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Prokaryotic large ribosomal subunit

January 01, 1970

50S is the larger subunit of the 70S ribosome of prokaryotes, i.e. bacteria and archaea. It is the site of inhibition for antibiotics such as macrolides, chloramphenicol, clindamycin, and the pleuromutilins. It includes the 5S ribosomal RNA and 23S ribosomal RNA.

Atomic structure of the 50S Subunit from Haloarcula marismortui. Proteins are shown in blue and the two RNA strands in orange and yellow.[1] The small patch of green in the center of the subunit is the active site.
Atomic structure of the 50S large subunit of the ribosome, facing the 30S small ribosomal subunit. Proteins are colored in blue and RNA in ochre. The active site, adenine 2486, is highlighted in red. Image created from PDB: 3CC2​ using PyMol

Despite having the same sedimentation rate, bacterial and archaeal ribosomes can be quite different.

Structure edit

50S, roughly equivalent to the 60S ribosomal subunit in eukaryotic cells, is the larger subunit of the 70S ribosome of prokaryotes. The 50S subunit is primarily composed of proteins but also contains single-stranded RNA known as ribosomal RNA (rRNA). rRNA forms secondary and tertiary structures to maintain the structure and carry out the catalytic functions of the ribosome.

X-ray crystallography has yielded electron density maps allowing the structure of the 50S in Haloarcula marismortui (archaeon) to be determined to 2.4Å resolution[1]and of the 50S in the Deinococcus radiodurans (bacterium) to 3.3Å. [2] The large ribosomal subunit (50S) is approximately twice as massive as the small ribosomal subunit (30S). The model of Hm 50S, determined in 2000 by Nenad Ban and colleagues in the laboratory of Thomas Steitz and the laboratory of Peter Moore, includes 2711 of the 2923 nucleotides of 23S rRNA, all 122 nucleotides of its 5S rRNA, and structure of 27 of its 31 proteins.[1]

Ribosomal RNA edit

The secondary structure of 23S is divided into six large domains, within which domain V is most important in its peptidyl transferase [3] activity. Each domain contains normal secondary structure (e.g., base triple, tetraloop, cross-strand purine stack) and is also highly symmetric in tertiary structure; proteins intervene between their helices. At tertiary structure level, the large subunit rRNA is a single gigantic domain while the small subunit contains three structural domains. This difference reflects the lesser flexibility of the large subunit required by its function. While its core is conserved, it accommodates expansion segments on its periphery.[4][5]

Difference between bacteria and archaeal versions edit

See also: Ribosome § Archaeal ribosomes

A cryoEM structure of the 50S subunit from the archaeon Methanothermobacter thermautotrophicus has been determined. It shares the 50S size/sedimentation rate and the two rRNA count, but its 23S expansion segments have more in common with eukaryotes.[6]

A cryoEM reconstruction of the native 50S subunit of the extremely halophilic Archaean Halococcus morrhuae (classified under Euryarchaeota; Stenosarchaea group) is available. The 50S subunit contains a 108‐nucleotide insertion in its 5S rRNA,[7] which at subnanometer resolution, is observed to emerge from a four‐way junction without affecting the parental canonical 5S rRNA structure.[4]

Due to the differences, archaeal 50S are less sensitive to some antibiotics that target bacterial 50S.[8][9]

Function edit

50S includes the activity that catalyzes peptide bond 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 after synthesis.

Promotes the peptidyl transfer reaction and prevents peptidyl hydrolysis edit

An induced-fit mechanism has been revealed for how 50S catalyzes the peptidyl transfer reaction and prevents peptidyl hydrolysis. The amino group of an aminoacyl-tRNA (binds to A site) attacks the carbon of a carbonyl group of a peptidyl-tRNA (binds to P site) and finally yields a peptide extended by one amino acid esterified to the A site tRNA bound to the ribosomal A site and a deacylated tRNA in the P site.

