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PDBsum entry 1dd5
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Ribosome PDB id
1dd5

 

 

 

 

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Contents
Protein chain
184 a.a. *
Ligands
ACY ×2
Waters ×65
* Residue conservation analysis
PDB id:
1dd5
Name: Ribosome
Title: Crystal structure of thermotoga maritima ribosome recycling factor, rrf
Structure: Ribosome recycling factor. Chain: a. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.55Å     R-factor:   0.230     R-free:   0.277
Authors: M.Selmer,S.Al-Karadaghi,G.Hirokawa,A.Kaji,A.Liljas
Key ref:
M.Selmer et al. (1999). Crystal structure of Thermotoga maritima ribosome recycling factor: a tRNA mimic. Science, 286, 2349-2352. PubMed id: 10600747 DOI: 10.1126/science.286.5448.2349
Date:
08-Nov-99     Release date:   22-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9X1B9  (RRF_THEMA) -  Ribosome-recycling factor from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
Seq:
Struc: 		185 a.a.
184 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1126/science.286.5448.2349 Science 286:2349-2352 (1999)
PubMed id: 10600747  
 
 
Crystal structure of Thermotoga maritima ribosome recycling factor: a tRNA mimic.
M.Selmer, S.Al-Karadaghi, G.Hirokawa, A.Kaji, A.Liljas.
 
  ABSTRACT  
 
Ribosome recycling factor (RRF), together with elongation factor G (EF-G), catalyzes recycling of ribosomes after one round of protein synthesis. The crystal structure of RRF was determined at 2.55 angstrom resolution. The protein has an unusual fold where domain I is a long three-helix bundle and domain II is a three-layer beta/alpha/beta sandwich. The molecule superimposes almost perfectly with a transfer RNA (tRNA) except that the amino acid-binding 3' end is missing. The mimicry suggests that RRF interacts with the posttermination ribosomal complex in a similar manner to a tRNA, leading to disassembly of the complex. The structural arrangement of this mimicry is entirely different from that of other cases of less pronounced mimicry of tRNA so far described.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. (A) A portion of the 2.9 Å MAD map after DM contoured at 1.0 with O (34) superimposed on residue 4-24 (H1, left) and 157-176 (H6, right) of the final refined model. (B) Molmol (34) ribbon representation of RRF. The chain starts from domain I (green), then goes through domain II (red) and back to domain I (blue). The conserved and conservatively substituted amino acids are marked with orange (all known sequences) and yellow (for bacteria and chloroplast). 		Figure 3.
Fig. 3. (A) Stereo ribbon representation of the superposition of RRF (blue) and yeast tRNA^Phe (red) with Molmol (34). (B) Comparison of EF-G (36) and the ternary complex of EF-Tu + GDPNP + aatRNA (32). EF-G (left) is similar in shape to EF-Tu + GDPNP + aatRNA (right). Domain III-IV of EF-G (purple) imitates the shape of the tRNA (red) bound to EF-Tu (yellow). The remaining domains of EF-G (green) are structurally similar to EF-Tu. RRF (A) imitates the tRNA in a totally different manner. (C) Grasp (34) surface representation of the superposition of RRF (blue) and yeast tRNA^Phe (red). The shapes and sizes of the surfaces are nearly identical except for the acceptor end of tRNA (to the right), which has no corresponding part in RRF.
 
