Crystallization and preliminary X-ray analysis of the Rieske-type [2Fe-2S] ferredoxin component of biphenyl dioxygenase from Pseudomonas sp. strain KKS102

Anaerobic crystallization of proteins

Crystallization has been a bottleneck in the X-ray crystallography of proteins. Although many techniques have been developed to overcome this obstacle, the impurities caused by chemical reactions during crystallization have not been sufficiently considered. Oxidation of proteins, which can lead to poor reproducibility of the crystallization, is a prominent example. Protein oxidization in the crystallization droplet causes inter-molecular disulfide bridge formation, formation of oxidation film, and precipitation of proteins. These changes by oxidation are typically irreversible. The best approach for preventing protein oxidization during crystallization is anaerobic crystallization. Here we review the anaerobic crystallization of proteins, which was originally developed to trap a reaction intermediate of the enzyme in the crystal. We also summarize representative anaerobic crystallizations from our laboratory and the general setup of anaerobic crystallization.

Complete genome sequence of Acidovorax sp. strain KKS102, a polychlorinated-biphenyl degrader

We report the complete genome sequence of Acidovorax sp. strain KKS102, a polychlorinated-biphenyl-degrading strain isolated from a soil sample in Tokyo. The genome contains a single circular 5,196,935-bp chromosome and no plasmids.

Crystal Structure of the Radical SAM Enzyme Catalyzing Tricyclic Modified Base Formation in tRNA

Wyosine and its derivatives, such as wybutosine, found in eukaryotic and archaeal tRNAs, are tricyclic hypermodified nucleosides. In eukaryotes, wybutosine exists exclusively in position 37, 3'-adjacent to the anticodon, of tRNA(Phe), where it ensures correct translation by stabilizing the codon-anticodon base-pairing during the ribosomal decoding process. Recent studies revealed that the wyosine biosynthetic pathway consists of multistep enzymatic reactions starting from a guanosine residue. Among these steps, TYW1 catalyzes the second step to form the tricyclic ring structure, by cyclizing N(1)-methylguanosine. In this study, we solved the crystal structure of TYW1 from Methanocaldococcus jannaschii at 2.4 A resolution. TYW1 assumes an incomplete TIM barrel with (alpha/beta)(6) topology, which closely resembles the reported structures of radical SAM enzymes. Hence, TYW1 was considered to catalyze the cyclization reaction by utilizing the radical intermediate. Comparison with other radical SAM enzymes allowed us to build a model structure complexed with S-adenosylmethionine and two [4Fe-4S] clusters. Mutational analyses in yeast supported the validity of this complex model structure, which provides a structural insight into the radical reaction involving two [4Fe-4S] clusters to create a complex tricyclic base.

Molecular mechanism of the redox-dependent interaction between NADH-dependent ferredoxin reductase and Rieske-type [2Fe-2S] ferredoxin

The electron transfer system of the biphenyl dioxygenase BphA, which is derived from Acidovorax sp. (formally Pseudomonas sp.) strain KKS102, is composed of an FAD-containing NADH-ferredoxin reductase (BphA4) and a Rieske-type [2Fe-2S] ferredoxin (BphA3). Biochemical studies have suggested that the whole electron transfer process from NADH to BphA3 comprises three consecutive elementary electron-transfer reactions, in which BphA3 and BphA4 interact transiently in a redox-dependent manner. Initially, BphA4 receives two electrons from NADH. The reduced BphA4 then delivers one electron each to the [2Fe-2S] cluster of the two BphA3 molecules through redox-dependent transient interactions. The reduced BphA3 transports the electron to BphA1A2, a terminal oxygenase, to support the activation of dioxygen for biphenyl dihydroxylation. In order to elucidate the molecular mechanisms of the sequential reaction and the redox-dependent interaction between BphA3 and BphA4, we determined the crystal structures of the productive BphA3-BphA4 complex, and of free BphA3 and BphA4 in all the redox states occurring in the catalytic cycle. The crystal structures of these reaction intermediates demonstrated that each elementary electron transfer induces a series of redox-dependent conformational changes in BphA3 and BphA4, which regulate the interaction between them. In addition, the conformational changes induced by the preceding electron transfer seem to induce the next electron transfer. The interplay of electron transfer and induced conformational changes seems to be critical to the sequential electron-transfer reaction from NADH to BphA3.

Crystallization and preliminary X-ray analysis of the reduced Rieske-type [2Fe-2S] ferredoxin derived from Pseudomonas sp. strain KKS102

The reduced form of BphA3, a Rieske-type [2Fe-2S] ferredoxin component of the biphenyl dioxygenase BphA from Pseudomonas sp. strain KKS102, was crystallized by the sitting-drop vapour-diffusion method under anaerobic conditions. The crystal belongs to space group P3(1)21, with unit-cell parameters a = b = 49.6, c = 171.9 A, and diffracts to a resolution of 1.95 A. A molecular-replacement calculation using oxidized BphA3 as a search model yielded a satisfactory solution.