When the A site is unoccupied, nucleotide U2620 (E. coli U2585), A2486 (2451) and 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 the A site because the optimal attacking angle is 105 degrees from the plane of the ester group. When a tRNA with a complete[?] CCA sequence at its acceptor stem is bound to the A site, C74 of the tRNA stacking with U2590 (2555) induces a conformational change in the ribosome, resulting in movement of U2541 (2506), U2620 (2585) through G2618 (2583). The displacement of bases allows the ester group to adopt a new conformation accessible to nucleophilic attack from the A site.

The N3 (nitrogen) of A2486 (2451) is closest to the peptide bond being synthesized and may function as a general base to facilitate the nucleophilic attack by the amino group of the aminoacyl-tRNA (in the A site). The pKa of A2486 (2451) is about 5 units higher in order to hydrogen 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 of A2486 (2450). This buried phosphate can stabilize the normally rare imino tautomers of both bases, resulting in an increase in the negative charge density on N3.

Helps protein formation edit

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 a prerequisite for the next round of protein synthesis. The large ribosomal subunit has a role in protein folding both in vitro and in vivo. The large ribosomal subunit provides a hydrophobic surface for the hydrophobic collapse step of protein folding. The newly synthesized protein needs full access to the large subunit to fold; this process may take a period of time (5 minutes for beta-galactosidase[citation needed]).

See also edit

References edit

  1. ^ a b c Nissen, P.; Hansen, J.; Ban, N.; Moore, P.; Steitz, T. (2000). "The complete atomic structure of the large ribosomal subunit at 2.4 A resolution". Science. 289 (5481): 905–920. Bibcode:2000Sci...289..905B. CiteSeerX 10.1.1.58.2271. doi:10.1126/science.289.5481.905. PMID 10937989.
  2. ^ Schluenzen, F.; Tocilj, A.; Zarivach, R.; Harms, J.; Gluehmann, M.; Janell, D.; Bashan, A.; Bartels, H.; Agmon, I.; Franceschi, F.; Yonath, A. (2000). "Structure of functionally activated small ribosomal subunit at 3.3 Å resolution". Cell. 102 (5): 615–623. doi:10.1016/S0092-8674(00)00084-2. PMID 11007480.
  3. ^ Tirumalai MR, Rivas M, Tran Q, Fox GE (November 10, 2021). "The Peptidyl Transferase Center: a Window to the Past". Microbiol Mol Biol Rev. 85 (4): e0010421. doi:10.1128/MMBR.00104-21. PMC 8579967. PMID 34756086.
  4. ^ a b Tirumalai, MR; Kaelber, JT; Park, DR; Tran, Q; Fox, GE (31 August 2020). "Cryo-electron microscopy visualization of a large insertion in the 5S ribosomal RNA of the extremely halophilic archaeon Halococcus morrhuae". FEBS Open Bio. 10 (10): 1938–1946. doi:10.1002/2211-5463.12962. PMC 7530397. PMID 32865340.
  5. ^ Penev PI, Fakhretaha-Aval S, Patel VJ, Cannone JJ, Gutell RR, Petrov AS, Williams LD, Glass JB (August 2020). "Supersized ribosomal RNA expansion segments in Asgard archaea". Genome Biology and Evolution. 12 (10): 1694–1710. doi:10.1093/gbe/evaa170. PMC 7594248. PMID 32785681.
  6. ^ Greber, Basil J.; Boehringer, Daniel; Godinic-Mikulcic, Vlatka; Crnkovic, Ana; Ibba, Michael; Weygand-Durasevic, Ivana; Ban, Nenad (May 2012). "Cryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Complex with Initiation Factor 6 and Implications for Ribosome Evolution". Journal of Molecular Biology. 418 (3–4): 145–160. doi:10.1016/j.jmb.2012.01.018. PMC 3879142. PMID 22306461.
  7. ^ Luehrsen, KR.; Nicholson, DE; Eubanks, DC; Fox, GE (May 1981). "An archaebacterial 5S rRNA contains a long insertion sequence". Nature. 293 (5835): 755–756. Bibcode:1981Natur.293..755L. doi:10.1038/293755a0. PMID 6169998. S2CID 4341755.
  8. ^ Khelaifia, S.; Drancourt, M. (September 2012). "Susceptibility of archaea to antimicrobial agents: applications to clinical microbiology". Clinical Microbiology and Infection. 18 (9): 841–848. doi:10.1111/j.1469-0691.2012.03913.x. PMID 22748132.
  9. ^ Thombre, Rebecca S.; Shinde, Vinaya; Thaiparambil, Elvina; Zende, Samruddhi; Mehta, Sourabh (13 September 2016). "Antimicrobial Activity and Mechanism of Inhibition of Silver Nanoparticles against Extreme Halophilic Archaea". Frontiers in Microbiology. 7: 1424. doi:10.3389/fmicb.2016.01424. PMC 5020055. PMID 27679615. The haloarchaea used in the current study were resistant to nalidixic acid, streptomycin, gentamicin, tetracycline, erythromycin, chloramphenicol, cephalothin, and clindamycin.
  • Nissen, P.; Hansen, J.; Ban, N.; Moore, P.; Steitz, T. (2000). "The structural basis of ribosome activity in peptide bond synthesis". Science. 289 (5481): 920–929. Bibcode:2000Sci...289..920N. doi:10.1126/science.289.5481.920. PMID 10937990.
  • Schmeing, T.; Huang, K.; Strobel, S.; Steitz, T. (2005). "An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA". Nature. 438 (7067): 520–524. Bibcode:2005Natur.438..520M. doi:10.1038/nature04152. PMID 16306996. S2CID 4333559.
  • Basu, A.; Ghosh, J.; Bhattacharya, A.; Pal, S.; Chowdhury, S.; DasGupta, C. (2003). "Splitting of ribosome into its subunits by unfolded polypeptide chains". Current Science. 84: 1123–1125.