  The above figures are reprinted by permission from the AAAs: Science (1999, 286, 2349-2352) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20007320 S.Arragain, R.Garcia-Serres, G.Blondin, T.Douki, M.Clemancey, J.M.Latour, F.Forouhar, H.Neely, G.T.Montelione, J.F.Hunt, E.Mulliez, M.Fontecave, and M.Atta (2010).
Post-translational modification of ribosomal proteins: structural and functional characterization of RimO from Thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase.
  J Biol Chem, 285, 5792-5801.
PDB code: 2qgq
19736993 K.H.Lee, L.Saleh, B.P.Anton, C.L.Madinger, J.S.Benner, D.F.Iwig, R.J.Roberts, C.Krebs, and S.J.Booker (2009).
Characterization of RimO, a new member of the methylthiotransferase subclass of the radical SAM superfamily.
  Biochemistry, 48, 10162-10174.  
18252828 B.P.Anton, L.Saleh, J.S.Benner, E.A.Raleigh, S.Kasif, and R.J.Roberts (2008).
RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli.
  Proc Natl Acad Sci U S A, 105, 1826-1831.  
18234219 R.D.Pai, W.Zhang, B.S.Schuwirth, G.Hirokawa, H.Kaji, A.Kaji, and J.H.Cate (2008).
Structural Insights into ribosome recycling factor interactions with the 70S ribosome.
  J Mol Biol, 376, 1334-1347.  
18206363 S.Petry, A.Weixlbaumer, and V.Ramakrishnan (2008).
The termination of translation.
  Curr Opin Struct Biol, 18, 70-77.  
17660830 A.Weixlbaumer, S.Petry, C.M.Dunham, M.Selmer, A.C.Kelley, and V.Ramakrishnan (2007).
Crystal structure of the ribosome recycling factor bound to the ribosome.
  Nat Struct Mol Biol, 14, 733-737.
PDB codes: 2v46 2v47 2v48 2v49
17643374 C.Barat, P.P.Datta, V.S.Raj, M.R.Sharma, H.Kaji, A.Kaji, and R.K.Agrawal (2007).
Progression of the ribosome recycling factor through the ribosome dissociates the two ribosomal subunits.
  Mol Cell, 27, 250-261.  
17540027 E.V.Koonin (2007).
The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life.
  Biol Direct, 2, 15.  
16855312 A.Liljas (2006).
On the complementarity of methods in structural biology.
  Acta Crystallogr D Biol Crystallogr, 62, 941-945.  
16809861 A.Seshadri, and U.Varshney (2006).
Mechanism of recycling of post-termination ribosomal complexes in eubacteria: a new role of initiation factor 3.
  J Biosci, 31, 281-289.  
16487710 G.Hirokawa, N.Demeshkina, N.Iwakura, H.Kaji, and A.Kaji (2006).
The ribosome-recycling step: consensus or controversy?
  Trends Biochem Sci, 31, 143-149.  
17064285 S.B.Conners, E.F.Mongodin, M.R.Johnson, C.I.Montero, K.E.Nelson, and R.M.Kelly (2006).
Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.
  FEMS Microbiol Rev, 30, 872-905.  
16859496 T.Hosaka, J.Xu, and K.Ochi (2006).
Increased expression of ribosome recycling factor is responsible for the enhanced protein synthesis during the late growth phase in an antibiotic-overproducing Streptomyces coelicolor ribosomal rpsL mutant.
  Mol Microbiol, 61, 883-897.  
15949442 A.V.Zavialov, V.V.Hauryliuk, and M.Ehrenberg (2005).
Splitting of the posttermination ribosome into subunits by the concerted action of RRF and EF-G.
  Mol Cell, 18, 675-686.  
15616575 D.N.Wilson, F.Schluenzen, J.M.Harms, T.Yoshida, T.Ohkubo, R.Albrecht, J.Buerger, Y.Kobayashi, and P.Fucini (2005).
X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit.
  EMBO J, 24, 251-260.
PDB code: 1y69
16043503 H.Liang, and L.F.Landweber (2005).
Molecular mimicry: quantitative methods to study structural similarity between protein and RNA.
  RNA, 11, 1167-1172.  
