Computational Structure Analysis and Function Prediction of an Uncharacterized Protein (I6U7D0) of Pyrococcus furiosus COM1 (original) (raw)
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Pyrococcus furiosus is a hyperthermophilic archaea. A hypothetical protein of this archaea, PF0847, was selected for computational analysis. Basic local alignment search tool and multiple sequence alignment (MSA) tool were employed to search for related proteins. Both the secondary and tertiary structure prediction were obtained for further analysis. Three-dimensional model was assessed by PROCHECK and QMEAN6 programs. To get insights about the physical and functional associations of the protein, STRING network analysis was performed. Binding of the SAM (S-adenosyl-l-methionine) ligand with our protein, fetched from an antibiotic-related methyltransferase (PDB code: 3P2K: D), showed high docking energy and suggested the function of the protein as methyltransferase. Finally, we tried to look for a specific function of the proposed methyltransferase, and binding of the geneticin bound to the eubacterial 16S rRNA A-site (PDB code: 1MWL) in the active site of the PF0847 gave us the indication to predict the protein responsible for aminoglycoside antibiotic resistance.
The crystal structure of hypothetical methyltransferase from Thermus thermophilus HB8
Proteins: Structure, Function, and Bioinformatics, 2006
A large number of new protein structures have been determined by development of the field of structural genomics. Some of them are called "hypothetical proteins" due to missing information on their biological functions. In such cases, the three-dimensional structure is one of the important clues to infer the molecular function.
Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 Å resolution
Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2007
The hypothetical protein PF0899 is a 95-residue peptide from the hyperthermophilic archaeon Pyrococcus furiosus that represents a gene family with six members. P. furiosus ORF PF0899 has been cloned, expressed and crystallized and its structure has been determined by the Southeast Collaboratory for Structural Genomics (http://www.secsg.org). The structure was solved using the SCA2Structure pipeline from multiple data sets and has been refined to 1.85 Å against the highest resolution data set collected (a presumed gold derivative), with a crystallographic R factor of 21.0% and R free of 24.0%. The refined structure shows some structural similarity to a wedge-shaped domain observed in the structure of the major capsid protein from bacteriophage HK97, suggesting that PF0899 may be a structural protein.
Nucleic Acids Research, 2010
The S-adenosyl-L-methionine dependent methylation of adenine 58 in the T-loop of tRNAs is essential for cell growth in yeast or for adaptation to high temperatures in thermophilic organisms. In contrast to bacterial and eukaryotic tRNA m 1 A58 methyltransferases that are site-specific, the homologous archaeal enzyme from Pyrococcus abyssi catalyzes the formation of m 1 A also at the adjacent position 57, m 1 A57 being a precursor of 1-methylinosine. We report here the crystal structure of P. abyssi tRNA m 1 A57/58 methyltransferase ( Pab TrmI), in complex with S-adenosyl-L-methionine or S-adenosyl-L-homocysteine in three different space groups. The fold of the monomer and the tetrameric architecture are similar to those of the bacterial enzymes. However, the inter-monomer contacts exhibit unique features. In particular, four disulfide bonds contribute to the hyperthermostability of the archaeal enzyme since their mutation lowers the melting temperature by 16.5 C. His78 in conserved motif X, which is present only in TrmIs from the Thermococcocales order, lies near the active site and displays two alternative conformations. Mutagenesis indicates His78 is important for catalytic efficiency of Pab TrmI. When A59 is absent in tRNA Asp , only A57 is modified. Identification of the methylated positions in tRNAAsp by mass spectrometry confirms that Pab TrmI methylates the first adenine of an AA sequence.
Proteins: Structure, Function, and Genetics, 2001
The crystal structure of YecO from Haemophilus influenzae (HI0319), a protein annotated in the sequence databases as hypothetical, and that has not been assigned a function, has been determined at 2.2-Å resolution. The structure reveals a fold typical of S-adenosyl-L-methioninedependent (AdoMet) methyltransferase enzymes. Moreover, a processed cofactor, S-adenosyl-L-homocysteine (AdoHcy), is bound to the enzyme, further confirming the biochemical function of HI0319 and its sequence family members. An active site arginine, shielded from bulk solvent, interacts with an anion, possibly a chloride ion, which in turn interacts with the sulfur atom of AdoHcy. The AdoHcy and nearby protein residues delineate a small solvent-excluded substrate binding cavity of 162 Å 3 in volume. The environment surrounding the cavity indicates that the substrate molecule contains a hydrophobic moiety and an anionic group. Many of the residues that define the cavity are invariant in the HI0319 sequence family but are not conserved in other methyltransferases. Therefore, the substrate specificity of YecO enzymes is unique and differs from the substrate specificity of all other methyltransferases sequenced to date. Examination of the Enzyme Commission list of methyltransferases prompted a manual inspection of 10 possible substrates using computer graphics and suggested that the ortho-substituted benzoic acids fit best in the active site. Proteins 2001;45:397-407.
Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase
Structure, 2000
Background: Methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr), catalyzes a key step in the Wood-Ljungdahl pathway of carbon dioxide fixation. It transfers the N 5 -methyl group from methyltetrahydrofolate (CH 3 -H 4 folate) to a cob(I)amide center in another protein, the corrinoid iron-sulfur protein. MeTr is a member of a family of proteins that includes methionine synthase and methanogenic enzymes that activate the methyl group of methyltetra-hydromethano(or -sarcino)pterin. We report the first structure of a protein in this family.
Nucleic acids research, 2008
The 5-methyluridine is invariably found at position 54 in the T)C loop of tRNAs of most organisms. In Pyrococcus abyssi, its formation is catalyzed by the S-adenosyl-L-methionine-dependent tRNA (uracil-54, C5)-methyltransferase ( Pab TrmU54), an enzyme that emerged through an ancient horizontal transfer of an RNA (uracil, C5)-methyltransferaselike gene from bacteria to archaea. The crystal structure of Pab TrmU54 in complex with S-adenosyl-L-homocysteine at 1.9 Å resolution shows the protein organized into three domains like Escherichia coli RumA, which catalyzes the same reaction at position 1939 of 23S rRNA. A positively charged groove at the interface between the three domains probably locates part of the tRNA-binding site of Pab TrmU54. We show that a mini-tRNA lacking both the D and anticodon stem-loops is recognized by Pab TrmU54. These results were used to model yeast tRNA Asp in the Pab TrmU54 structure to get further insights into the different RNA specificities of RumA and Pab TrmU54. Interestingly, the presence of two flexible loops in the central domain, unique to Pab TrmU54, may explain the different substrate selectivities of both enzymes. We also predict that a large T)C loop conformational change has to occur for the flipping of the target uridine into the Pab TrmU54 active site during catalysis. Pab TrmU54 (same color code as ) is shown in the same orientation as that of RumA in A. The target uridine, as seen in the RumAÁAdoHCysÁmini-rRNA structure, and AdoHCys are shown in grey and cyan stick representations, respectively.
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.
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.