Bacterial Ribosomes

Joachim Frank, State University of New York at Albany, NY, USA Rajendra K Agrawal, Wadsworth Center, Albany, NY, USA
Ribosomes are complex ribonucleoproteins that provide the platform for protein biosynthesis in all organisms.

Secondary article
Article Contents
. Introduction . The Small Subunit . The Large Subunit . Interactions with mRNA, tRNA and Elongation Factors . Polysomes and Secretion

Introduction
Translation of genetic information encoded in the base sequence of messenger RNA (mRNA) into the amino acid sequence of polypeptides takes place on ribosomes. This process involves the binding of a ribosome to an initiation sequence of nucleotides near the 5 end of mRNA, movement of the ribosome along the mRNA through a distance of a triplet of bases (one codon) after each peptide bond is formed, followed by release of both the completed polypeptide chain and the ribosome, once the termination codon at the 3 end of the mRNA is reached. The translation is mediated by transfer RNA (tRNA), an elbow-shaped molecule that exists in more than 20 varieties, for the 20 amino acids. Its anticodon end recognizes the mRNA codon, by forming wobble or WatsonCrick base pairings, while its amino acid acceptor end, also known as the CCA end, carries the corresponding amino acid. Thus the placement of tRNAs in the order stipulated by the genetic code induces the correct placement of amino acids in the polypeptide chain. Ribosomes carry out protein synthesis in all organisms using the same basic mechanism, and are therefore believed to have common structural features. The bacterial 70S ribosome (Figure 1), from Escherichia coli, which is the most extensively studied ribosome, provides the frame of reference for studies of ribosomes from all other sources. It is simplest in design, due to the absence of additional control and feedback functions that are required in multicellular organisms. In all organisms the ribosomes are composed of two unequal subunits, comprising single copies of 50 or more dierent, mostly basic proteins and several ribosomal RNA (rRNA) molecules (Table 1). In bacteria, the small (30S) and large subunit (50S) (Figure 2) associate in the course of the initiation process that is started by the interaction of mRNA and initiator tRNA with the small subunit and facilitated by three protein molecules called initiation factors. Upon association of the subunits which can also be induced in vitro in an mRNA- or tRNAfree system by raising the Mg2 1 concentration to 6 mmol L 2 1 or above a characteristic space is formed between the subunits (the intersubunit space) that facilitates binding of tRNA molecules at a succession of sites on both subunits. The structure and arrangement of the subunits, as well as the topology of the intersubunit space (Frank and Agrawal, 1998), have been elucidated by threedimensional cryoelectron microscopy of the E. coli ribosome (Figure 1) at resolutions ranging from 2.5 nm (Frank et al., 1995; Stark et al., 1995) to 1.5 nm (Malhotra et al., 1998). The same technique has been used to determine the 3-dimensional binding positions of tRNA and certain protein factors such as initiation and elongation factors, that catalyse specic steps of the protein synthesis process.

The Small Subunit

Figure 1 Cryoelectron microscopy of the Escherichia coli ribosome, with the small subunit (50S) in yellow, the large subunit in blue. The space between the subunits (intersubunit space) is where most of the ligands interact with the ribosome.

The small (30S) subunit is made up of 21 dierent proteins, designated S1S21, and one 16S rRNA molecule, which comprises 1542 nucleotides. The amino acid sequences of all 21 proteins and the nucleotide sequence of 16S rRNA are known. Small-subunit proteins range from 8.4 kDa to
1

ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net

Bacterial Ribosomes

Table 1 Important statistics of the E. coli ribosome and its subunits Ribosome 70S 30S 50S Molecular weight ( 103) 2700 950 1750 Number of proteins 54 21 34 Number of rRNAs 16S, 5S, 23S 16S 5S, 23S

Figure 2 Morphology of Escherichia coli ribosomal subunits, and locations of ribosomal proteins, as determined by immunoelectron microscopy. Top row: Three-dimensional cryoelectron microscopy maps of (a) the 30S subunit, (b) the 50S subunit and (c) the 70S ribosome (Frank et al ., 1995). Bottom row: Models of the two subunits and the 70S ribosome, as derived from visual interpretation of 2D projections from conventional electron microscopy of negatively stained specimen with approximate locations of some of the ribosomal proteins, marked by numbers. Locations of r-protein are determined by immunoelectron microscopy. Reproduced from Sto ffler-Meilicke and Sto ffler (1990) with permission by the American Society for Microbiology Press, Washington DC.

