Page last updated: 2024-10-24

rRNA binding

Definition

Target type: molecularfunction

Binding to a ribosomal RNA. [GOC:jl]

Ribosomal RNA (rRNA) binding is a fundamental molecular function that plays a crucial role in protein synthesis. rRNA molecules, which are essential components of ribosomes, are responsible for catalyzing the formation of peptide bonds between amino acids. rRNA binding proteins, such as ribosomal proteins and translation factors, interact with specific regions of rRNA to facilitate various steps in the translation process.

The molecular function of rRNA binding encompasses several key aspects:

1. **Ribosome assembly:** rRNA binding proteins participate in the assembly of ribosomal subunits by interacting with rRNA and providing structural support. They help to fold and stabilize the rRNA molecule, ensuring the proper formation of the ribosome's functional structure.

2. **Translation initiation:** During translation initiation, rRNA binding proteins facilitate the binding of mRNA to the ribosome. They interact with the 5' cap of mRNA and guide it to the small ribosomal subunit, allowing the ribosome to initiate translation.

3. **Translation elongation:** During translation elongation, rRNA binding proteins contribute to the movement of the ribosome along the mRNA, as well as the recruitment of tRNA molecules carrying amino acids. They interact with the ribosome's A, P, and E sites, ensuring accurate codon-anticodon pairing and polypeptide chain elongation.

4. **Translation termination:** rRNA binding proteins are involved in the termination of translation by recognizing stop codons in mRNA and facilitating the release of the newly synthesized polypeptide chain from the ribosome.

5. **Regulation of translation:** rRNA binding proteins can regulate translation by influencing the accessibility of mRNA to the ribosome, affecting the rate of translation, and modulating the stability of mRNA transcripts.

6. **Ribosome biogenesis:** rRNA binding proteins are essential for the synthesis and processing of rRNA molecules. They participate in the transcription, modification, and maturation of rRNA, ensuring the proper formation of functional rRNA molecules.

Overall, rRNA binding is a complex and multifaceted molecular function that is essential for protein synthesis and cellular function. The precise interactions between rRNA binding proteins and rRNA molecules are crucial for the efficient and accurate translation of genetic information into proteins.'
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Proteins (52)