External links edit

January 01, 1970
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This article needs additional citations for verification Please help improve this article by adding citations to reliable sources Unsourced material may be challenged and removed Find sources Prokaryotic large ribosomal subunit news newspapers books scholar JSTOR October 2011 Learn how and when to remove this message 50S is the larger subunit of the 70S ribosome of prokaryotes i e bacteria and archaea It is the site of inhibition for antibiotics such as macrolides chloramphenicol clindamycin and the pleuromutilins It includes the 5S ribosomal RNA and 23S ribosomal RNA Atomic structure of the 50S Subunit from Haloarcula marismortui Proteins are shown in blue and the two RNA strands in orange and yellow 1 The small patch of green in the center of the subunit is the active site Atomic structure of the 50S large subunit of the ribosome facing the 30S small ribosomal subunit Proteins are colored in blue and RNA in ochre The active site adenine 2486 is highlighted in red Image created from PDB 3CC2 using PyMol Despite having the same sedimentation rate bacterial and archaeal ribosomes can be quite different Contents 1 Structure 1 1 Ribosomal RNA 1 2 Difference between bacteria and archaeal versions 2 Function 2 1 Promotes the peptidyl transfer reaction and prevents peptidyl hydrolysis 2 2 Helps protein formation 3 See also 4 References 5 External linksStructure edit50S roughly equivalent to the 60S ribosomal subunit in eukaryotic cells is the larger subunit of the 70S ribosome of prokaryotes The 50S subunit is primarily composed of proteins but also contains single stranded RNA known as ribosomal RNA rRNA rRNA forms secondary and tertiary structures to maintain the structure and carry out the catalytic functions of the ribosome X ray crystallography has yielded electron density maps allowing the structure of the 50S in Haloarcula marismortui archaeon to be determined to 2 4A resolution 1 and of the 50S in the Deinococcus radiodurans bacterium to 3 3A 2 The large ribosomal subunit 50S is approximately twice as massive as the small ribosomal subunit 30S The model of Hm 50S determined in 2000 by Nenad Ban and colleagues in the laboratory of Thomas Steitz and the laboratory of Peter Moore includes 2711 of the 2923 nucleotides of 23S rRNA all 122 nucleotides of its 5S rRNA and structure of 27 of its 31 proteins 1 Ribosomal RNA edit The secondary structure of 23S is divided into six large domains within which domain V is most important in its peptidyl transferase 3 activity Each domain contains normal secondary structure e g base triple tetraloop cross strand purine stack and is also highly symmetric in tertiary structure proteins intervene between their helices At tertiary structure level the large subunit rRNA is a single gigantic domain while the small subunit contains three structural domains This difference reflects the lesser flexibility of the large subunit required by its function While its core is conserved it accommodates expansion segments on its periphery 4 5 Difference between bacteria and archaeal versions edit See also Ribosome Archaeal ribosomes A cryoEM structure of the 50S subunit from the archaeon Methanothermobacter thermautotrophicus has been determined It shares the 50S size