61 kDa, S21 protein being the smallest and S1 the largest protein. Except for S1, S2 and S6, all are basic in nature. Interactions between the various basic proteins and the negatively charged rRNA molecule help to stabilize the overall architecture of the 30S subunit. The 16S rRNA component of the subunit, which was originally thought to act merely as a scaold, in fact plays an active role in the initiation, elongation and termination steps of protein
2

biosynthesis (Dahlberg, 1989; Green and Noller, 1997). For example, the anti-ShineDalgarno sequence, which is situated near the 3 end of the 16S rRNA moiety, helps in establishing proper alignment of mRNA with the subunit at the initiation step of protein synthesis, by base-pairing with the ShineDalgarno sequence of mRNA present in the upstream 5 region. The decoding site, where the codonanticodon interaction takes place, lies within 1 or

ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net

Bacterial Ribosomes

2 nm of the 1400th nucleotide residue, which is a cytosine (C) residue. This C residue and many other segments of the 16S rRNA are phylogenetically conserved in all species and thus provide clues to their functional signicance. Several antibiotics that inhibit specic steps of the translation process interact with specic regions of 16S rRNA. For example, the aminoglycoside class of antibiotics bind to the decoding region of 16S RNA and interfere with decoding and translocation of tRNA. The overall secondary structure of the small-subunit rRNA from dierent sources is also conserved. The secondary structure of the 16S rRNA has been divided into three major domains; the 3-end domain, the middle domain and the 5-end domain. The 16S rRNA folds into the tertiary structure and spans the whole 30S subunit, as various small-subunit proteins interact with small segments of the 16S rRNA. Some of the proteins have multiple RNA-binding sites and probably interact with several regions of rRNA. These proteins presumably play the role of preserving the three-dimensional architecture of the 30S subunit, by protecting rRNA from the action of RNAase enzymes, and also help in ne-tuning various functions of the ribosomal rRNAs. Many of the functionally important rRNA regions and ribosomal proteins have been localized on the surface of the subunit (reviewed by Sto er-Meilicke and Sto er, 1990; see Figure 2d). So far, the structures of seven of the 21 proteins from dierent bacterial species have been (partially or fully) solved, either by X-ray crystallography or by three-dimensional nuclear magnetic resonance (NMR) techniques.

16S rRNA and proteins like S7, S9, S14 and S13, whereas the main body comprises the major portion of the 5 end of the rRNA and proteins like S4, S5, S12 and S17. The cleft between platform and head is the site where anticodoncodon interaction between mRNA and tRNA takes place. The cleft is continuous with a channel that leads through the neck between body and head and is thought to be the conduit for mRNA. Association with the large subunit involves the head, the rim of the platform and part of the body (Lata et al., 1996).

The Large Subunit

The large 50S subunit, which confers the peptidyltransferase and most of the translocase activities to the ribosome, is much more complex in composition. It is composed of two rRNA molecules (5S and 23S) and 34 dierent proteins, designated L1L34. The large-subunit proteins vary in size from 5.3 kDa to 29.7 kDa, protein L34 being smallest and L2 the largest. Thus the largest protein in the whole 70S ribosome, the S1 protein, is present in the small 30S subunit. The 5S and 23S rRNAs are comprised of 120 and 2904 nucleotides, respectively. As in the case of the 30S subunit, amino acid and nucleotide sequences of all 34 proteins and the two rRNA molecules, respectively, are known. All proteins are present in single copies and are mostly basic in nature except L7 and L12 proteins, which are acidic and exist in two copies. These two proteins have the same amino acid sequence but dier in the N-terminus, which is N-acetylated in L7. Of the 34 dierent proteins, the structures of eight large-subunit proteins have been solved, either fully or partially, using either X-ray crystallography or three-dimensional NMR techniques. As in the case of the small subunit rRNA, the secondary structure of the large-subunit rRNA is phylogenetically conserved. Being larger in size than the 16S rRNA, the 23S rRNA is divided into six domains, and appears to play a major role in the function of the 50S subunit. For example, the peptidyltransferase activity of the ribosome lies within domain V, whereas a small portion of domain II is involved in the elongation factor-dependent guanosine triphosphatase (GTPase) activity of the ribosome. As in 16S rRNA, various specic regions of 23S rRNA are sites for interaction with a variety of antibiotics that inhibit particular steps of bacterial protein synthesis.

