Article

Crystal Structures of the Catalytic Domains of Pseudouridine Synthases RluC and RluD from Escherichia coli

Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi, Yokohama 230-0045, Japan.
Biochemistry (Impact Factor: 3.02). 05/2004; 43(15):4454-63. DOI: 10.1021/bi036079c
Source: PubMed

ABSTRACT

The most frequent modification of RNA, the conversion of uridine bases to pseudouridines, is found in all living organisms and often in highly conserved locations in ribosomal and transfer RNA. RluC and RluD are homologous enzymes which each convert three specific uridine bases in Escherichia coli ribosomal 23S RNA to pseudouridine: bases 955, 2504, and 2580 in the case of RluC and 1911, 1915, and 1917 in the case of RluD. Both have an N-terminal S4 RNA binding domain. While the loss of RluC has little phenotypic effect, loss of RluD results in a much reduced growth rate. We have determined the crystal structures of the catalytic domain of RluC, and full-length RluD. The S4 domain of RluD appears to be highly flexible or unfolded and is completely invisible in the electron density map. Despite the conserved topology shared by the two proteins, the surface shape and charge distribution are very different. The models suggest significant differences in substrate binding by different pseudouridine synthases.

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    • "Three-dimensional structure of proteins P44197 and P44720 was predicted using the homology modeling (Marti-Renom et al. 2000) on MODELLER module present in the Discovery Studio 3.5 (Accelrys 2013). We have identified templates using sequence similarity search methods PSI-BLAST (Altschul et al. 1997) and found pseudouridine synthases RluC (Mizutani et al. 2004) and aminodeoxychorismate lyase from Escherichia coli (PDB id: 2RIF) as a suitable template for P44197 and P44720, respectively. The template and query sequences were aligned and finally used for modeling protein structure in MODELLER (Eswar et al. 2007). "

    Full-text · Dataset · Jun 2014
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    • "Three-dimensional structure of proteins P44197 and P44720 was predicted using the homology modeling (Marti-Renom et al. 2000) on MODELLER module present in the Discovery Studio 3.5 (Accelrys 2013). We have identified templates using sequence similarity search methods PSI-BLAST (Altschul et al. 1997) and found pseudouridine synthases RluC (Mizutani et al. 2004) and aminodeoxychorismate lyase from Escherichia coli (PDB id: 2RIF) as a suitable template for P44197 and P44720, respectively. The template and query sequences were aligned and finally used for modeling protein structure in MODELLER (Eswar et al. 2007). "
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    ABSTRACT: Haemophilus influenzae is a small pleomorphic Gram-negative bacteria which causes several chronic diseases, including bacteremia, meningitis, cellulitis, epiglottitis, septic arthritis, pneumonia, and empyema. Here we extensively analyzed the sequenced genome of H. influenzae strain Rd KW20 using protein family databases, protein structure prediction, pathways and genome context methods to assign a precise function to proteins whose functions are unknown. These proteins are termed as hypothetical proteins (HPs), for which no experimental information is available. Function prediction of these proteins would surely be supportive to precisely understand the biochemical pathways and mechanism of pathogenesis of Haemophilus influenzae. During the extensive analysis of H. influenzae genome, we found the presence of eight HPs showing lyase activity. Subsequently, we modeled and analyzed three-dimensional structure of all these HPs to determine their functions more precisely. We found these HPs possess cystathionine-β-synthase, cyclase, carboxymuconolactone decarboxylase, pseudouridine synthase A and C, D-tagatose-1,6-bisphosphate aldolase and aminodeoxychorismate lyase-like features, indicating their corresponding functions in the H. influenzae. Lyases are actively involved in the regulation of biosynthesis of various hormones, metabolic pathways, signal transduction, and DNA repair. Lyases are also considered as a key player for various biological processes. These enzymes are critically essential for the survival and pathogenesis of H. influenzae and, therefore, these enzymes may be considered as a potential target for structure-based rational drug design. Our structure–function relationship analysis will be useful to search and design potential lead molecules based on the structure of these lyases, for drug design and discovery.
    Full-text · Article · Jun 2014
  • Source
    • "Three-dimensional structure of proteins P44197 and P44720 was predicted using the homology modeling (Marti-Renom et al. 2000) on MODELLER module present in the Discovery Studio 3.5 (Accelrys 2013). We have identified templates using sequence similarity search methods PSI-BLAST (Altschul et al. 1997) and found pseudouridine synthases RluC (Mizutani et al. 2004) and aminodeoxychorismate lyase from Escherichia coli (PDB id: 2RIF) as a suitable template for P44197 and P44720, respectively. The template and query sequences were aligned and finally used for modeling protein structure in MODELLER (Eswar et al. 2007). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Haemophilus influenzae is a small pleomorphic Gram-negative bacteria which causes several chronic diseases, including bacteremia, meningitis, cellulitis, epiglottitis, septic arthritis, pneumonia, and empyema. Here we extensively analyzed the sequenced genome of H. influenzae strain Rd KW20 using protein family databases, protein structure prediction, pathways and genome context methods to assign a precise function to proteins whose functions are unknown. These proteins are termed as hypothetical proteins (HPs), for which no experimental information is available. Function prediction of these proteins would surely be supportive to precisely understand the biochemical pathways and mechanism of pathogenesis of Haemophilus influenzae. During the extensive analysis of H. influenzae genome, we found the presence of eight HPs showing lyase activity. Subsequently, we modeled and analyzed three-dimensional structure of all these HPs to determine their functions more precisely. We found these HPs possess cystathionine-beta-synthase, cyclase, carboxymuconolactone decarboxylase, pseudouridine synthase A and C, D-tagatose-1,6-bisphosphate aldolase and aminodeoxychorismate lyase-like features, indicating their corresponding functions in the H. influenzae. Lyases are actively involved in the regulation of biosynthesis of various hormones, metabolic pathways, signal transduction, and DNA repair. Lyases are also considered as a key player for various biological processes. These enzymes are critically essential for the survival and pathogenesis of H. influenzae and, therefore, these enzymes may be considered as a potential target for structure-based rational drug design. Our structure-function relationship analysis will be useful to search and design potential lead molecules based on the structure of these lyases, for drug design and discovery.
    Full-text · Article · Jun 2014
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