Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 Å resolution (original) (raw)
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Pyrococcus furiosus is a hyperthermophilic Archaea. An uncharacterized protein of this Achaea, I6U7D0 (UniProt accession) containing 349 residues was selected for in silico analysis. Various bioinformatic tools were used to predict the structure and function of this protein. Sequence similarity was searched through UniProt and non-redundant database using BLASTp program of NCBI and homology was found with methyltransferases. Multiple sequence alignment was used to locate the conserved residues. The secondary and three dimensional structures were predicted. The validation of the three dimensional structure was obtained through PROCHECK, Verify3D and ERRAT program. CASTp server was used to predict the active site of the protein. Molecular docking with the ligand ACY (Acetic Acid) was performed using Molegro Virtual Docker to visualize the interactions between the ligand and amino acid residues in the protein. Finally, all the accumulated results suggested the biological function of the target protein to be a methyltransferase
Modeling the structure of pyrococcus furiosus rubredoxin by homology to other X-ray structures
Protein Science, 2008
The three-dimensional structure of rubredoxin from the hyperthermophilic archaebacterium, Pyrococcus furiosus, has been modeled from the X-ray crystal structures of three homologous proteins from Clostridiumpusteuriunum, Desulfovibrio gigas, and Desulfovibrio vulgaris. All three homology models are similar. When comparing the positions of all heavy atoms and essential hydrogen atoms to the recently solved crystal structure (Day, M.W., et al., 1992, Protein Sci. I, 1494-1507) of the same protein, the homology models differ from the X-ray structure by 2.09 A root mean square (RMS). The X-ray and the zinc-substituted NMR structures (Blake, P.R., et al., 1992b, Protein Sci. I, 1508-1521) show a similar level of difference (2.05 A RMS). On average, the homology models are closer to the X-ray structure than to the NMR structures (2.09 vs. 2.42 A RMS).
Dps-like protein from the hyperthermophilic archaeon Pyrococcus furiosus
Journal of Inorganic Biochemistry, 2006
Oxidative stress is a universal phenomenon experienced by organisms in all domains of life. Proteins like those in the ferritin-like diiron carboxylate superfamily have evolved to manage this stress. Here we describe the cloning, isolation, and characterization of a Dpslike protein from the hyperthermophilic archaeon Pyrococcus furiosus (PfDps-like). Phylogenetic analysis, primary structure alignments and higher order structural predictions all suggest that the P. furiosus protein is related to proteins within the broad superfamily of ferritin-like di-iron carboxylate proteins. The recombinant PfDps protein self-assembles into a 12 subunit quaternary structure with an outer shell diameter of 10nmandaninteriordiameterof10 nm and an interior diameter of 10nmandaninteriordiameterof5 nm. Dps proteins functionally manage the toxicity of oxidative stress by sequestering intracellular ferrous iron and using it to reduce H 2 O 2 in a two electron process to form water. The iron is converted to a benign form as Fe(III) within the protein cage. This Dps-mediated reduction of hydrogen peroxide, coupled with the protein's capacity to sequester iron, contributes to its service as a multifunctional antioxidant.
Molecular & Cellular Proteomics, 2009
Virtually all cellular processes are carried out by dynamic molecular assemblies or multiprotein complexes, the compositions of which are largely undefined. They cannot be predicted solely from bioinformatics analyses nor are there well defined techniques currently available to unequivocally identify protein complexes (PCs). To address this issue, we attempted to directly determine the identity of PCs from native microbial biomass using Pyrococcus furiosus, a hyperthermophilic archaeon that grows optimally at 100°C, as the model organism. Novel PCs were identified by large scale fractionation of the native proteome using non-denaturing, sequential column chromatography under anaerobic, reducing conditions. A total of 967 distinct P. furiosus proteins were identified by mass spectrometry (nano LC-ESI-MS/MS), representing ϳ80% of the cytoplasmic proteins. Based on the co-fractionation of proteins that are encoded by adjacent genes on the chromosome, 106 potential heteromeric PCs containing 243 proteins were identified, only 20 of which were known or expected. In addition to those of unknown function, novel and uncharacterized PCs were identified that are proposed to be involved in the metabolism of amino acids (10), carbohydrates (four), lipids (two), vitamins and metals (three), and DNA and RNA (nine). A further 30 potential PCs were classified as tentative, and the remaining potential PCs (13) were classified as weakly interacting. Some major advantages of native biomass fractionation for PC identification are that it provides a road map for the (partial) purification of native forms of novel and uncharacterized PCs, and the results can be utilized for the recombinant production of low abundance PCs to provide enough material for detailed structural and biochemical analyses. Molecular & Cellular Proteomics 8: 735-751, 2009.