Morphological features
Knowledge of morphological features of the two subunits helps in deducing their functional roles. The overall shape of the small subunit (Figure 2a), as determined by cryoelectron microscopy, is that of an elongate, at ellipsoid (largest width: 17.2 nm; length: 24.0 nm). Three major parts can be recognized: the body, the adjoining head and the platform. As yet, the exact locations of the various segments of rRNA and ribosomal proteins in the ribosome are unknown. However, a number of biophysical and biochemical studies have helped in reaching a consensus three-dimensional model of the subunit. These studies include neutron scattering (Capel et al., 1987), resulting in a positioning of all 21 proteins inside the 30S subunit; various biochemical protection and crosslinking experiments, which established the proximity of the proteins to specic rRNA segments; immunoelectron microscopy of ribosomal proteins; and positioning of various rRNA segments, by hybridizing complementary biotinylated oligonucleotides and tagging these with avidin. For example, the platform includes mainly the 3 end of the 16S rRNA and proteins like S6, S11, S15 and S18. The head region comprises the middle portion of the

Morphological features
The overall shape of the large subunit (Figures 1 and 2b) is hemispherical (diameter: 23.6 nm), with the relatively at side facing the small subunit, and the convex side facing the solvent. Three protrusions give the large subunit a characteristic crown appearance when viewed at face on: (1) a mushroom-shaped protuberance identied by
3

ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net

Bacterial Ribosomes

immunoelectron microscopy as protein L1; (2) the central protuberance, formed in part by 5S rRNA; and (3) the stalk, a exible structure made up of four copies of L7/L12 proteins, present as two dimers. It has been suggested that one copy of protein from each dimer gives rise to the extended stalk. Although the approximate positions of most of the proteins in the 50S subunit are known (Figure 2e) from neutron scattering (May et al., 1992) and immunoelectron microscopy (reviewed by Sto er-Meilicke and Sto er, 1990), because of the complexity of its composition, progress in molecular model building has been rather slow, as compared to that for the 30S subunit. On the at face of the 50S subunit, a deep groove, termed the interface canyon, runs across the entire width of the subunit. tRNA localization studies using cryoelectron microscopy have shown the interface canyon to contain the sites of tRNA acceptor end binding. At the bottom of the interface canyon there is the entrance to a tunnel, which traverses the subunit and exits at a site where the nascent polypeptide was localized by immunoelectron microscopy (Bernabeu and Lake, 1982).

Interactions with mRNA, tRNA and Elongation Factors

As mentioned in the Introduction, the ribosome needs to interact with various other molecules to synthesize the polypeptide chain. In this section, the interaction of the ribosome with various ligands during dierent stages of the protein synthesis will be described.

Interaction with mRNA and formation of the initiation complex

All mRNAs are single-stranded polyribonucleotides containing a central coding region, which determines the amino acid sequence of the gene product, along with anking sequences adjacent to the initiation and termina-

increases the rate of dissociation. IF-2 plays a central role in binding fMet-tRNAf to the 30S subunit preinitiation complex by specic recognition of the N-formylmethionine residue attached to the tRNA, thus restricting this interaction to charged initiator tRNA. In addition to its antiassociation activity, IF-3 is also involved in the decoding of the initiation codon. All three IFs are known to interact with the 3 end segment of 16S rRNA, which is mainly present in the platform region of the subunit. In the following step, the initiator tRNA and mRNA bind to the 30SIF-1IF-2IF-3 complex as IF-3 is released. From in vitro experiments, it has been suggested that the binding of mRNA precedes that of the initiator tRNA. The proper positioning of mRNA on the 30S subunit is ascertained by binding of its ShineDalgarno sequence, usually consisting of 39 bases on the 5 side (upstream), with the complementary anti-ShineDalgarno sequence located near the 3 end of the 16S rRNA, which is exposed on the platform of the 30S subunit. In the nal step of the initiation of protein synthesis, the 50S subunit joins the preinitiation complex. This step involves the hydrolysis of GTP due to the GTPase activity of IF-2 and release of IF-1, IF-2, guanosine diphosphate (GDP) and Pi, processes that are essential for allowing the fMet-tRNAf to engage in the formation of the rst peptide bond. It has been found that as it associates with the 50S subunit, the 30S subunit undergoes a drastic change of conformation accompanied by the formation of a channel between the head and main body (Lata et al., 1996). This channel has been proposed to be the conduit of mRNA during the elongation steps of protein synthesis (Frank et al., 1995; Lata et al., 1996; Mueller et al ., 1997; also see section on small subunit above). The three-dimensional binding position of fMet-tRNAf in the P site of the 70S ribosome has been established by cryoelectron microscopy and image reconstruction (Malhotra et al., 1998).