15768033 H.Takagi, Y.Kakuta, T.Okada, M.Yao, I.Tanaka, and M.Kimura (2005).
Crystal structure of archaeal toxin-antitoxin RelE-RelB complex with implications for toxin activity and antitoxin effects.
  Nat Struct Mol Biol, 12, 327-331.
PDB code: 1wmi
15949441 N.Gao, A.V.Zavialov, W.Li, J.Sengupta, M.Valle, R.P.Gursky, M.Ehrenberg, and J.Frank (2005).
Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
  Mol Cell, 18, 663-674.
PDB codes: 1zn0 1zn1
16199751 N.S.Singh, G.Das, A.Seshadri, R.Sangeetha, and U.Varshney (2005).
Evidence for a role of initiation factor 3 in recycling of ribosomal complexes stalled on mRNAs in Escherichia coli.
  Nucleic Acids Res, 33, 5591-5601.  
16055531 S.M.Stagg, and S.C.Harvey (2005).
Exploring the flexibility of ribosome recycling factor using molecular dynamics.
  Biophys J, 89, 2659-2666.  
15612924 T.Yamami, K.Ito, T.Fujiwara, and Y.Nakamura (2005).
Heterologous expression of Aquifex aeolicus ribosome recycling factor in Escherichia coli is dominant lethal by forming a complex that lacks functional co-ordination for ribosome disassembly.
  Mol Microbiol, 55, 150-161.  
15937186 V.Oganesyan, N.Oganesyan, P.D.Adams, J.Jancarik, H.A.Yokota, R.Kim, and S.H.Kim (2005).
Crystal structure of the "PhoU-like" phosphate uptake regulator from Aquifex aeolicus.
  J Bacteriol, 187, 4238-4244.
PDB codes: 1t72 1t8b
15661844 V.S.Raj, H.Kaji, and A.Kaji (2005).
Interaction of RRF and EF-G from E. coli and T. thermophilus with ribosomes from both origins--insight into the mechanism of the ribosome recycling step.
  RNA, 11, 275-284.  
15522083 G.Hirokawa, H.Inokuchi, H.Kaji, K.Igarashi, and A.Kaji (2004).
In vivo effect of inactivation of ribosome recycling factor - fate of ribosomes after unscheduled translation downstream of open reading frame.
  Mol Microbiol, 54, 1011-1021.  
15210970 K.Hanawa-Suetsugu, S.Sekine, H.Sakai, C.Hori-Takemoto, T.Terada, S.Unzai, J.R.Tame, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2004).
Crystal structure of elongation factor P from Thermus thermophilus HB8.
  Proc Natl Acad Sci U S A, 101, 9595-9600.
PDB code: 1ueb
14747728 K.Saikrishnan, S.K.Kalapala, M.Bidya Sagar, A.R.Rao, U.Varshney, and M.Vijayan (2004).
Purification, crystallization and preliminary X-ray studies of Mycobacterium tuberculosis RRF.
  Acta Crystallogr D Biol Crystallogr, 60, 368-370.  
15189156 L.D.Kapp, and J.R.Lorsch (2004).
The molecular mechanics of eukaryotic translation.
  Annu Rev Biochem, 73, 657-704.  
15178758 R.K.Agrawal, M.R.Sharma, M.C.Kiel, G.Hirokawa, T.M.Booth, C.M.Spahn, R.A.Grassucci, A.Kaji, and J.Frank (2004).
Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: functional implications.
  Proc Natl Acad Sci U S A, 101, 8900-8905.
PDB codes: 1t1m 1t1o
15228531 T.Fujiwara, K.Ito, T.Yamami, and Y.Nakamura (2004).
Ribosome recycling factor disassembles the post-termination ribosomal complex independent of the ribosomal translocase activity of elongation factor G.
  Mol Microbiol, 53, 517-528.  
12555080 D.E.Brodersen, and V.Ramakrishnan (2003).
Shape can be seductive.
  Nat Struct Biol, 10, 78-80.  
12853640 E.Teyssier, G.Hirokawa, A.Tretiakova, B.Jameson, A.Kaji, and H.Kaji (2003).
Temperature-sensitive mutation in yeast mitochondrial ribosome recycling factor (RRF).
  Nucleic Acids Res, 31, 4218-4226.  
12869707 S.Marzi, W.Knight, L.Brandi, E.Caserta, N.Soboleva, W.E.Hill, C.O.Gualerzi, and J.S.Lodmell (2003).
