PDBsum entry 1vjw

Oxidoreductase

PDB id: 1vjw

Contents

Protein chain

59 a.a. *

Ligands

SF4

Waters ×40

* Residue conservation analysis

PDB id:

1vjw

Name:

Oxidoreductase

Title:

Structure of oxidoreductase (NADP+(a),ferredoxin(a))

Structure:

Ferredoxin(a). Chain: a. Engineered: yes

Source:

Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.75Å R-factor: 0.159

Authors:

S.Macedo-Ribeiro,B.Darimont,R.Sterner,R.Huber

Key ref:

S.Macedo-Ribeiro et al. (1996). Small structural changes account for the high thermostability of 1[4Fe-4S] ferredoxin from the hyperthermophilic bacterium Thermotoga maritima. Structure, 4, 1291-1301. PubMed id: 8939753 DOI: 10.1016/S0969-2126(96)00137-2

Date:

09-Oct-96 Release date: 23-Dec-96

Protein chain

P46797  (FER_THEMA) -  Ferredoxin from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 60 a.a.

Struc: 59 a.a.

DOI no: 10.1016/S0969-2126(96)00137-2

Structure 4:1291-1301 (1996)

PubMed id: 8939753

Small structural changes account for the high thermostability of 1[4Fe-4S] ferredoxin from the hyperthermophilic bacterium Thermotoga maritima.

S.Macedo-Ribeiro, B.Darimont, R.Sterner, R.Huber.

ABSTRACT

BACKGROUND: The characterization of the structural features that account for the high thermostability of some proteins is of great scientific and biotechnological interest. Proteins from hyperthermophilic organisms with optimum growth temperatures of 80 degrees C and higher generally show high intrinsic stabilities. The comparison of high resolution X-ray structures of these proteins with their counterparts from mesophilic organisms has therefore helped to identify potentially stabilizing forces in a number of cases. Small monomeric proteins which comprise only a single domain, such as ferredoxins, are especially suitable for such comparisons since the search for determinants of protein stability is considerably simplified. RESULTS: The 1.75 A crystal ferredoxin from Thermotoga maritima (FdTm) was determined and compared with other monocluster-containing ferredoxins with different degrees of thermostability. CONCLUSIONS: A comparison of the three-dimensional structure of FdTm with that of ferredoxins from mesophilic organisms suggests that the very high thermostability of FdTm is unexpectedly achieved without large changes of the overall protein structure. Instead, an increased number of potentially stabilizing features is observed in FdTm, compared with mesophilic ferredoxins. These include stabilization of alpha helices, replacement of residues in strained conformation by glycines, strong docking of the N-terminal methionine and an overall increase in the number of hydrogen bonds. Most of these features stabilize several secondary structure elements and improve the overall rigidity of the polypeptide backbone. The decreased flexibility will certainly play a relevant role in shielding the iron-sulfur cluster against physiologically high temperatures and further improve the functional integrity of FdTm.

Selected figure(s)

Figure 1.
Figure 1. Representation of the Fd[Tm] structure. (a) Stereo view of the Cα backbone; each fifth residue is labeled. (b) Schematic representation of the Fd[Tm] structure. B1, B2: β sheets; H1, H2: α helices; A–E: turns. Iron atoms of the cluster are shown in red and all sulfur atoms are shown in yellow. Figure 1. Representation of the Fd[Tm] structure. (a) Stereo view of the Cα backbone; each fifth residue is labeled. (b) Schematic representation of the Fd[Tm] structure. B1, B2: β sheets; H1, H2: α helices; A–E: turns. Iron atoms of the cluster are shown in red and all sulfur atoms are shown in yellow.

Figure 5.
Figure 5. Conserved folding topology within monocluster-type ferredoxins. Least-square superposition of the Cα tracings of Fd[Tm] (blue), Fd[Dg] (orange), Fd[Daf] (green) and Fd[Bt] (violet). For clarity only the Fd[Tm] cluster is shown and residue labels refer to Fd[Tm]. Figure 5. Conserved folding topology within monocluster-type ferredoxins. Least-square superposition of the Cα tracings of Fd[Tm] (blue), Fd[Dg] (orange), Fd[Daf] (green) and Fd[Bt] (violet). For clarity only the Fd[Tm] cluster is shown and residue labels refer to Fd[Tm].

The above figures are reprinted by permission from Cell Press: Structure (1996, 4, 1291-1301) copyright 1996.

Figures were selected by an automated process.