Interaction with tRNAs and the elongation cycle

Three primary binding positions of the tRNA on the ribosome have been characterized by a variety of biochemical and biophysical experiments: the A (aminoacyl) site, where a new tRNA carrying a covalently bound amino acid enters the ribosome; the P (peptidyl) site, the site where the rst initiator tRNA binds and where subsequently the A-site tRNA moves after the formation of a new peptide bond; and the E (exit) site, where the deacylated P-site tRNA moves before leaving the ribosome. A- and P-site positions each involve two binding sites, one on the small, the other on the large subunit. In addition, both A- and P-site tRNAs are bound to their cognate mRNA codons. The E-site tRNA may also still be bound to the mRNA (Nierhaus, 1990), although it has been suggested that it is

tion codons. The polycistronic mRNA of prokaryotes usually has a 5 leader sequence starting with either A or G. Accurate translation of mRNA requires the selection of the appropriate reading frame by precise interactions between the AUG initiation codon (or in rare cases, alternative initiation codons), charged initiator tRNA, and the small ribosomal subunit. A methionine-carrying initiator tRNA, termed Met-tRNAf, which is formylated, recognizes both the initiation codon of mRNA and the ribosomal P site. As mentioned earlier, three initiation factors, called IF-1, IF-2 and IF-3, are involved in the formation of the initiation complex. IF-3, also known as antiassociation factor, helps in maintaining the pool of dissociated subunits, while IF-1
4

ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net

Bacterial Ribosomes

primarily associated with the large subunit (Moazed and Noller, 1989a). The tRNA-binding sites on the small subunit, through anticodon ends, are along the cleft; those on the large subunit, through CCA ends, are along the interface canyon. If the structural features of the 50S subunit are used as the frame of reference, the A site is on the L7/L12 stalk side and the E site is on the L1 protein side, while the P site is located between these two positions. Three-dimensional binding positions of tRNA in the A, P and E sites have been inferred by cryoelectron microscopy (Agrawal et al., 1996 ; Stark et al., 1997a) at low resolution. Of these, the position of P-site tRNA is known with highest accuracy, with an estimated uncertainty of 0.10.2 nm (Malhotra et al., 1998). The movement of the tRNA through the ribosome involves a sequence of events during which two protein factors, called elongation factors, interact with the ribosome to facilitate two separate steps: one involving elongation factor Tu and resulting in the incorporation of a new tRNA at the free A site, and the other involving elongation factor G, eecting translocation of tRNAs occupying the A and P sites to the P and E sites, respectively. This sequence of events takes place in a cyclic fashion, with each cycle (elongation cycle) adding a new amino acid to the growing polypeptide chain (Figure 3).

Interaction with the aminoacyl-tRNA EF-Tu GTP ternary complex

After the formation of the initiation complex, which has an fMet-tRNAf at the P site, subsequent binding of aminoacyl-tRNA takes place at the ribosomal A site. Initially, the aminoacyl-tRNA enters the ribosome in the form of a complex with elongation factor Tu (EF-Tu) and GTP, known as the ternary complex. The anticodon end of the tRNA of the ternary complex interacts with the A site on the 30S subunit while EF-Tu protects its aminoacyl end (which is yet to occupy the actual A-site position on the 50S subunit) from forming a peptide bond. This state of the tRNA is known as the A/T state or sometimes also as the low-anity state, which is probably required for the proofreading of the mRNA codon. If cognate anticodon codon interaction occurs, GTP hydrolysis is triggered, EFTuGDP is released, and the aminoacyl end of the tRNA is freed up to occupy the A site on the 50S subunit and engage in peptide bond formation. This state is also known as A/A state or the high-anity state of the tRNA in the A site, and the corresponding conformational state of the ribosome is referred to as the pretranslocational state. Cryoelectron microscopic visualization (Stark et al., 1997b) has revealed the binding position of the ternary complex on the ribosome, in a complex where release of EF-Tu after the GTP hydrolysis was blocked by use of the antibiotic kirromycin. A low-resolution model of the X-ray structure of the aminoacyl-tRNAEF-TuGDPNP (5-guanylyli-

