PDBsum entry 1fhh

Electron transport

PDB id: 1fhh

Contents

Protein chain

53 a.a. *

Metals

_FE

Waters ×59

* Residue conservation analysis

PDB id:

1fhh

Name:

Electron transport

Title:

X-ray crystal structure of oxidized rubredoxin

Structure:

Rubredoxin. Chain: a. Synonym: rd. Engineered: yes. Other_details: oxidized

Source:

Clostridium pasteurianum. Organism_taxid: 1501. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.50Å R-factor: 0.197

Authors:

T.Min,C.E.Ergenekan,M.K.Eidsness,T.Ichiye,C.Kang

Key ref:

T.Min et al. (2001). Leucine 41 is a gate for water entry in the reduction of Clostridium pasteurianum rubredoxin. Protein Sci, 10, 613-621. PubMed id: 11344329 DOI: 10.1110/gad.34501

Date:

01-Aug-00 Release date: 14-Mar-01

Protein chain

P00268  (RUBR_CLOPA) -  Rubredoxin from Clostridium pasteurianum

Seq: 54 a.a.

Struc: 53 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1110/gad.34501

Protein Sci 10:613-621 (2001)

PubMed id: 11344329

Leucine 41 is a gate for water entry in the reduction of Clostridium pasteurianum rubredoxin.

T.Min, C.E.Ergenekan, M.K.Eidsness, T.Ichiye, C.Kang.

ABSTRACT

Biological electron transfer is an efficient process even though the distances between the redox moieties are often quite large. It is therefore of great interest to gain an understanding of the physical basis of the rates and driving forces of these reactions. The structural relaxation of the protein that occurs upon change in redox state gives rise to the reorganizational energy, which is important in the rates and the driving forces of the proteins involved. To determine the structural relaxation in a redox protein, we have developed methods to hold a redox protein in its final oxidation state during crystallization while maintaining the same pH and salt conditions of the crystallization of the protein in its initial oxidation state. Based on 1.5 A resolution crystal structures and molecular dynamics simulations of oxidized and reduced rubredoxins (Rd) from Clostridium pasteurianum (Cp), the structural rearrangements upon reduction suggest specific mechanisms by which electron transfer reactions of rubredoxin should be facilitated. First, expansion of the [Fe-S] cluster and concomitant contraction of the NH...S hydrogen bonds lead to greater electrostatic stabilization of the extra negative charge. Second, a gating mechanism caused by the conformational change of Leucine 41, a nonpolar side chain, allows transient penetration of water molecules, which greatly increases the polarity of the redox site environment and also provides a source of protons. Our method of producing crystals of Cp Rd from a reducing solution leads to a distribution of water molecules not observed in the crystal structure of the reduced Rd from Pyrococcus furiosus. How general this correlation is among redox proteins must be determined in future work. The combination of our high-resolution crystal structures and molecular dynamics simulations provides a molecular picture of the structural rearrangement that occurs upon reduction in Cp rubredoxin.

Selected figure(s)

Figure 2.
Fig. 2. The electron density map (2F0--Fc) around residue 41 for (a) the reduced form and (b) the oxidized form. In the reduced form, there are two different conformations of Leu 41 side chain. When the side chain of Leu 41 is in the open conformation, a water molecule (depicted by a star) can be placed in the electron density on the other side in hydrogen bonding distance of the S> atom of Cys 9.

Figure 3.
Fig. 3. Local structure of the reduced form around Fe---S cluster and Leu 41 in its open conformation (open water gate). Placing the side chain of Leu 41 away from Cys 9 S> allows the string of water molecules to approach the Cys 9 S>, with the first water forming a hydrogen bond with Cys 9 S>.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2001, 10, 613-621) copyright 2001.

Figures were selected by an automated process.