PDBsum entry 1b13

Electron transport

PDB id: 1b13

Contents

Protein chain

54 a.a. *

Metals

_FE

Waters ×40

* Residue conservation analysis

PDB id:

1b13

Name:

Electron transport

Title:

Clostridium pasteurianum rubredoxin g10a mutant

Structure:

Protein (rubredoxin). Chain: a. Engineered: yes. Mutation: yes

Source:

Clostridium pasteurianum. Organism_taxid: 1501. Strain: jm109. Cellular_location: cytoplasm. Gene: clorub. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.50Å R-factor: 0.171 R-free: 0.191

Authors:

M.J.Maher,J.M.Guss,M.C.J.Wilce,A.G.Wedd

Key ref:

M.J.Maher et al. (1999). Rubredoxin from Clostridium pasteurianum. Structures of G10A, G43A and G10VG43A mutant proteins. Mutation of conserved glycine 10 to valine causes the 9-10 peptide link to invert. Acta Crystallogr D Biol Crystallogr, 55, 962-968. PubMed id: 10216292 DOI: 10.1107/S0907444999001900

Date:

26-Nov-98 Release date: 27-May-99

Protein chain

P00268  (RUBR_CLOPA) -  Rubredoxin from Clostridium pasteurianum

Seq: 54 a.a.

Struc: 54 a.a.*

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

DOI no: 10.1107/S0907444999001900

Acta Crystallogr D Biol Crystallogr 55:962-968 (1999)

PubMed id: 10216292

Rubredoxin from Clostridium pasteurianum. Structures of G10A, G43A and G10VG43A mutant proteins. Mutation of conserved glycine 10 to valine causes the 9-10 peptide link to invert.

M.J.Maher, Z.Xiao, M.C.Wilce, J.M.Guss, A.G.Wedd.

ABSTRACT

The four cysteine ligands which coordinate the Fe atom in the electron-transfer protein rubredoxin lie on loops of the polypeptide which form approximate local twofold symmetry. The cysteine ligands in the protein from Clostridium pasteurianum lie at positions 6, 9, 39 and 42. Two glycine residues adjacent to the cysteine ligands at positions 10 and 43 are conserved in all rubredoxins, consistent with the proposal that a beta-carbon substituent at these positions would eclipse adjacent peptide carbonyl groups [Adman et al. (1975). Proc. Natl Acad. Sci. USA, 72, 4854-4858]. X-ray crystal structures of the three mutant proteins G10A, G43A and G10VG43A are reported. The crystal structures of the single-site mutations are isomorphous with the native protein, space group R3; unit-cell parameters are a = 64.3, c = 32.9 A for G10A and a = 64.4, c = 32.8 A for G43A. The crystals of the double mutant, G10VG43A, were in space group P43212, unit-cell parameters a = 61.9, c = 80.5 A, with two molecules per asymmetric unit. The observed structural perturbations support the hypothesis that mutation of the conserved glycine residues would introduce strain into the polypeptide. In particular, in the G10VG43A protein substitution of valine at Gly10 causes the 9-10 peptide link to invert, relieving steric interaction between Cys9 O and Val10 Cbeta. This dramatic change in conformation is accompanied by the loss of the 10N-HcO6 hydrogen bond, part of the chelate loop Thr5-Tyr11. The new conformation allows retention of the 11N-HcS9 hydrogen bond, but converts it from a type II to a type I hydrogen bond. This occurs at the cost of a less tightly packed structure. The structural insights allow rationalization of 1H NMR data reported previously for the 113CdII-substituted proteins and of the negative shifts observed in the FeIII/FeII mid-point potentials upon mutation.

Selected figure(s)

Figure 1.
Figure 1 N-H S interactions (broken lines) around the Fe(S-Cys)[4] centre in CpRd (generated from the coordinates of 5rxn in the Protein Data Bank). The pseudo-twofold axis (see text) is perpendicular to the page, passing though the Fe atom.

Figure 3.
Figure 3 Electron-density difference map for the G10VG434A structure in the region of residue 10. Colour coding as in Fig. 2-. Major positive peaks are associated with the Gly10 C^ atom, indicating the position of the additional Pr^i side chain of Val10.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 962-968) copyright 1999.

Figures were selected by an automated process.