ProteinDefinitionTaxonomy
50S ribosomal protein L25A large ribosomal subunit protein bL25 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P68919]Escherichia coli K-12
30S ribosomal protein S21A small ribosomal subunit protein bS21 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P68679]Escherichia coli K-12
50S ribosomal protein L5A large ribosomal subunit protein uL5 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P62399]Escherichia coli K-12
50S ribosomal protein L22A 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 L4A large ribosomal subunit protein uL4 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P60723]Escherichia coli K-12
50S ribosomal protein L24A 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 L3A large ribosomal subunit protein uL3 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P60438]Escherichia coli K-12
50S ribosomal protein L2A large ribosomal subunit protein uL2 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P60422]Escherichia coli K-12
50S ribosomal protein L18A large ribosomal subunit protein uL18 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0C018]Escherichia coli K-12
30S ribosomal protein S17A small ribosomal subunit protein uS17 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0AG63]Escherichia coli K-12
30S ribosomal protein S14A small ribosomal subunit protein uS14 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0AG59]Escherichia coli K-12
50S ribosomal protein L6A 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 L21A large ribosomal subunit protein bL21 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0AG48]Escherichia coli K-12
30S ribosomal protein S15A small ribosomal subunit protein uS15 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0ADZ4]Escherichia coli K-12
50S ribosomal protein L23A large ribosomal subunit protein uL23 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0ADZ0]Escherichia coli K-12
50S ribosomal protein L16A large ribosomal subunit protein uL16 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0ADY7]Escherichia coli K-12
50S ribosomal protein L14A large ribosomal subunit protein uL14 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0ADY3]Escherichia coli K-12
30S ribosomal protein S8A small ribosomal subunit protein uS8 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7W7]Escherichia coli K-12
30S ribosomal protein S5A small ribosomal subunit protein uS5 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7W1]Escherichia coli K-12
30S ribosomal protein S4A small ribosomal subunit protein uS4 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7V8]Escherichia coli K-12
30S ribosomal protein S3A small ribosomal subunit protein uS3 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7V3]Escherichia coli K-12
30S ribosomal protein S20A small ribosomal subunit protein bS20 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7U7]Escherichia coli K-12
30S ribosomal protein S19A small ribosomal subunit protein uS19 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7U3]Escherichia coli K-12
30S ribosomal protein S18A small ribosomal subunit protein bS18 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7T7]Escherichia coli K-12
30S ribosomal protein S13A small ribosomal subunit protein uS13 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7S9]Escherichia coli K-12
30S ribosomal protein S12A small ribosomal subunit protein uS12 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7S3]Escherichia coli K-12
30S ribosomal protein S11A small ribosomal subunit protein uS11 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7R9]Escherichia coli K-12
50S ribosomal protein L31A large ribosomal subunit protein bL31 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7M9]Escherichia coli K-12
50S ribosomal protein L29A large ribosomal subunit protein uL29 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7M6]Escherichia coli K-12
50S ribosomal protein L28A large ribosomal subunit protein bL28 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7M2]Escherichia coli K-12
50S ribosomal protein L27A large ribosomal subunit protein bL27 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7L8]Escherichia coli K-12
50S ribosomal protein L20A 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 L1A large ribosomal subunit protein uL1 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7L0]Escherichia coli K-12
50S ribosomal protein L19A 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 L11A 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 L10A large ribosomal subunit protein uL10 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A7J3]Escherichia coli K-12
50S ribosomal protein L15A large ribosomal subunit protein uL15 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P02413]Escherichia coli K-12
30S ribosomal protein S7A small ribosomal subunit protein uS7 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P02359]Escherichia coli K-12
30S ribosomal protein S6A small ribosomal subunit protein bS6 that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P02358]Escherichia coli K-12
40S ribosomal protein S5A eukaryotic-type small ribosomal subunit protein uS7 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P46782]Homo sapiens (human)
40S ribosomal protein S9A eukaryotic-type small ribosomal subunit protein uS4 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P46781]Homo sapiens (human)
Lysine-specific demethylase 2BA lysine-specific demethylase 2B that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q8NHM5]Homo sapiens (human)
2-5A-dependent ribonucleaseA 2-5A-dependent ribonuclease that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q05823]Homo sapiens (human)
60S ribosomal protein L8A eukaryotic-type large ribosomal subunit protein uL2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P62917]Homo sapiens (human)
60S ribosomal protein L23aA eukaryotic-type large ribosomal subunit protein uL23 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P62750]Homo sapiens (human)
40S ribosomal protein S4, X isoformA small ribosomal subunit protein eS4, X isoform that is encoded in the genome of human. [PRO:DNx, UniProtKB:P62701]Homo sapiens (human)
40S ribosomal protein S11A eukaryotic-type small ribosomal subunit protein uS17 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P62280]Homo sapiens (human)
40S ribosomal protein S18A eukaryotic-type small ribosomal subunit protein uS13 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P62269]Homo sapiens (human)
60S ribosomal protein L37A large ribosomal subunit protein eL37 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P61927]Homo sapiens (human)
60S ribosomal protein L9A eukaryotic-type large ribosomal subunit protein uL6 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P32969]Homo sapiens (human)
40S ribosomal protein S4, Y isoform 1A small ribosomal subunit protein eS4, Y isoform 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P22090]Homo sapiens (human)
NucleophosminA nucleophosmin that is encoded in the genome of human. [PRO:DNx, UniProtKB:P06748]Homo sapiens (human)

Compounds (35)

CompoundDefinitionClassesRoles
deferipronedeferiprone : A member of the class of 4-pyridones that is pyridin-4(1H)-one substituted at positions 1 and 2 by methyl groups and at position 3 by a hydroxy group. A lipid-soluble iron-chelator used for treatment of thalassaemia.