Ribosomal localization of translation initiation factor IF2.
  RNA, 9, 958-969.  
12575998 Y.Nakamura, and K.Ito (2003).
Making sense of mimic in translation termination.
  Trends Biochem Sci, 28, 99.  
12093730 G.Buchwald, A.Friebel, J.E.Galán, W.D.Hardt, A.Wittinghofer, and K.Scheffzek (2002).
Structural basis for the reversible activation of a Rho protein by the bacterial toxin SopE.
  EMBO J, 21, 3286-3295.
PDB code: 1gzs
11980724 G.Hirokawa, M.C.Kiel, A.Muto, M.Selmer, V.S.Raj, A.Liljas, K.Igarashi, H.Kaji, and A.Kaji (2002).
Post-termination complex disassembly by ribosome recycling factor, a functional tRNA mimic.
  EMBO J, 21, 2272-2281.  
12086623 K.Ito, T.Fujiwara, T.Toyoda, and Y.Nakamura (2002).
Elongation factor G participates in ribosome disassembly by interacting with ribosome recycling factor at their tRNA-mimicry domains.
  Mol Cell, 9, 1263-1272.  
12356746 L.Chavatte, A.Seit-Nebi, V.Dubovaya, and A.Favre (2002).
The invariant uridine of stop codons contacts the conserved NIKSR loop of human eRF1 in the ribosome.
  EMBO J, 21, 5302-5311.  
12372306 L.Lancaster, M.C.Kiel, A.Kaji, and H.F.Noller (2002).
Orientation of ribosome recycling factor in the ribosome from directed hydroxyl radical probing.
  Cell, 111, 129-140.  
11813010 M.Ehrenberg, and T.Tenson (2002).
A new beginning of the end of translation.
  Nat Struct Biol, 9, 85-87.  
11866090 S.Ejiri (2002).
Moonlighting functions of polypeptide elongation factor 1: from actin bundling to zinc finger protein R1-associated nuclear localization.
  Biosci Biotechnol Biochem, 66, 1.  
12351820 T.R.Schneider, and G.M.Sheldrick (2002).
Substructure solution with SHELXD.
  Acta Crystallogr D Biol Crystallogr, 58, 1772-1779.  
11909526 V.Ramakrishnan (2002).
Ribosome structure and the mechanism of translation.
  Cell, 108, 557-572.  
12762054 A.Kaji, M.C.Kiel, G.Hirokawa, A.R.Muto, Y.Inokuchi, and H.Kaji (2001).
The fourth step of protein synthesis: disassembly of the posttermination complex is catalyzed by elongation factor G and ribosome recycling factor, a near-perfect mimic of tRNA.
  Cold Spring Harb Symp Quant Biol, 66, 515-529.  
11387230 A.R.Rao, and U.Varshney (2001).
Specific interaction between the ribosome recycling factor and the elongation factor G from Mycobacterium tuberculosis mediates peptidyl-tRNA release and ribosome recycling in Escherichia coli.
  EMBO J, 20, 2977-2986.  
11779511 B.Vestergaard, L.B.Van, G.R.Andersen, J.Nyborg, R.H.Buckingham, and M.Kjeldgaard (2001).
Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1.
  Mol Cell, 8, 1375-1382.
PDB code: 1gqe
12762045 G.R.Andersen, and J.Nyborg (2001).
Structural studies of eukaryotic elongation factors.
  Cold Spring Harb Symp Quant Biol, 66, 425-437.  
11494321 J.Frank (2001).
Cryo-electron microscopy as an investigative tool: the ribosome as an example.
  Bioessays, 23, 725-732.  
11230150 O.N.Voloshin, B.E.Ramirez, A.Bax, and R.D.Camerini-Otero (2001).
A model for the abrogation of the SOS response by an SOS protein: a negatively charged helix in DinI mimics DNA in its interaction with RecA.
  Genes Dev, 15, 415-427.  
11489855 S.Karlin, J.Mrázek, A.Campbell, and D.Kaiser (2001).
Characterizations of highly expressed genes of four fast-growing bacteria.
  J Bacteriol, 183, 5025-5040.  
11214182 T.Fujiwara, K.Ito, and Y.Nakamura (2001).
Functional mapping of ribosome-contact sites in the ribosome recycling factor: a structural view from a tRNA mimic.