Structure determination of fibrillarin from the hyperthermophilic archaeon Pyrococcus furiosus
Biochemical and Biophysical Research Communications - BIOCHEM BIOPHYS RES COMMUN, 2004
The methyltransferase fibrillarin is the catalytic component of ribonucleoprotein complexes that direct site-specific methylation of precursor ribosomal RNA and are critical for ribosome biogenesis in eukaryotes and archaea. Here we report the crystal structure of a fibrillarin ortholog from the hyperthermophilic archaeon Pyrococcus furiosus at 1.97Å resolution. Comparisons of the X-ray structures of fibrillarin orthologs from Methanococcus jannashii and Archaeoglobus fulgidus reveal nearly identical backbone configurations for the catalytic C-terminal domain with the exception of a unique loop conformation at the S-adenosyl-l-methionine (AdoMet) binding pocket in P. furiosus. In contrast, the N-terminal domains are divergent which may explain why some forms of fibrillarin apparently homodimerize (M. jannashii) while others are monomeric (P. furiosus and A. fulgidus). Three positively charged amino acids surround the AdoMet-binding site and sequence analysis indicates that this is a...
Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3
2005
Background: Although 2,061 proteins of Pyrococcus horikoshii OT3, a hyperthermophilic archaeon, have been predicted from the recently completed genome sequence, the majority of proteins show no similarity to those from other organisms and are thus hypothetical proteins of unknown function. Because most proteins operate as parts of complexes to regulate biological processes, we systematically analyzed protein-protein interactions in Pyrococcus using
Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii
Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2005
The Pyrococcus horikoshii OT3 protein PH0500 is highly conserved within the Pyrococcus genus of hyperthermophilic archaea and shows low amino-acid sequence similarity with a family of PIN-domain proteins. The protein has been expressed, purified and crystallized in two crystal forms: PH0500-I and PH0500-II. The structure was determined at 2.0 Å by the multiple anomalous dispersion method using a selenomethionyl derivative of crystal form PH0500-I (PH0500-I-Se). The structure of PH0500-I has been refined at 1.75 Å resolution to an R factor of 20.9% and the structure of PH0500-II has been refined at 2.0 Å resolution to an R factor of 23.4%. In both crystal forms as well as in solution the molecule appears to be a dimer. Searches of the databases for protein-fold similarities confirmed that the PH0500 protein is a PIN-domain protein with possible exonuclease activity and involvement in DNA or RNA editing.
Carbohydrate Research, 2014
An oligosaccharide chain attached to the asparagine residue in a structurally defined peptide was produced by an in vitro oligosaccharide-transfer reaction, using membrane fractions that contained the oligosaccharyltransferase from the hyperthermophilic archaeon, Pyrococcus furiosus. The chemical structure of the N-glycan was elucidated by sugar analysis, NMR spectroscopy, and MS spectrometry, which revealed the structure. The shorter glycan structures lacking one or two xylose residues were also transferred by the P. furiosus oligosaccharyltransferase. The archaeal N-glycans are known to exhibit a high degree of structural variation. The structure of the P. furiosus N-glycan is novel and unique. The present data will be useful for structural and functional studies of the P. furiosus oligosaccharyltransferase.
Structure, 2002
revealed distinct differences from any known carboxypeptidase. Biochemical char-Columbus, Ohio 43210 2 Noyes Laboratories 127-72 acterization of the TaqCP demonstrated that it had a novel size and sequence and an unexpected metal bind-Division of Chemistry and Chemical Engineering California Institute of Technology ing motif [3]. TaqCP was found to be missing the HXXE(X) 123-132 H motif characteristic of classical metallo-Pasadena, California 91125 carboxypeptidases (CPA, CPB, and CPT) and instead contained the HEXXH motif [4, 5] common to other families of metalloproteases (thermolysin and deformylase) Summary