Deferiprone: A pyridone derivative and iron chelator that is used in the treatment of IRON OVERLOAD in patients with THALASSEMIA.
4-pyridonesiron chelator;
protective agent
imatinibaromatic amine;
benzamides;
N-methylpiperazine;
pyridines;
pyrimidines
antineoplastic agent;
apoptosis inducer;
tyrosine kinase inhibitor
chloramphenicolAmphenicol: 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
butylparabenorganic molecular entity
framycetinframycetin : 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)
aminoglycosideallergen;
antibacterial drug;
Escherichia coli metabolite
erythromycinerythromycin : 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
neamineneamine : 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
florfenicolflorfenicol : 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 418antibiotic G 418: from Micromonospora rhodorangea
paromomycinparomomycin : 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
puromycinpuromycinsantiinfective 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
netilmicinNetilmicin: Semisynthetic 1-N-ethyl derivative of SISOMYCIN, an aminoglycoside antibiotic with action similar to gentamicin, but less ear and kidney toxicity.
linezolidacetamides;
morpholines;
organofluorine compound;
oxazolidinone
antibacterial drug;
protein synthesis inhibitor
zithromaxazithromycin : 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 antibioticantibacterial drug;
environmental contaminant;
xenobiotic
pd 173955PD 173955: inhibits src family-selective tyrosine kinase; structure in first sourcearyl sulfide;
dichlorobenzene;
methyl sulfide;
pyridopyrimidine
tyrosine kinase inhibitor
tiamulintiamulin : 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
vitexinC-glycosyl compound;
trihydroxyflavone
antineoplastic agent;
EC 3.2.1.20 (alpha-glucosidase) inhibitor;
plant metabolite;
platelet aggregation inhibitor
hyperosidequercetin 3-O-beta-D-galactopyranoside : A quercetin O-glycoside that is quercetin with a beta-D-galactosyl residue attached at position 3. Isolated from Artemisia capillaris, it exhibits hepatoprotective activity.beta-D-galactoside;
monosaccharide derivative;
quercetin O-glycoside;
tetrahydroxyflavone
hepatoprotective agent;
plant metabolite
myricetin7-hydroxyflavonol;
hexahydroxyflavone
antineoplastic agent;
antioxidant;
cyclooxygenase 1 inhibitor;
food component;
geroprotector;
hypoglycemic agent;
plant metabolite
ellagic acidcatechols;
cyclic ketone;
lactone;
organic heterotetracyclic compound;
polyphenol
antioxidant;
EC 1.14.18.1 (tyrosinase) inhibitor;
EC 2.3.1.5 (arylamine N-acetyltransferase) inhibitor;
EC 2.4.1.1 (glycogen phosphorylase) inhibitor;
EC 2.5.1.18 (glutathione transferase) inhibitor;
EC 2.7.1.127 (inositol-trisphosphate 3-kinase) inhibitor;
EC 2.7.1.151 (inositol-polyphosphate multikinase) inhibitor;
EC 2.7.4.6 (nucleoside-diphosphate kinase) inhibitor;
EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor;
EC 5.99.1.2 (DNA topoisomerase) inhibitor;
EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor;
food additive;
fungal metabolite;
geroprotector;
plant metabolite;
skin lightening agent
josamycinacetate ester;
aldehyde;
disaccharide derivative;
glycoside;
macrolide antibiotic;
tertiary alcohol;
tertiary amino compound
antibacterial drug;
metabolite
bosutinib4-((2,4-dichloro-5-methoxyphenyl)amino)-6-methoxy-7-(3-(4-methyl-1-piperazinyl)propoxy)-3-quinolinecarbonitrile: a Src kinase inhibitor; structure in first sourceaminoquinoline;
aromatic ether;
dichlorobenzene;
N-methylpiperazine;
nitrile;
tertiary amino compound
antineoplastic agent;
tyrosine kinase inhibitor
albocyclinealbocycline: macrolide antibiotic isolated from Streptomyces bruneogriseus nov. sp. MCRL-0129; specifically anti-staphylococcal, including antibiotic-resistant strains; structuremacrolide
evernimicin
gentamicin sulfate
gentamicin sulfate
crizotinibcrizotinib : A 3-[1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-[1-(piperidin-4-yl)pyrazol-4-yl]pyridin-2-amine that has R configuration at the chiral centre. The active enantiomer, it acts as a kinase inhibitor and is used for the treatment of patients with locally advanced or metastatic non-small cell lung cancer (NSCLC)

Crizotinib: A piperidine and aminopyridine derivative that acts as an inhibitor of RECEPTOR PROTEIN-TYROSINE KINASES, including ANAPLASTIC LYMPHOMA KINASE (ALK) and HEPATOCYTE GROWTH FACTOR RECEPTOR (HGFR; c-Met). It is used in the treatment of NON-SMALL CELL LUNG CANCER.
3-[1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-[1-(piperidin-4-yl)pyrazol-4-yl]pyridin-2-amineantineoplastic agent;
biomarker;
EC 2.7.10.1 (receptor protein-tyrosine kinase) inhibitor
pristinamycin iibvirginiamycin M2: structure in first source
cem 101solithromycin: an antibacterial fluoroketolide; structure in first source
tetracyclinetetracycline : 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.
eravacyclineeravacycline: has antibacterial activitytetracyclines
3-[[2-(2-pyridinyl)-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)-4-pyrimidinyl]amino]propanoic acidorganonitrogen heterocyclic compound
ceritinibceritinib : A member of the class of aminopyrimidines that is 2,6-diamino-5-chloropyrimidine in which the amino groups at positions 2 and 6 are respectively carrying 2-methoxy-4-(piperidin-4-yl)-5-methylphenyl and 2-(isopropylsulfonyl)phenyl substituents. Used for the treatment of ALK-positive metastatic non-small cell lung cancer.

ceritinib: an anaplastic lymphoma kinase inhibitor
aminopyrimidine;
aromatic ether;
organochlorine compound;
piperidines;
secondary amino compound;
sulfone
antineoplastic agent;
EC 2.7.10.1 (receptor protein-tyrosine kinase) inhibitor
PF-06446846PF-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