrogen bonds involving water molecules are gray dotted lines. The corresponding Phe residues in native FdI are shown based on least squares superposition of native FdI onto each mutant FdI. Atoms are colored orange (Fe), yellow (S), red (O), blue (N), purple (His C) and gray (C). a, The F2H mutant structure refined at 1.62 Å resolution. Contacts <4 Å from His 2 atoms to sulfur atoms of the [[4Fe−4S](Cys[4])]^2- center include N 1−S (3.64 Å) and C −S (3.63 Å). Both conformers of Glu 46 are shown. b, The F25H mutant structure refined at 1.75 Å resolution. Contacts <4 Å from His 25 atoms to sulfur atoms of the [[4Fe−4S](Cys[4])]^2- center are N epsilon 2−S (3.80 Å) and C epsilon 1−S (3.68 Å), from His 25 atoms to Cys 20 N 1−S (3.88 Å) and C epsilon 1−S (3.79 Å), and from His 25 atoms to Cys 16 ([[3Fe−4S](Cys[3])]^2- center) N epsilon 2−S (3.74 Å) and C 2−S (3.94 Å). The solvent-accessible surface of the c, FdI F2H and d, F25H mutants. The electron density of each His residue is also shown. Atoms and their corresponding surfaces are colored as in (a,b). His 2 is completely buried except for a small portion of C epsilon 1 (purple dots in (c)). His 25 is also completely buried except for a contact of N 1 to a water molecule as shown in (b). Electron density maps are calculated with [A] coefficients and contoured at 1.5 .

Figure 4.
Figure 4. Protonation of His 25, not of the cluster, causes the pH dependence of reduction potential of the [[3Fe−4S](Cys[3])]^2-/3- center in F25H. a, CD spectra of native FdI and F25H FdI reduced by sodium dithionite at different pH values: pH 6.0 (thin line) and pH 8.0 (thick line). All samples were in 50 mM TAPS, 50 mM PIPES and 2 mM sodium dithionite. The observed spectral change for native FdI is due to protonation of a [2]-S for the [[3Fe−4S](Cys[3])]^3- center^26. b, The thermodynamics of the one-electron reduction of the [[3Fe−4S](Cys[3])]^2- cluster as measured from the temperature dependence of E^0'. The total free energy change ( G) is shown along with its enthalpic ( H) and entropic (-T S[red]) components. Data are for native FdI at pH 8.5 (no associated proton transfer), F25H FdI at pH 9.5 (no associated proton transfer), wild type FdI at pH 5.0 (associated protonation of the cluster) and F25H FdI at pH 5.0 (associated protonation of H25). Errors are 0.5 kJmol^-1 for G[red] and 2 kJ mol for S[red] and H[red].

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 188-192) copyright 2002.

Figures were selected by an automated process.