Crystal structure of ribosomal protein L30e from the extreme thermophile Thermococcus celer: thermal stability and RNA binding.
We report here the high-resolution crystal structure of the ribosomal protein L30e from the hyperthermophilic archaeon Thermococcus celer determined at cryo-temperature. When it is compared with its mesophilic homologue, L30e from yeast, a number of structural features that can enhance thermostability are revealed. Disordered residues corresponding to a large RNA-binding loop in yeast L30e are well structured in the T. celer protein. The overall charge of T. celer L30e is near neutral, whereas that of the yeast homologue is highly positive. This is the result of an increase in the number of acidic residues at the expense of polar residues, Asn, Ser, and Thr. Extensive ion pair networks are found on the molecular surface. Exposed nonpolar surface areas are reduced in the T. celer protein. Its side chain atoms preferably form hydrogen bonds with main chain atoms. Taken together, these factors contribute to high protein stability. The roles of well-conserved L30e residues are studied and found to be important in defining a very compact overall structure and in maintaining the structure of the RNA binding site. By comparing it with the yeast homologue, we also identified the residues that are responsible for RNA binding and built a model to illustrate how L30e binds to an RNA kink turn motif.
Chen
Yu Wai
YW
Cambridge University Chemical Laboratory and Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, UK.
Bycroft
Mark
M
Wong
Kam-Bo
KB
D000596:Amino Acids / Q000032:analysis; D019843:Archaeal Proteins / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D003460:Crystallization; D018360:Crystallography, X-Ray; D006358:Hot Temperature; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding; D017510:Protein Folding; D017433:Protein Structure, Secondary; D020871:RNA Stability; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D012269:Ribosomal Proteins / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D012270:Ribosomes / Q000737:chemistry / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry; D055672:Static Electricity; D019712:Thermococcus / Q000737:chemistry*; D013816:Thermodynamics
D000596:Amino Acids; D019843:Archaeal Proteins; D016601:RNA-Binding Proteins; D012269:Ribosomal Proteins; D029701:Saccharomyces cerevisiae Proteins; C035201:ribosomal protein L30