50S

Svedberg

A svedberg is a non-SI physical unit used for sedimentation coefficients.  It characterizes the behaviour of a particle type in sedimentation processes, notably centrifugation.  The svedberg is technically a measure of time, and is defined as exactly 10-13 seconds A svedberg (symbol S, sometimes...

is the larger subunit of the 70S ribosome

Ribosome

A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....

 of prokaryote

Prokaryote

The prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles...

s. It is the site of inhibition for antibiotics such as macrolides, chloramphenicol

Chloramphenicol

Chloramphenicol is a bacteriostatic antimicrobial that became available in 1949. It is considered a prototypical broad-spectrum antibiotic, alongside the tetracyclines, and as it is both cheap and easy to manufacture it is frequently found as a drug of choice in the third world.Chloramphenicol is...

, clindamycin

Clindamycin

Clindamycin rINN is a lincosamide antibiotic. It is usually used to treat infections with anaerobic bacteria but can also be used to treat some protozoal diseases, such as malaria...

, and the pleuromutilin

Pleuromutilin

Pleuromutilin and its derivatives are antibacterial drugs that inhibit protein synthesis in bacteria by binding to the peptidyl transferase component of the 50S subunit of ribosomes....

s. It includes the subunits 5S

5S ribosomal RNA

5S ribosomal RNA is a component of the large ribosomal subunit in both prokaryotes and eukaryotes .Eukaryotic 5S rRNA is synthesised by RNA polymerase III, whereas most other eukaroytic rRNAs are cleaved from a 45S precursor transcribed by RNA polymerase I...

 and 23S

23S ribosomal RNA

The 23S rRNA is a 2904 nt long component of the large prokaryotic subunit The ribosomal peptidyl transferase activity resides in this rRNA...

.

Structure

50S, roughly equivalent to the 60S

60S

60S is the large ribosomal subunit in eukaryotes. It corresponds to 50S in prokaryotes.It consists of the following:* 5S* 28S* 5.8SThe following is a list of proteins contained within the 60S ribosome:...

 ribosomal subunit in eukaryotic

Eukaryote

A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear...

 cells, is the large subunit of the 70S ribosome of prokaryote

Prokaryote

The prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles...

s. The 50S subunit is primarily composed of proteins but also contains single-stranded RNA

RNA

Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....

 known as ribosomal RNA

Ribosomal RNA

Ribosomal ribonucleic acid is the RNA component of the ribosome, the enzyme that is the site of protein synthesis in all living cells. Ribosomal RNA provides a mechanism for decoding mRNA into amino acids and interacts with tRNAs during translation by providing peptidyl transferase activity...

 (rRNA). rRNA forms secondary and tertiary structures to maintain the structure and carry out the catalytic functions of the ribosome.

Electron microscopy and x-ray crystallography

X-ray crystallography

X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...

 have yielded electron density maps allowing the structure of 50S in Haloarcula marismortui to be determined up to 2.4-angstrom

Ångström

The angstrom or ångström, is a unit of length equal to 1/10,000,000,000 of a meter . Its symbol is the Swedish letter Å....

 resolution. The large ribosomal subunit (50S) is approximately twice as massive as the small ribosomal subunit (30S

30S

30S is the smaller subunit of the 70S ribosome of prokaryotes. It is a complex of ribosomal RNA and ribonucleoproteins that functions in mRNA translation...

). The model of 50S determined in 2000 by the Steitz lab includes 2711 of the 2923 nucleotide

Nucleotide

Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...

s of 23S rRNA, all 122 nucleotides of its 5S rRNA, and structure of 27 of its 31 protein

Protein

Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

s.

Ribosomal proteins

Ribosomal proteins are mostly on the surface of the 50S subunit, though some extend into the active site

Active site

In biology the active site is part of an enzyme where substrates bind and undergo a chemical reaction. The majority of enzymes are proteins but RNA enzymes called ribozymes also exist. The active site of an enzyme is usually found in a cleft or pocket that is lined by amino acid residues that...

. Seventeen proteins are globular and the remaining 13 either have protruding extensions or are entirely extended. The proteins do not shield all rRNA surfaces but act like mortar

Mortar (masonry)

Mortar is a workable paste used to bind construction blocks together and fill the gaps between them. The blocks may be stone, brick, cinder blocks, etc. Mortar becomes hard when it sets, resulting in a rigid aggregate structure. Modern mortars are typically made from a mixture of sand, a binder...

 filling the gaps and cracks between “RNA bricks”. The main function of protein is to stabilize the tertiary structure and orientation of the rRNA. The burial of a large amount of surface area may be required to provide the free energy

Thermodynamic free energy

The thermodynamic free energy is the amount of work that a thermodynamic system can perform. The concept is useful in the thermodynamics of chemical or thermal processes in engineering and science. The free energy is the internal energy of a system less the amount of energy that cannot be used to...

 required to immobilize the structure of molecules, thus making it possible to form interior protein-poor catalytic regions. Some ribosomal proteins may also aid in interactions with elongation factors.

Prokaryotic elongation factors

In prokaryotes, three elongation factors are required for translation: EF-Tu, EF-Ts, and EF-G.*EF-Tu mediates the entry of the aminoacyl tRNA into a free site of the ribosome....

