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Provides information on a study which focused on the multiline electron paramagnetic resonance (EPR) signals in a photosynthetic oxygen-evolving complex, from oriented photosystem II membranes, and the Mn cluster's magnetic structure. Function of photosynthetic water cleavage; In-depth look at the extended X-ray absorption fine structure spectroscopy; Methodology used to conduct the study; Results of the study.

ADP-ribose pyrophosphatase (ADPRase) catalyzes the divalent metal ion-dependent hydrolysis of ADP-ribose to ribose 5′-phosphate and AMP. This enzyme plays a key role in regulating the intracellular ADP-ribose levels, and prevents nonenzymatic ADP-ribosylation. To elucidate the pyrophosphatase hydrolysis mechanism employed by this enzyme, structural changes occurring on binding of substrate, metal and product were investigated using crystal structures of ADPRase from an extreme thermophile, Thermus thermophilus HB8. Seven structures were determined, including that of the free enzyme, the Zn2+-bound enzyme, the binary complex with ADP-ribose, the ternary complexes with ADP-ribose and Zn2+ or Gd3+, and the product complexes with AMP and Mg2+ or with ribose 5′-phosphate and Zn2+. The structural and functional studies suggested that the ADP-ribose hydrolysis pathway consists of four reaction states: bound with metal (I), metal and substrate (II), metal and substrate in the transition state (III), and products (IV). In reaction state II, Glu-82 and Glu-70 abstract a proton from a water molecule. This water molecule is situated at an ideal position to carry out nucleophilic attack on the adenosyl phosphate, as it is 3.6 A away from the target phosphorus and almost in line with the scissile bond. [ABSTRACT FROM AUTHOR]

Uracil-DNA glycosylase (UDG; EC 3.2.2.-) removes uracil from DNA to initiate DNA base excision repair. Since hydrolytic deamination of cytosine to uracil is one of the most frequent DNA-damaging events in all cells, UDG is an essential enzyme for maintaining the integrity of genomic information. For the first time, we report the crystal structure of a family 4 UDG from Thermus thermophilus HB8 (TthUDG) complexed with uracil, solved at 1.5 A˚ resolution. As opposed to UDG enzymes in its other families, TthUDG possesses a [4Fe–4S] cluster. This iron–sulfur cluster, which is distant from the active site, interacts with loop structures and has been suggested to be unessential to the activity but necessary for stabilizing the loop structures. In addition to the iron–sulfur cluster, salt-bridges and ion pairs on the molecular surface and the presence of proline on loops and turns is thought to contribute to the enzyme's thermostability. Despite very low levels of sequence identity with Escherichia coli and human UDGs (family 1) and E. coli G:T/U mismatch-specific DNA glycosylase (MUG) (family 2), the topology and order of secondary structures of TthUDG are similar to those of these distant relatives. Furthermore, the coordinates of the core structure formed by β-strands are almost the same. Positive charge is distributed over the active-site groove, where TthUDG would bind DNA strands, as do UDG enzymes in other families. TthUDG recognizes uracil specifically in the same manner as does human UDG (family 1), rather than guanine in the complementary strand DNA, as does E. coli MUG (family 2). These results suggest that the mechanism by which family 4 UDGs remove uracils from DNA is similar to that of family 1 enzymes. [Copyright &y& Elsevier]

Small protein B (SmpB) is required for trans-translation, binding specifically to tmRNA. We show here the solution structure of SmpB from an extremely thermophilic bacterium, Thermus thermophilus HB8, determined by heteronuclear nuclear magnetic resonance methods. The core of the protein consists of an antiparallel β-barrel twisted up from eight β-strands, each end of which is capped with the second or third helix, and the first helix is located beside the barrel. Its C-terminal sequence (20 residues), which is rich in basic residues, shows a poorly structured form, as often seen in isolated ribosomal proteins. The results are discussed in relation to the oligonucleotide binding fold. [Copyright &y& Elsevier]

Investigates the purification and crystallization of RNA polymerase (RNAP) holoenzyme from Thermus thermophilus. Molecular mechanism of RNAP; Structure of RNAP core enzyme; Process for holoenzyme purification of T. thermophilus cells.