  RNA, 7, 64-70.  
11327859 T.Yoshida, S.Uchiyama, H.Nakano, H.Kashimori, H.Kijima, T.Ohshima, Y.Saihara, T.Ishino, H.Shimahara, T.Yoshida, K.Yokose, T.Ohkubo, A.Kaji, and Y.Kobayashi (2001).
Solution structure of the ribosome recycling factor from Aquifex aeolicus.
  Biochemistry, 40, 2387-2396.
PDB code: 1ge9
12762049 Y.Nakamura, M.Uno, T.Toyoda, T.Fujiwara, and K.Ito (2001).
Protein tRNA mimicry in translation termination.
  Cold Spring Harb Symp Quant Biol, 66, 469-475.  
  11152126 B.E.Ramirez, O.N.Voloshin, R.D.Camerini-Otero, and A.Bax (2000).
Solution structure of DinI provides insight into its mode of RecA inactivation.
  Protein Sci, 9, 2161-2169.
PDB codes: 1f0a 1ghh
10999601 G.Bertram, H.A.Bell, D.W.Ritchie, G.Fullerton, and I.Stansfield (2000).
Terminating eukaryote translation: domain 1 of release factor eRF1 functions in stop codon recognition.
  RNA, 6, 1236-1247.  
11073222 J.Carnes, L.Frolova, S.Zinnen, G.Drugeon, M.Phillippe, J.Justesen, A.L.Haenni, L.Leinwand, L.L.Kisselev, and M.Yarus (2000).
Suppression of eukaryotic translation termination by selected RNAs.
  RNA, 6, 1468-1479.  
11029437 K.Atarashi, and A.Kaji (2000).
Inhibitory effect of heterologous ribosome recycling factor on growth of Escherichia coli.
  J Bacteriol, 182, 6154-6160.  
11084369 L.L.Kisselev, and R.H.Buckingham (2000).
Translational termination comes of age.
  Trends Biochem Sci, 25, 561-566.  
10937867 M.Sprinzl, S.Brock, Y.Huang, P.Milovnik, M.Nanninga, M.Nesper-Brock, H.Rütthard, and K.Szkaradkiewicz (2000).
Regulation of GTPases in the bacterial translation machinery.
  Biol Chem, 381, 367-375.  
10937868 M.V.Rodnina, H.Stark, A.Savelsbergh, H.J.Wieden, D.Mohr, N.B.Matassova, F.Peske, T.Daviter, C.O.Gualerzi, and W.Wintermeyer (2000).
GTPases mechanisms and functions of translation factors on the ribosome.
  Biol Chem, 381, 377-387.  
10675317 P.Nissen, M.Kjeldgaard, and J.Nyborg (2000).
Macromolecular mimicry.
  EMBO J, 19, 489-495.  
11828416 S.Connell, and K.Nierhaus (2000).
Translational termination not yet at its end.
  Chembiochem, 1, 250-253.  
10982835 S.K.Choi, D.S.Olsen, A.Roll-Mecak, A.Martung, K.L.Remo, S.K.Burley, A.G.Hinnebusch, and T.E.Dever (2000).
Physical and functional interaction between the eukaryotic orthologs of prokaryotic translation initiation factors IF1 and IF2.
  Mol Cell Biol, 20, 7183-7191.  
11168582 T.Ishino, K.Atarashi, S.Uchiyama, T.Yamami, Y.Saihara, T.Yoshida, H.Hara, K.Yokose, Y.Kobayashi, and Y.Nakamura (2000).
Interaction of ribosome recycling factor and elongation factor EF-G with E. coli ribosomes studied by the surface plasmon resonance technique.
  Genes Cells, 5, 953-963.  
11073219 T.Toyoda, O.F.Tin, K.Ito, T.Fujiwara, T.Kumasaka, M.Yamamoto, M.B.Garber, and Y.Nakamura (2000).
Crystal structure combined with genetic analysis of the Thermus thermophilus ribosome recycling factor shows that a flexible hinge may act as a functional switch.
  RNA, 6, 1432-1444.
PDB code: 1eh1
10899132 Y.Inokuchi, A.Hirashima, Y.Sekine, L.Janosi, and A.Kaji (2000).
Role of ribosome recycling factor (RRF) in translational coupling.
  EMBO J, 19, 3788-3798.  
10830162 Y.Nakamura, K.Ito, and M.Ehrenberg (2000).
Mimicry grasps reality in translation termination.
  Cell, 101, 349-352.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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