1WTF

Crystal structure of Bacillus thermoproteolyticus Ferredoxin Variants Containing Unexpected [3Fe-4S] Cluster that is linked to Coenzyme A at 1.6 A Resolution

Summary for 1WTF

• Entry DOI: 10.2210/pdb1wtf/pdb
• Descriptor: Ferredoxin, SULFATE ION, COENZYME A, ... (5 entities in total)
• Functional Keywords: 3fe-4s cluster, coenzyme a, ferredoxin, complex, electron transport
• Biological source: Bacillus thermoproteolyticus
• Total number of polymer chains: 4
• Total formula weight: 37333.28

Authors

Shirakawa, T.,Takahashi, Y.,Wada, K.,Hirota, J.,Takao, T.,Ohmori, D.,Fukuyama, K. (deposition date: 2004-11-22, release date: 2005-11-08, Last modification date: 2024-11-13)

Primary citation

Shirakawa, T.,Takahashi, Y.,Wada, K.,Hirota, J.,Takao, T.,Ohmori, D.,Fukuyama, K.
Identification of variant molecules of Bacillus thermoproteolyticus ferredoxin: crystal structure reveals bound coenzyme A and an unexpected [3Fe-4S] cluster associated with a canonical [4Fe-4S] ligand motif
Biochemistry, 44:12402-12410, 2005

PubMed Abstract: During the purification of recombinant Bacillus thermoproteolyticus ferredoxin (BtFd) from Escherichia coli, we have noted that some Fe-S proteins were produced in relatively small amounts compared to the originally identified BtFd carrying a [4Fe-4S] cluster. These variants could be purified into three Fe-S protein components (designated as V-I, V-II, and V-III) by standard chromatography procedures. UV-vis and EPR spectroscopic analyses indicated that each of these variants accommodates a [3Fe-4S] cluster. From mass spectrometric and protein sequence analyses together with native and SDS gel electrophoresis, we established that V-I and V-II contain the polypeptide of BtFd associated with acyl carrier protein (ACP) and with coenzyme A (CoA), respectively, and that V-III is a BtFd dimer linked by a disulfide bond. The crystal structure of the BtFd-CoA complex (V-II) determined at 1.6 A resolution revealed that each of the four complexes in the crystallographic asymmetric unit possesses a [3Fe-4S] cluster that is coordinated by Cys(11), Cys(17), and Cys(61). The polypeptide chain of each complex is superimposable onto that of the original [4Fe-4S] BtFd except for the segment containing Cys(14), the fourth ligand to the [4Fe-4S] cluster of BtFd. In the variant molecules, the side chain of Cys(14) is rotated away to the molecular surface, forming a disulfide bond with the terminal sulfhydryl group of CoA. This covalent modification may have occurred in vivo, thereby preventing the assembly of the [4Fe-4S] cluster as observed previously for Desulfovibrio gigas ferredoxin. Possibilities concerning how the variant molecules are formed in the cell are discussed.

PubMed: 16156653
DOI: 10.1021/bi0508441

Experimental method

X-RAY DIFFRACTION (1.6 Å)