Abstract Background: Transfer RNAs from an extreme thermophile, Thermus thermophilus , commonly possess 2′-O-methylguanosine at position 18 (Gm18) in the D-loop. This modification is post-transcriptionally introduced by tRNA (Gm18) methyltransferase. Results: Partial amino acid sequence data were obtained from purified T. thermophilus tRNA (Gm18) methyltransferase by peptide sequencing and mass spectrometry. The sequence data were used to screen the T. thermophilus genome database currently in progress, resulting in the identification of the corresponding gene. Purified recombinant enzyme showed a strict specificity for methylation at the 2′-OH of G18 in tRNA. Sequence alignment with other known or putative methyltransferases elucidates that tRNA (Gm18) methyltransferases have specific conserved region as well as three consensus motifs found in RNA ribose 2′-O-methyltransferases. The enzyme truncated at its N and C termini by limited tryptic digestion still retained binding activity for S-adenosyl-l-homocysteine, but lost the catalytic activity. Conclusion: This is the first report describing the identification of a methyltransferase gene of the trmH family through the analysis of a purified protein. Further, our results indicate that a restricted region(s) in the terminal amino acid residues of T. thermophilus tRNA (Gm18) methyltransferase are responsible for tRNA recognition and a main part of the enzyme is allocated for a catalytic core. [ABSTRACT FROM AUTHOR]

The CsaA protein was first characterized in Bacillus subtilis as a molecular chaperone with export-related activities. Here we report the 2.0 Å-resolution crystal structure of the Thermus thermophilus CsaA protein, designated ttCsaA. Atomic structure and experiments in solution revealed a homodimer as the functional unit. The structure of the ttCsaA monomer is reminiscent of the well known oligonucleotide-binding fold, with the addition of extensions at the N- and C-termini that form an extensive dimer interface. The two identical, large, hydrophobic cavities on the protein surface are likely to constitute the substrate binding sites. The CsaA proteins share essential sequence similarity with the tRNA-binding protein Trbp111. Structure-based sequence analysis suggests a close structural resemblance between these proteins, which may extend to the architecture of the binding sites at the atomic level. These results raise the intriguing possibility that CsaA proteins possess a second, tRNA-binding activity in addition to their export-related function. [ABSTRACT FROM AUTHOR]

The MutM [formamidopyrimidine DNA glycosylase (Fpg)] protein is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidatively damaged bases (N-glycosylase activity) and cleaves both the 3′- and 5±-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity). The crystal structure of MutM from an extreme thermophilc, Thermus thermophilus HB8, was determined at 1.9 Å resolution with multiwavelength anomalous diffraction phasing using the intrinsic Zn2+ ion of the zinc finger. MutM is composed of two distinct and novel domains connected by a flexible hinge. There is a large, electrostatically positive cleft lined by highly conserved residues between the domains. On the basis of the three-dimensional structure and taking account of previous biochemical experiments, we propose a DNA-binding mode and reaction mechanism for MutM. The locations of the putative catalytic residues and the two DNA-binding motifs (the zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes. [ABSTRACT FROM AUTHOR]

An ADP-ribose pyrophosphatase from Thermus thermophilus HB8 was overproduced in Escherichia coli and purified. Gel-filtration chromatography showed the protein to be in a dimeric state. This protein catalyses the Mg[SUP2+]- or Zn[SUP2+] -dependent hydrolysis of ADP-ribose to AMP and ribose-5′-phosphate. It was crystallized in the absence and the presence of ADP-ribose by the hanging-drop vapour-diffusion method. Complete data sets were collected to 1.50 Å resolution from the complexed form. Both crystals belong to space group P3[SUB1]21 or P3[SUB2]21 and contain one molecule in the asymmetric unit. [ABSTRACT FROM AUTHOR]

Knots in polypeptide chains have been found in very few proteins. Only two proteins are considered to have a shallow 'trefoil' knot, which tucks a few residues at one end of the chain through a loop exposed on the protein surface. Recently, another protein was found by a mathematical algorithm to have a deep 'figure-of-eight' knot which had not been visually identified. In the present study, the crystal structure of a hypothetical RNA 2'-O-ribose methyltransferase from Thermus thermophilus (RrmA) was determined at 2.4 A resolution and a deep trefoil knot was found for the first time. The present knot is formed by the threading of a 44-residue polypeptide chain through a 41-residue loop and is better defined than the previously reported knots. Two of the three catalytic residues conserved in the 2'-O-ribose methyltransferase family are located in the knotting loop and in the knotted carboxy-terminal chain, which is the first observation that the enzyme active site is constructed right on the knot. On the other hand, the amino-terminal domain exhibits a geometrical similarity to the ribosomal proteins which recognize an internal loop of RNA.