PDBsum entry 1m2a

Electron transport

PDB id: 1m2a

Contents

Protein chains

103 a.a. *

Ligands

FES ×2

SO4

Metals

_ZN ×4

Waters ×187

* Residue conservation analysis

PDB id:

1m2a

Name:

Electron transport

Title:

Crystal structure at 1.5 angstroms resolution of the wild type thioredoxin-like [2fe-2s] ferredoxin from aquifex aeolicus

Structure:

[2fe-2s] ferredoxin. Chain: a, b. Synonym: aafd4. Engineered: yes

Source:

Aquifex aeolicus. Organism_taxid: 63363. Gene: fdx4. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.50Å R-factor: 0.184 R-free: 0.216

Authors:

A.P.Yeh,X.I.Ambroggio,S.L.A.Andrade,O.Einsle,C.Chatelet,J.Meyer, D.C.Rees

Key ref:

A.P.Yeh et al. (2002). High resolution crystal structures of the wild type and Cys-55-->Ser and Cys-59-->Ser variants of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus. J Biol Chem, 277, 34499-34507. PubMed id: 12089152 DOI: 10.1074/jbc.M205096200

Date:

22-Jun-02 Release date: 18-Sep-02

Protein chains

O66511  (FER2_AQUAE) -  Ferredoxin, 2Fe-2S from Aquifex aeolicus (strain VF5)

Seq: 111 a.a.

Struc: 103 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1074/jbc.M205096200

J Biol Chem 277:34499-34507 (2002)

PubMed id: 12089152

High resolution crystal structures of the wild type and Cys-55-->Ser and Cys-59-->Ser variants of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus.

A.P.Yeh, X.I.Ambroggio, S.L.Andrade, O.Einsle, C.Chatelet, J.Meyer, D.C.Rees.

ABSTRACT

ferredoxin (Fd4) from Aquifex aeolicus adopts a thioredoxin-like ferredoxins. Crystal structures of the Cys-55 --> Ser (C55S) and Cys-59 --> Ser (C59S) variants of this protein have been determined to 1.25 A and 1.05 A resolution, respectively, whereas the resolution of the wild type (WT) has been extended to 1.5 A. The cluster, cluster-containing protein, namely, pronounced distortions in the cysteine coordination to the cluster and a Calpha-H-Sgamma hydrogen bond between cluster ligands Cys-55 and Cys-9. These features may contribute to the unusual clusters in WT and variants of this ferredoxin. The structures of the two variants of Fd4, in which single cluster are replaced by serine, establish the metric details of serine-ligated Fe-S active sites with unprecedented accuracy. Both the cluster and its surrounding protein matrix change in subtle ways to accommodate this ligand substitution, particularly in terms of distortions of the Fe(2)S(2) inorganic core from planarity and displacements of the polypeptide chain. These high resolution structures illustrate how the interactions between polypeptide chains and Fe-S active sites reflect combinations of flexibility and rigidity on the part of both partners; these themes are also evident in more complex systems, as exemplified by changes associated with serine ligation of the nitrogenase P cluster.

Selected figure(s)

Figure 3.
Fig. 3. A, stereoview of the [2Fe-2S] cluster and its ligands from the WT ( cyan), C55S (yellow), and C59S (purple) structures upon superposition of the corresponding 101 C atoms of the three structures, showing the varying degree of positional shifts that occur in the inorganic core as well as residues 55 and 59 caused by the cysteine to serine substitutions. B, stereoview of the same region, viewed from a direction perpendicular to that in A, illustrates the varying degrees to which the inorganic core is distorted in each structure. The color scheme is the same as in A.

Figure 4.
Fig. 4. Stereoview comparing the P cluster of nitrogenase in the oxidized (transparent ball-and-stick model in cyan) and reduced (solid ball-and-stick model in gray) states (39, 40). In the oxidized state, one of the irons is coordinated by the side chain of Ser- 188, whereas in the reduced state this iron is shifted and coordinates an inorganic sulfur in the cluster instead. The coloring scheme is as in Fig. 3. PDB entries 2MIN (oxidized) and 3MIN (reduced) were used for this figure.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 34499-34507) copyright 2002.

Figures were selected by the author.

Author's comment

These high resolution structures illustrate how the interactions between polypeptide chains and Fe-S active sites reflect combinations of flexibility and rigidity on the part of both partners; these themes are also evident in more complex systems, as exemplified by changes associated with serine ligation of the nitrogenase P cluster.
Jacques Meyer