sedimentation rate and the two rRNA count but its 23S expansion segments have more in common with eukaryotes 6 A cryoEM reconstruction of the native 50S subunit of the extremely halophilic Archaean Halococcus morrhuae classified under Euryarchaeota Stenosarchaea group is available The 50S subunit contains a 108 nucleotide insertion in its 5S rRNA 7 which at subnanometer resolution is observed to emerge from a four way junction without affecting the parental canonical 5S rRNA structure 4 Due to the differences archaeal 50S are less sensitive to some antibiotics that target bacterial 50S 8 9 Function edit50S includes the activity that catalyzes peptide bond 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 after synthesis Promotes the peptidyl transfer reaction and prevents peptidyl hydrolysis edit An induced fit mechanism has been revealed for how 50S catalyzes the peptidyl transfer reaction and prevents peptidyl hydrolysis The amino group of an aminoacyl tRNA binds to A site attacks the carbon of a carbonyl group of a peptidyl tRNA binds to P site and finally yields a peptide extended by one amino acid esterified to the A site tRNA bound to the ribosomal A site and a deacylated tRNA in the P site When the A site is unoccupied nucleotide U2620 E coli U2585 A2486 2451 and 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 the A site because the optimal attacking angle is 105 degrees from the plane of the ester group When a tRNA with a complete CCA sequence at its acceptor stem is bound to the A site C74 of the tRNA stacking with U2590 2555 induces a conformational change in the ribosome resulting in movement of U2541 2506 U2620 2585 through G2618 2583 The displacement of bases allows the ester group to adopt a new conformation accessible to nucleophilic attack from the A site The N3 nitrogen of A2486 2451 is closest to the peptide bond being synthesized and may function as a general base to facilitate the nucleophilic attack by the amino group of the aminoacyl tRNA in the A site The pKa of A2486 2451 is about 5 units higher in order to hydrogen 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 of A2486 2450 This buried phosphate can stabilize the normally rare imino tautomers of both bases resulting in an increase in the negative charge density on N3 Helps protein formation edit 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 a prerequisite for the next round of protein synthesis The large ribosomal subunit has a role in protein folding both in vitro and in vivo The large ribosomal subunit provides a hydrophobic surface for the hydrophobic collapse step of protein folding The newly synthesized protein needs full access to the large subunit to fold this process may take a period of time 5 minutes for beta galactosidase citation needed See also editProkaryotic small ribosomal subunit 30S Ribosomal RNA 23S methyl RNA motifReferences edit a b c Nissen P Hansen J Ban N Moore P Steitz T 2000 The complete atomic structure of the large ribosomal subunit at 2 4 A resolution Science 289 5481 905 920 Bibcode 2000Sci 289 905B CiteSeerX 10 1 1 58 2271 doi 10 1126 science 289 5481 905 PMID 10937989 Schluenzen F Tocilj A Zarivach R Harms J Gluehmann M Janell D Bashan A Bartels H Agmon I Franceschi F Yonath A 2000 Structure of functionally activated small ribosomal subunit at 3 3 A