large ribosomal subunit rRNA binding
Definition
Target type: molecularfunction
Binding to large ribosomal subunit RNA (LSU rRNA), a constituent of the large ribosomal subunit. In S. cerevisiae, this is the 25S rRNA. [GOC:elh]
Large ribosomal subunit rRNA binding is a crucial molecular function that plays a central role in protein synthesis. Ribosomes, the protein synthesis machinery of cells, are composed of two subunits: a small subunit (SSU) and a large subunit (LSU). The LSU is responsible for catalyzing peptide bond formation, a critical step in protein elongation. This catalytic activity is facilitated by the presence of ribosomal RNA (rRNA), a highly conserved and essential component of the LSU. rRNA molecules within the LSU exhibit complex structures that are responsible for binding to various components involved in protein synthesis, including messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal proteins.
The large ribosomal subunit rRNA binding function encompasses the interactions between the LSU rRNA and these components. These interactions are essential for proper ribosome assembly, mRNA and tRNA binding, and the accurate positioning of the tRNA molecules within the ribosome's active site. The rRNA within the LSU provides a framework for the correct positioning of the A, P, and E sites, which are crucial for tRNA binding and peptide bond formation.
Specifically, the large ribosomal subunit rRNA interacts with the following components:
- **mRNA:** The rRNA within the LSU helps to position and stabilize mRNA on the ribosome, ensuring that the correct codons are aligned with the tRNA anticodons. This interaction is critical for accurate translation.
- **tRNA:** The rRNA within the LSU provides binding sites for both the A and P sites, facilitating the interaction of tRNA molecules with the mRNA and the ribosome. This interaction allows for the delivery of amino acids to the ribosome and the formation of peptide bonds.
- **Ribosomal proteins:** The rRNA within the LSU interacts with a variety of ribosomal proteins, which contribute to the overall structure and function of the LSU. These interactions are essential for maintaining the integrity of the ribosome and its catalytic activity.
In summary, the large ribosomal subunit rRNA binding function is fundamental to protein synthesis. It ensures the proper assembly of the LSU, the accurate positioning of mRNA and tRNA molecules within the ribosome, and the efficient catalysis of peptide bond formation. This process is critical for the production of all proteins essential for cellular function and organismal survival.'
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Proteins (12)
| Protein | Definition | Taxonomy |
|---|---|---|
| 50S ribosomal protein L22 | A large ribosomal subunit protein uL22 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P61175] | Escherichia coli K-12 |
| 50S ribosomal protein L24 | A large ribosomal subunit protein uL24 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P60624] | Escherichia coli K-12 |
| 50S ribosomal protein L6 | A large ribosomal subunit protein uL6 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0AG55] | Escherichia coli K-12 |
| 50S ribosomal protein L14 | A large ribosomal subunit protein uL14 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0ADY3] | Escherichia coli K-12 |
| 50S ribosomal protein L13 | A large ribosomal subunit protein uL13 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0AA10] | Escherichia coli K-12 |
| 50S ribosomal protein L20 | A large ribosomal subunit protein bL20 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7L3] | Escherichia coli K-12 |
| 50S ribosomal protein L19 | A large ribosomal subunit protein bL19 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7K6] | Escherichia coli K-12 |
| 50S ribosomal protein L11 | A large ribosomal subunit protein uL11 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7J7] | Escherichia coli K-12 |
| 50S ribosomal protein L10 | A large ribosomal subunit protein uL10 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7J3] | Escherichia coli K-12 |
| 60S ribosomal protein L23 | A eukaryotic-type large ribosomal subunit protein uL14 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P62829] | Homo sapiens (human) |
| 60S ribosomal protein L12 | A eukaryotic-type large ribosomal subunit protein uL11 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P30050] | Homo sapiens (human) |
| 60S acidic ribosomal protein P0 | A eukaryotic-type large ribosomal subunit protein uL10 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P05388] | Homo sapiens (human) |
Compounds (23)
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| chloramphenicol | Amphenicol: Chloramphenicol and its derivatives. | C-nitro compound; carboxamide; diol; organochlorine compound | antibacterial drug; antimicrobial agent; Escherichia coli metabolite; geroprotector; Mycoplasma genitalium metabolite; protein synthesis inhibitor |
| framycetin | framycetin : A tetracyclic antibacterial agent derived from neomycin, being a glycoside ester of neamine and neobiosamine B. Framycetin: A component of NEOMYCIN that is produced by Streptomyces fradiae. On hydrolysis it yields neamine and neobiosamine B. (From Merck Index, 11th ed) | aminoglycoside | allergen; antibacterial drug; Escherichia coli metabolite |