Figure 3 The elongation cycle, showing three-dimensional positions of tRNAs and elongation factors, as obtained by cryoelectron microscopy technique, overlaid on the 1.5-nm resolution map of the Escherichia coli 70S ribosome. Top: tRNA positions in the pretranslocational state. The aminoacyl-tRNA (pink) is present in the A site and peptidyl-tRNA (green), carrying a growing polypeptide chain, in the P site. Right: Posttranslocational state. After peptide bond formation, A- (pink) and P(green) site tRNAs have moved to P (green) and E (yellow) sites, respectively, in an EF-G-dependent translocation reaction. EF-G (purple) momentarily interacts with ribosome to facilitate the translocation reaction. Bottom: Posttranslocational state with tRNAs occupying P and E sites. EF-G has been released, after GTP hydrolysis in GDP form, to vacate the overlapping binding site for the next ternary complex. Left: At this stage, a new aminoacyl-tRNA (grey, then pink) enters into the cycle in the form of a ternary complex with EF-Tu (red) and GTP, and binds to the ribosome in the A/T state. Recently, another E site, the E2 site (brown), has been suggested, in which the deacylated tRNA temporarily resides without maintaining codon anticodon interaction. While the EF-Tu part of the ternary complex leaves the ribosome, following GTP hydrolysis, aminoacyltRNA moves to its proper A-site position to engage in peptide-bond formation, and deacylated tRNA is released from the E2 site.

midodiphosphate) complex (Nissen et al., 1995) has been docked into the inferred binding position (Figure 3). Following dissociation from the ribosome, the EF-Tu GDP complex interacts with another elongation factor, EF-Ts, resulting in the formation of an EF-TuEF-Ts heterodimer and release of GDP. Reaction of the heterodimer with GTP regenerates the EF-TuGTP complex required for binding aminoacyl-tRNA. The peptide bond formation takes place by a transpeptidation reaction between the carboxyl group of the peptidyl chain on the P-site tRNA and the amino group of the amino acid of the A-site tRNA. The transpeptidation reaction, also known as the peptidyltransferase reaction, is catalysed by a portion of domain V of 23S rRNA, also known as the peptidyltransferase centre of the

ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net

Bacterial Ribosomes

ribosome, which is presumably located near the mouth of the proposed polypeptide tunnel (see below).

Interaction with EF-G

After peptide bond formation, elongation factor G (EF-G) promotes the step of translocation (from the pretranslocational to the posttranslocational state) in which the tRNAs move from the A and P sites to the P and E sites, respectively (Figure 3, bottom) and mRNA advances by one codon. Thus the ribosome is readied for interaction with the ternary complex containing the tRNA cognate to the new codon. It is not clear whether this translocation is achieved in one step, by going from the pretranslocational state (Figure 3, top) to the posttranslocational state (Figure 3, bottom), or whether it involves an intermediate state as suggested by Moazed and Noller (1989b). X-ray crystallography has shown that the structure of EF-G (Czworkowski et al., 1994; varsson et al., 1994) is very similar in shape and charge pattern to the GTP form of the ternary complex (Nissen et al., 1995). Like the EF-Tu ternary complex, EF-G binds to the ribosome in a GTP complex form, and the translocation step is also accompanied, or possibly triggered, by GTP hydrolysis. Cryoelectron microscopy has shown that EF-G interacts primarily with ve dierent sites on the ribosome, two of which are on the small subunit, and three on the large subunit (Agrawal et al., 1998). As the binding sites are similar to those found for the ternary complex, EF-G and the ternary complex appear to present a case of molecular mimicry (Nissen et al., 1995): the GTP-binding domain of both molecules interacts with the same site on the 50S subunit, and the EF-G domain which mimics the anticodon arm of the ternary complex interacts with the 30S subunit at the same position where the anticodon arm of the tRNA within the ternary complex interacts with the 30S subunit. Cryoelectron microscopy and other biophysical studies indicate that the ribosome undergoes a conformational change from the pre- to the posttranslocational state. It is likely that this conformational change is powered by the hydrolysis of GTP. After the release of EF-G in its GDP form from the ribosome, a new ternary complex, aminoacyl-tRNAEF-TuGTP, binds to the ribosome in the posttranslocational state (Figure 3, left) that is characterized by two tRNAs being bound to the P and E sites. It is conceivable that during the A-site occupation by the newcoming tRNA, the codonanticodon interaction of the E-site bound tRNA breaks and the deacylated tRNA moves into another, nal exit position (E2 position), where it clings to the L1 protein (Figure 3, left), and is nally ejected. Subsequently, the ribosome enters the next elongation cycle. The elongation cycle is terminated when one of the three termination codons, UAA, UAG or UGA, in the A site results in the binding of a release factor instead
6

