Thermophiles structures

Kakuta, Y., Tahara, M., Maetani, S., Yao, M., Tanaka, I., and Kimura, M. (2004). Crystal structure of the regulatory subunit of archaeal initiation factor 2B (aIF2B) from hyper-thermophilic archaeon Pyrococcus horikoshii OT3 A proposed structure of the regulatory subcomplex of eukaryotic IF2B. Biochem. Biophys. Res. Commun. 319, 725—732. 

H. Kuhl, J. Kruip, A. Seidler, A. Krieger-Liszkay, M. Bunker, D. Bald, J.A. Scheidig, M. Rogner (2000) Towards structural determination of the water-splitting enzyme. Purification, crystallization, and preliminary crystallographic studies of photosystem II from a thermophilic cyanobacterium. J. Biol. Chem., 275 20652-20659... 

The only other E. coli ribosomal protein whose crystallization has so far been reported is L29 (Appelt et al., 1981). On the other hand, attempts to crystallize ribosomal proteins from the thermophilic Bacillus stearothermophilus have been more successful. Protein BL17, which according to its amino acid sequence (Kimura et al., 1980) corresponds to protein L9 from the E. coli ribosome (Kimura et al., 1982), was the first intact ribosomal protein to give crystals useful for X-ray structural analysis (Appelt et al., 1979). Several other B. stearothermophUus ribosomal proteins, namely BL6 and BL30 (Appelt eteU., 1981,1983) from the large and BS5 (Appelt et al., 1983) from the small subunit have been crystallized, and the determination of their three-dimensional structure at a resolution of better than 3 A is now in progress. Furthermore, crystals of aB. stearothermophilus ribosomal protein complex, which corresponds to the complex (L7/L12)4 LIO from E. coli ribosome, have been obtained (Liljas and Newcomer, 1981). 

Analyses of soluble proteins from complete genomes of 20 thermophilic or mesophilic microorganisms revealed that higher amounts of Glu and Asp residues and lower amounts of Gin and Asn residues are present in proteins of thermophiles compared to proteins of mesophiles. " This result suggests that Gin and Asn residues destabilize protein structure at high temperature, possibly through their deamidation. 

Figure 14.3. Composition and structural organization of atp genes in E. coli (Ecoli) (accession no. J01594), thermophilic bacterium PS3 (PS3) (accession no. X07804), C. pasteurianum (Cpast) (accession no. AF283808), M. thermoacetica (Mthe) (accession no. U64318), and A. woodii. (Awoo) (U10505). The size of each gene (in base pairs) is also shown.

TlFd (59 amino acids, stable up to 90 °C) contains a single cluster that can exist in both 3Fe-4S and 4Fe-4S forms. The molecular and electronic structures were solved by NMR whereas the X-ray structure is still unknown. Compared to other mesophilic and thermophilic Fds, TTFd showed several structural adjustments such as the addition of a third strand of jS-sheet, a likely Lys2-Glu38 salt bridge from this /1-sheet and the N-terminus and a more hydrophobic and compact interaction between the large /S-sheet and the long helix. According to the authors, each of these modifications contributes to the extraordinary protein thermostability. 

Cytochromes are electron-transfer proteins having one or several haem groups. Cytochrome c binds to the protein by one or, more commonly two, thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. Cytochrome c has been proved to be a useful model system for studying the relationship between protein structure and thermostability due to the availability of its three-dimensional structure from a wide variety of organisms, both mesophiles and thermophiles. 

The solution structure of the 87-residue cytochrome cg from the thermophilic cyanobacterium Synechococcus elongatus (optimal temperature for photosynthetic activity = 57 °C) was determined by multidimensional NMR spectroscopy and molecular dynamics calculations and exhibited the overall topology of class I c cytochromes with four a-helices and a small antiparallel /1-sheet near Met58, one of the axial haem ligands. ... 

The small protein B (SmpB) is an essential component of the tmRNA-SmpB system used by prokaryotes for releasing stalled ribosome from damaged messanger RNAs and targeting incompletely synthesized protein fragments for degradation. The solution structure of SmpB from the thermophilic A. aeoUcus... 

A combination of crystallographic and NMR methods was used to obtain the high-resolution structure of the domain of a Hsp from the thermophilic T. thermophilus (Tm > 100 °C) and to compare it to the homologous domain of Hsp from E. coli T = 65 °C). It was found that the structure of the domain of the T. thermophilus Hsp contained additional salt bridges which could be responsible for the higher thermostability. ... 

The C-terminal domain (85 amino acid residues, not completely denatured at 90 °C) of the so-called a subunit of the RNAP from the extremely thermophilic eubacterium T. thermophilus (Tt) has been expressed uniformly N/ C-labelled and structurally characterized by the NMR spectroscopy. The tertiary structure of the domain, comprising a helical turn and four helices, was found to be almost identical to that of the corresponding domain from the mesophilic E. coli, despite 32% sequence homology. The interaction of the Tt domain with a variety of DNAs at 37 °C and 50 °C was investigated by chemical shift perturbation of the NMR signals and the DNA binding site was localized. ... 

Several NMR studies have been carried out in order to reveal the three-dimensional structure of CBMs and to understand the mechanism by which CBMs from thermophilic organisms bind to their polysaccharide ligands (CBM22, CBM4, and CBM4-2 ). It has been found that CBMs are composed mainly of jS-strand and contain a planar hydrophobic platform comprising aromatic residues that bind to the surface of the polysaccharide. 

Within the cellulosome complex, type I dockerin domain is responsible for incorporating its associated glycosyl hydrolase in the bacterial cellulosome via interaction with a reception domain, the cohesin domain. The three-dimensional solution structure of the 69-residue dockerin domain from the thermophilic Clostridium thermocellum (Topt = 55-65 °C) was solved by NMR and was found to consist of two Ca " -binding loop-helix motifs connected by a linker. Each Ca " -binding subdomain is stabilized by a cluster of buried hydrophobic sidechains. Recently, the NMR sequence-specific resonance assignment of type II cohesin module from C. thermocellum has been published. ... 

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