resolution Cell 102 5 615 623 doi 10 1016 S0092 8674 00 00084 2 PMID 11007480 Tirumalai MR Rivas M Tran Q Fox GE November 10 2021 The Peptidyl Transferase Center a Window to the Past Microbiol Mol Biol Rev 85 4 e0010421 doi 10 1128 MMBR 00104 21 PMC 8579967 PMID 34756086 a b Tirumalai MR Kaelber JT Park DR Tran Q Fox GE 31 August 2020 Cryo electron microscopy visualization of a large insertion in the 5S ribosomal RNA of the extremely halophilic archaeon Halococcus morrhuae FEBS Open Bio 10 10 1938 1946 doi 10 1002 2211 5463 12962 PMC 7530397 PMID 32865340 Penev PI Fakhretaha Aval S Patel VJ Cannone JJ Gutell RR Petrov AS Williams LD Glass JB August 2020 Supersized ribosomal RNA expansion segments in Asgard archaea Genome Biology and Evolution 12 10 1694 1710 doi 10 1093 gbe evaa170 PMC 7594248 PMID 32785681 Greber Basil J Boehringer Daniel Godinic Mikulcic Vlatka Crnkovic Ana Ibba Michael Weygand Durasevic Ivana Ban Nenad May 2012 Cryo EM Structure of the Archaeal 50S Ribosomal Subunit in Complex with Initiation Factor 6 and Implications for Ribosome Evolution Journal of Molecular Biology 418 3 4 145 160 doi 10 1016 j jmb 2012 01 018 PMC 3879142 PMID 22306461 Luehrsen KR Nicholson DE Eubanks DC Fox GE May 1981 An archaebacterial 5S rRNA contains a long insertion sequence Nature 293 5835 755 756 Bibcode 1981Natur 293 755L doi 10 1038 293755a0 PMID 6169998 S2CID 4341755 Khelaifia S Drancourt M September 2012 Susceptibility of archaea to antimicrobial agents applications to clinical microbiology Clinical Microbiology and Infection 18 9 841 848 doi 10 1111 j 1469 0691 2012 03913 x PMID 22748132 Thombre Rebecca S Shinde Vinaya Thaiparambil Elvina Zende Samruddhi Mehta Sourabh 13 September 2016 Antimicrobial Activity and Mechanism of Inhibition of Silver Nanoparticles against Extreme Halophilic Archaea Frontiers in Microbiology 7 1424 doi 10 3389 fmicb 2016 01424 PMC 5020055 PMID 27679615 The haloarchaea used in the current study were resistant to nalidixic acid streptomycin gentamicin tetracycline erythromycin chloramphenicol cephalothin and clindamycin Nissen P Hansen J Ban N Moore P Steitz T 2000 The structural basis of ribosome activity in peptide bond synthesis Science 289 5481 920 929 Bibcode 2000Sci 289 920N doi 10 1126 science 289 5481 920 PMID 10937990 Schmeing T Huang K Strobel S Steitz T 2005 An induced fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl tRNA Nature 438 7067 520 524 Bibcode 2005Natur 438 520M doi 10 1038 nature04152 PMID 16306996 S2CID 4333559 Basu A Ghosh J Bhattacharya A Pal S Chowdhury S DasGupta C 2003 Splitting of ribosome into its subunits by unfolded polypeptide chains Current Science 84 1123 1125 External links edithttp pathmicro med sc edu mayer antibiot htm https web archive org web 20110227235620 http www molgen mpg de ag ribo ag franceschi franceschi projects 50S antibiotics html https web archive org web 20080206051722 http www riboworld com antib 50santib eng shtml 23S Ribosomal RNA at the U S National Library of Medicine Medical Subject Headings MeSH 5S Ribosomal RNA at the U S National Library of Medicine Medical Subject Headings MeSH Retrieved from https en wikipedia org w index php title Prokaryotic large ribosomal subunit amp oldid 1219971719, wikipedia, wiki, book, books, library,

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