of aminoacyl-tRNA. In bacteria three release factors (RFs) have been identied, RF1, recognizing UAA or UAG, RF2 recognizing UAA or UGA, and RF3, which is a GTP protein and assists the binding interaction of RF1 and RF2 with the ribosome.

Polysomes and Secretion

Polysomes
In a bacterial cell, mRNA is physically accessible to the ribosomes while it is being synthesized by the RNA polymerase. Thus ribosomes bind to the 5 end of the mRNA and start translation even before the completed mRNA is released from the RNA polymerase. When several ribosomes are associated with a polycistronic mRNA in the cytoplasm, they are referred to as polyribosomes, or polysomes. Formation of polysomes helps in speeding up the rate of the protein synthesis. The number of ribosomes in a polysome depends on the length of the mRNA-coding sequence and on the relative rates of initiation, elongation and termination steps of protein synthesis. For example, if the rate of initiation is slower, as compared to the rates of elongation and termination, distances between two consecutive ribosomes will be increased, resulting in polysomes with a small number of ribosomes; on the other hand, a relatively higher rate of initiation results in a denser distribution of ribosome on the mRNA, resulting in polysomes with a high number of ribosomes.

Exit tunnel and secretion of polypeptides

As described before, polypeptide synthesis takes place on the 50S subunit of the ribosome. The growing peptide chain is attached to the CCA end of the P-site tRNA, which is found (Malhotra et al ., 1998) in the immediate vicinity to an opening of a tunnel starting at the bottom of the interface canyon and exiting at the bottom of the 50S subunit. Based on its proximity to the CCA end of the Psite tRNA and early immunoelectron microscopic localization of the exiting polypeptide (Bernabeu and Lake, 1982), this tunnel has been proposed to be involved in the release of polypeptide chain from the ribosome into the cytoplasm (Yonath et al., 1987; Frank et al., 1995). Some of the polypeptides are specically retained in the cytosol and folded by molecular chaperones, e.g. DnaK, DnaJ, GrpE, GroEL, GroES, etc., whereas others (approximately 20%) are inserted into membranes or secreted by specic mechanisms. Frequently, secretory proteins have a signal sequence at the N-terminal of the polypeptide, known as signal peptide. The signal peptides have a long hydrophobic region that is usually preceded by one or more positively charged residues and their primary

ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net

Bacterial Ribosomes

function is to help direct polypeptides to the periplasmic/ cytoplasmic membrane. All bacterial signal peptides have essentially similar structural features. All bacteria have a general secretory pathway involving cytosolic and plasma membrane proteins, e.g. Sec proteins. Several Sec proteins are known to be components of the general secretory pathway in E. coli. For example, SecA, SecD, SecE, SecF and SecY are present in the plasma membrane while SecB is present in the cytoplasm and probably binds to the presecretory protein complexes.