| erythromycin | erythromycin : Any of several wide-spectrum macrolide antibiotics obtained from actinomycete Saccharopolyspora erythraea (formerly known as Streptomyces erythraeus). erythromycin A : An erythromycin that consists of erythronolide A having 2,6-dideoxy-3-C-methyl-3-O-methyl-alpha-L-ribo-hexopyranosyl and 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl residues attahced at positions 4 and 6 respectively. Erythromycin: A bacteriostatic antibiotic macrolide produced by Streptomyces erythreus. Erythromycin A is considered its major active component. In sensitive organisms, it inhibits protein synthesis by binding to 50S ribosomal subunits. This binding process inhibits peptidyl transferase activity and interferes with translocation of amino acids during translation and assembly of proteins. | cyclic ketone; erythromycin | |
| neamine | neamine : 2-Deoxy-D-streptamine glycosylated at the 4-oxygen with a 6-amino-alpha-D-glucosaminyl group. neamine: fragment of NEOMYCIN B; structure in first source | 2,6-dideoxy-alpha-D-glucoside; aminoglycoside | antibacterial agent |
| florfenicol | florfenicol : A carboxamide that is the N-dichloroacetyl derivative of (1R,2S)-2-amino-3-fluoro-1-[4-(methanesulfonyl)phenyl]propan-1-ol. A synthetic veterinary antibiotic that is used for treatment of bovine respiratory disease and foot rot; also used in aquaculture. florfenicol: structure given in first source | organochlorine compound; organofluorine compound; secondary alcohol; secondary carboxamide; sulfone | antimicrobial agent |
| antibiotic g 418 | antibiotic G 418: from Micromonospora rhodorangea | ||
| paromomycin | paromomycin : An amino cyclitol glycoside that is the 1-O-(2-amino-2-deoxy-alpha-D-glucopyranoside) and the 3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranoside of 4,6-diamino-2,3-dihydroxycyclohexane (the 1R,2R,3S,4R,6S diastereoisomer). It is obtained from various Streptomyces species. A broad-spectrum antibiotic, it is used (generally as the sulfate salt) for the treatment of acute and chronic intestinal protozoal infections, but is not effective for extraintestinal protozoal infections. It is also used as a therapeutic against visceral leishmaniasis. Paromomycin: An aminoglycoside antibacterial and antiprotozoal agent produced by species of STREPTOMYCES. | amino cyclitol glycoside; aminoglycoside antibiotic | anthelminthic drug; antibacterial drug; antiparasitic agent; antiprotozoal drug |
| puromycin | puromycins | antiinfective agent; antimicrobial agent; antineoplastic agent; EC 3.4.11.14 (cytosol alanyl aminopeptidase) inhibitor; EC 3.4.14.2 (dipeptidyl-peptidase II) inhibitor; nucleoside antibiotic; protein synthesis inhibitor | |
| netilmicin | Netilmicin: Semisynthetic 1-N-ethyl derivative of SISOMYCIN, an aminoglycoside antibiotic with action similar to gentamicin, but less ear and kidney toxicity. | ||
| linezolid | acetamides; morpholines; organofluorine compound; oxazolidinone | antibacterial drug; protein synthesis inhibitor | |
| zithromax | azithromycin : A macrolide antibiotic useful for the treatment of bacterial infections. Azithromycin: A semi-synthetic macrolide antibiotic structurally related to ERYTHROMYCIN. It has been used in the treatment of Mycobacterium avium intracellulare infections, toxoplasmosis, and cryptosporidiosis. | macrolide antibiotic | antibacterial drug; environmental contaminant; xenobiotic |
| tiamulin | tiamulin : A carbotricyclic compound that is pleuromutilin in which the hydroxyacetate group is replaced by a 2-{[2-(diethylamino)ethyl]sulfanyl}acetate group. An antibacterial drug, tiamulin is used in veterinary medicine (generally as its hydrogen fumarate salt) for the treatment of swine dysentery caused by Serpulina hyodysenteriae. tiamulin: 81723 HFU and tiamutin are for fumarate salt; prevents senescence in ascomycete; pleuromutilin derivative; RN given refers to ((3aS-(3aalpha,4beta,5alpha,6alpha,8beta,9alpha,9abeta,10S*))-isomer | carbotricyclic compound; carboxylic ester; cyclic ketone; organic sulfide; secondary alcohol; semisynthetic derivative; tertiary amino compound; tetracyclic diterpenoid | antibacterial drug |
| hmr 3647 | |||
| josamycin | acetate ester; aldehyde; disaccharide derivative; glycoside; macrolide antibiotic; tertiary alcohol; tertiary amino compound | antibacterial drug; metabolite | |
| albocycline | albocycline: macrolide antibiotic isolated from Streptomyces bruneogriseus nov. sp. MCRL-0129; specifically anti-staphylococcal, including antibiotic-resistant strains; structure | macrolide | |
| evernimicin | |||
| gentamicin sulfate | |||
| gentamicin sulfate | |||
| pristinamycin iib | virginiamycin M2: structure in first source | ||
| cem 101 | solithromycin: an antibacterial fluoroketolide; structure in first source | ||
| tetracycline | tetracycline : A broad-spectrum polyketide antibiotic produced by the Streptomyces genus of actinobacteria. Tetracycline: A naphthacene antibiotic that inhibits AMINO ACYL TRNA binding during protein synthesis. | ||
| eravacycline | eravacycline: has antibacterial activity | tetracyclines | |
| PF-06446846 | PF-06446846 : A triazolopyridine that is 3H-[1,2,3]triazolo[4,5-b]pyridine substituted by a 4-{(3-chloropyridin-2-yl)[(3R)-piperidin-3-yl]carbamoyl}phenyl group at position 3. It is a potent inhibitor of PCSK9. PF-06446846: inhibits translation of PCSK9 ;structure in first source | benzamides; monochloropyridine; piperidines; tertiary carboxamide; triazolopyridine | antilipemic drug; EC 3.4.21.61 (kexin) inhibitor |