Ribosomal RNA

The secondary structure

Secondary structure

In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...

 of 23S is divided into six large domains, within which domain V is most important in its peptidyl transferase

Peptidyl transferase

The Peptidyl transferase is an aminoacyltransferase as well as the primary enzymatic function of the ribosome, which forms peptide links between adjacent amino acids using tRNAs during the translation process of protein biosynthesis....

 activity. Each domain contains normal secondary structure (e.g., base triple, tetraloop, cross-strand purine stack) and is also highly symmetric in tertiary structure and is protrude by proteins between their helices. At tertiary structure

Tertiary structure

In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.-Relationship to primary structure:...

 level, the large subunit rRNA is a single and gigantic domain while the small subunit contains three structural domains. This difference reflects the less flexibility of big subunit required by its function.

Function

50S includes the activity that catalyzes peptide bond

Peptide bond

This article is about the peptide link found within biological molecules, such as proteins. A similar article for synthetic molecules is being created...

 formation (peptidyl transfer reaction), prevents premature polypeptide hydrolysis, provides a binding site for the G-protein factors (assists initiation, elongation, and termination), and helps protein folding

Protein folding

Protein folding is the process by which a protein structure assumes its functional shape or conformation. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil....

 after synthesis.

Promotes peptidyl transfer reaction and prevents peptidyl hydrolysis

An induced-fit mechanism has been revealed for how 50S catalyze peptidyl transfer reaction and prevent peptidyl hydrolysis. The amino group of aminoacyl-tRNA (binds to A site) attacks the carbon of carbonyl

Carbonyl

In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom: C=O. It is common to several classes of organic compounds, as part of many larger functional groups....

 group of peptidyl-tRNA (binds to P site) and finally yields a peptide extended by one amino acid

Amino acid

Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...

 esterified to the A site bound-tRNA and a deacylated tRNA in the P site.

When A site is unoccupied, nucleotide U2620 (E. coli U2585) and A2486 (2451), C2106 (2063) sandwich the carbonyl group in the middle, forcing it into an orientation facing the A site. This orientation prevents any nucleophilic attack from A site because the optimal attacking angle is 105 degrees from the plane of the ester

Ester

Esters are chemical compounds derived by reacting an oxoacid with a hydroxyl compound such as an alcohol or phenol. Esters are usually derived from an inorganic acid or organic acid in which at least one -OH group is replaced by an -O-alkyl group, and most commonly from carboxylic acids and...

 group. When tRNA with compete CCA sequence at its acceptor stem is bound to A site, C74 of tRNA stacking with U2590 (2555) induces a conformational change in the ribosome, resulting in movement of U2541 (2506), U2620 (2585) through G2618 (2583). The displacements of bases allow ester group adopts a new conformation assessable to nucleophilic attack from A site.

The N3 (nitrogen

Nitrogen

Nitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless, and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere...

) of A2486 (2451) is nearest to the peptide bond being synthesized and may function as a general base to facilitate the nucleophilic attack by the amino group of aminoacyl-tRNA (in A site). The pKa of A2486 (2451) is about 5 units higher in order to hydrogen bond

Hydrogen bond

A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen must be covalently bonded to another electronegative atom to create the bond...

 with the amino group thus increasing its nucleophilicity. The elevation of pKa is achieved through a charge relay mechanism. A2486 (2451) interacts with G2482 (G2447), which hydrogen-bonds with the buried phosphate

Phosphate

A phosphate, an inorganic chemical, is a salt of phosphoric acid. In organic chemistry, a phosphate, or organophosphate, is an ester of phosphoric acid. Organic phosphates are important in biochemistry and biogeochemistry or ecology. Inorganic phosphates are mined to obtain phosphorus for use in...

 of A2486 (2450). This buried phosphate can stabilize normally rare imino tautomeric forms of both bases, resulting in an increase in negative charge density on N3.

Help protein formation

After initiation, elongation, and termination, there is a fourth step of the disassembly of the post-termination complex of ribosome, mRNA, and tRNA, which is prerequisite for the next round of protein synthesis. Large ribosomal subunit has a role in protein folding both in vitro

In vitro

In vitro refers to studies in experimental biology that are conducted using components of an organism that have been isolated from their usual biological context in order to permit a more detailed or more convenient analysis than can be done with whole organisms. Colloquially, these experiments...

and in vivo

In vivo

In vivo is experimentation using a whole, living organism as opposed to a partial or dead organism, or an in vitro controlled environment. Animal testing and clinical trials are two forms of in vivo research...

. Large ribosomal subunit provides a hydrophobic surface for the hydrophobic collapse step of protein folding. The newly synthesis protein needs fully access to the large subunit to fold and this process may take a period of time (5 minutes for beta-galactosidase

Beta-galactosidase

β-galactosidase, also called beta-gal or β-gal, is a hydrolase enzyme that catalyzes the hydrolysis of β-galactosides into monosaccharides. Substrates of different β-galactosidases include ganglioside GM1, lactosylceramides, lactose, and various glycoproteins...

).

External links

• http://pathmicro.med.sc.edu/mayer/antibiot.htm
• http://www.molgen.mpg.de/~ag_ribo/ag_franceschi/franceschi-projects-50S-antibiotics.html
• http://riboworld.com/antib/50santib-eng.shtml