References
varsson A, Brazhnikov E, Garber M et al . (1994) Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus. EMBO Journal 13: 36693677. Agrawal RK, Penczek P, Grassucci RA, Li Y, Leith A, Nierhaus KH and Frank J (1996) Direct visualization of A-, P-, and E-site transfer RNAs in the Escherichia coli ribosome. Science 271: 10001002. Agrawal RK, Penczek P, Grassucci RA and Frank J (1998) Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation. Proceedings of the National Academy of Sciences of the USA 95: 61346138. Bernabeu C and Lake JA (1982) Nascent polypeptide chains emerge from the exit domain of the large ribosomal subunit: Immune mapping of the nascent chain. Proceedings of the National Academy of Sciences of the USA 79: 31113115. Capel MS, Engleman DM, Freeborn BR et al. (1987) A complete mapping of the proteins in the small ribosomal subunit of Escherichia coli. Science 238: 14031406. Czworkowski J, Wang J, Steitz TA and Moore PB (1994) The crystal . structure of elongation factor G complexed with GDP, at 2.7A EMBO Journal 13: 36613668. Dahlberg AE (1989) The functional role of ribosomal RNA in protein synthesis. Cell 57: 525529. Frank J and Agrawal RK (1998) The movement of tRNA through the ribosome. Biophysical Journal 74: 589594. Frank J, Zhu J, Penczek P, Li Y, Srivastava S et al. (1995) A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome. Nature 376: 441444. Green R and Noller HF (1997) Ribosomes and translation. Annual Review of Biochemistry 66: 679716. Lata KR, Agrawal RK, Penczek P, Grassucci RA, Zhu J and Frank J (1996) Three-dimensional reconstruction of the Escherichia coli 30S ribosomal subunit in ice. Journal of Molecular Biology 262: 4352. Malhotra A, Penczek P, Agrawal RK et al. (1998) E. coli 70S ribosome at resolution by cryo-electron microscopy: Localization of fMET15 A and tting of L1 protein. Journal of Molecular Biology 280: tRNAMet f 103116. May RP, Nowotny V, Nowotny P, Voss H and Nierhaus KH (1992) Inter-protein distances within the large subunit from Escherichia coli ribosomes. EMBO Journal 11: 373378.

Moazed D and Noller HF (1989a) Interaction of tRNA with 23S RNA in ribosomal A, P and E sites. Cell 57: 585597. Moazed D and Noller HF (1989b) Intermediate states in the movement of transfer RNA in the ribosome. Nature 342: 142148. Mueller F, Stark H, Van Heel M, Rinke-Appel J and Brimacombe R (1997) A new model for the three-dimensional folding of Escherichia coli 16S ribosomal RNA. III. The topography of the functional center. Journal of Molecular Biology 271: 566587. Nierhaus KH (1990) The allosteric three-site model for the ribosomal elongation cycle: Feature and future. Biochemistry 29: 49975012. Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark BFC and Nyborg J (1995) Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science 270: 14641472. Stark H, Mu ller F, Orlova EV et al. (1995) The 70S ribosome at 23 A resolution: tting the ribosomal RNA. Structure 3: 815821. Stark H, Orlova EV, Rinke-Appel J et al. (1997a) Arrangement of tRNAs in pre- and posttranslocational ribosomes revealed by electron cryomicroscopy. Cell 88 : 1928. Stark H, Rodnina M, Rinke-Appel J, Brimacombe R, Wintermeyer W and van Heel M (1997b) Visualization of elongation factor Tu on the Escherichia coli ribosome. Nature 389: 403406. Sto er-Meilicke M and Sto er G (1990) Topography of the ribosomal proteins from Escherichia coli within the intact subunits as determined by immunoelectron microscopy and proteinprotein cross-linking. In: Hill WE, Dahlberg A, Garrett RA, Moore PB, Schlessinger D and Warner JR (eds) The Ribosome, Structure, Function, Evolution, pp. 123133. Washington DC: ASM Press. Yonath A, Leonard KR and Wittmann HG (1987) A tunnel in the large ribosomal subunit revealed by three-dimensional image reconstruction. Science 236 : 813816.

Further Reading
Hill WE, Moore P, Dahlberg A, Schlessinger R, Garrett R and Warner J (1990) The Ribosome: Structure, Function, and Evolution. Washington, DC: American Society for Microbiology. Liljas A and Al-Karadaghi S (1997) Structural aspects of protein synthesis. Nature Structural Biology 4: 767771. Matheson A, Dennis P, Davies J and Hill W (1995) Frontiers in Translation. Ottawa: National Research Council Canada. Moore PB (1998) The three-dimensional structure of the ribosome and its components. Annual Review of Biophysical Chemistry 27: 3558. Nierhaus KH (1993) Solution of the ribosome riddle: how the ribosome selects the correct aminoacyl-tRNA out of 41 similar contestants. Molecular Microbiology 9: 661669. Ramakrishnan V and White SW (1998) Ribosomal protein structures: insights into the architecture, machinery and evolution of the ribosome. Trends in Biochemical Sciences 23: 208212. Wilson KS and Noller HF (1998) Molecular movement inside the translation engine. Cell 92: 337349.

ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net