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PDBsum entry 1b23
Go to PDB code: 
protein dna_rna ligands metals links
Gene regulation/RNA PDB id
1b23

 

 

 

 

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Contents
Protein chain
405 a.a. *
DNA/RNA
Ligands
CYS
SO4 ×2
GNP
Metals
_MG ×3
Waters ×261
* Residue conservation analysis
PDB id:
1b23
Name: Gene regulation/RNA
Title: E. Coli cysteinyl-tRNA and t. Aquaticus elongation factor ef-tu:gtp ternary complex
Structure: Cysteinyl tRNA. Chain: r. Synonym: cys-tRNA. Engineered: yes. Other_details: aminoacyl link between a76 and cys77. Elongation factor tu. Chain: p. Synonym: ef-tu. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Thermus aquaticus. Organism_taxid: 271. Strain: yt-1. Gene: tufa. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.60Å     R-factor:   0.206     R-free:   0.263
Authors: P.Nissen,M.Kjeldgaard,S.Thirup,J.Nyborg
Key ref:
P.Nissen et al. (1999). The crystal structure of Cys-tRNACys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA. Structure, 7, 143-156. PubMed id: 10368282 DOI: 10.1016/S0969-2126(99)80021-5
Date:
04-Dec-98     Release date:   07-Dec-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Q01698  (EFTU_THEAQ) -  Elongation factor Tu from Thermus aquaticus
Seq:
Struc: 		406 a.a.
405 a.a.
Key:    Secondary structure  CATH domain

DNA/RNA chain
  G-G-C-G-C-G-U-4SU-A-A-C-A-A-A-G-C-G-G-H2U-H2U-A-U-G-U-A-G-C-G-G-A-PSU-U-G-C-A- 74 bases

 Enzyme reactions 
   Enzyme class: E.C.3.6.5.3  - protein-synthesizing GTPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: GTP + H2O = GDP + phosphate + H+
GTP
 + H2O
 = GDP
 + phosphate
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(99)80021-5 Structure 7:143-156 (1999)
PubMed id: 10368282  
 
 
The crystal structure of Cys-tRNACys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA.
P.Nissen, S.Thirup, M.Kjeldgaard, J.Nyborg.
 
  ABSTRACT  
 
BACKGROUND:. The translation elongation factor EF-Tu in its GTP-bound state forms a ternary complex with any aminoacylated tRNA (aa-tRNA), except initiator tRNA and selenocysteinyl-tRNA. This complex delivers aa-tRNA to the ribosomal A site during the elongation cycle of translation. The crystal structure of the yeast Phe-tRNAPhe ternary complex with Thermus aquaticus EF-Tu-GDPNP (Phe-TC) has previously been determined as one representative of this general yet highly discriminating complex formation. RESULTS: The ternary complex of Escherichia coli Cys-tRNACys and T. aquaticus EF-Tu-GDPNP (Cys-TC) has been solved and refined at 2.6 degrees resolution. Conserved and variable features of the aa-tRNA recognition and binding by EF-Tu-GTP have been revealed by comparison with the Phe-TC structure. New tertiary interactions are observed in the tRNACys structure. A 'kissing complex' is observed in the very close crystal packing arrangement. CONCLUSIONS: The recognition of Cys-tRNACys by EF-Tu-GDPNP is restricted to the aa-tRNA motif previously identified in Phe-TC and consists of the aminoacylated 3' end, the phosphorylated 5' end and one side of the acceptor stem and T stem. The aminoacyl bond is recognized somewhat differently, yet by the same primary motif in EF-Tu, which suggests that EF-Tu adapts to subtle variations in this moiety among all aa-tRNAs. New tertiary interactions revealed by the Cys-tRNACys structure, such as a protonated C16:C59 pyrimidine pair, a G15:G48 'Levitt pair' and an s4U8:A14:A46 base triple add to the generic understanding of tRNA structure from sequence. The structure of the 'kissing complex' shows a quasicontinuous helix with a distinct shape determined by the number of base pairs.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. Focus on the tertiary interactions in the E. coli Cys-tRNA^Cys molecule by (a) a stereographic representation and (b) a schematic clover leaf diagram. Residue numbers refer to the yeast tRNA^Phe standard, thus residues 17 and 47 are missing (see Figure 1b ). The acceptor stem has been omitted from (a) for clarity and the schematic diagram in (b) includes only the base–base interactions. Further, the variable loop in (b) has been wrapped into the clover leaf center to indicate the unique role of A46 in the tertiary interactions. Colour codes are as in Figure 2 . Part (b) was produced using ‘The Gimp’ (http://www.gimp.org).
 
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 143-156) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22245970 D.Takeshita, and K.Tomita (2012).
Molecular basis for RNA polymerization by Qβ replicase.
  Nat Struct Mol Biol, 19, 229-237.
PDB codes: 3avt 3avu 3avv 3avw 3avx 3avy
21151095 M.Y.Pavlov, A.Zorzet, D.I.Andersson, and M.Ehrenberg (2011).
Activation of initiation factor 2 by ligands and mutations for rapid docking of ribosomal subunits.
  EMBO J, 30, 289-301.  
19940162 A.Paleskava, A.L.Konevega, and M.V.Rodnina (2010).
Thermodynamic and kinetic framework of selenocysteyl-tRNASec recognition by elongation factor SelB.
  J Biol Chem, 285, 3014-3020.  
20832312 K.W.Lin, I.Yakymovych, M.Jia, M.Yakymovych, and S.Souchelnytskyi (2010).
Phosphorylation of eEF1A1 at Ser300 by TβR-I results in inhibition of mRNA translation.
  Curr Biol, 20, 1615-1625.  
20686685 M.Siwiak, and P.Zielenkiewicz (2010).
A comprehensive, quantitative, and genome-wide model of translation.
  PLoS Comput Biol, 6, e1000865.  
21119764 R.Giegé, and C.Sauter (2010).
Biocrystallography: past, present, future.
  HFSP J, 4, 109-121.  
19925799 S.E.Kolitz, and J.R.Lorsch (2010).
Eukaryotic initiator tRNA: finely tuned and ready for action.
  FEBS Lett, 584, 396-404.  
  19856359 J.Guo, C.E.Melançon, H.S.Lee, D.Groff, and P.G.Schultz (2009).
Evolution of amber suppressor tRNAs for efficient bacterial production of proteins containing nonnatural amino acids.
  Angew Chem Int Ed Engl, 48, 9148-9151.  
19452597 J.M.Schrader, S.J.Chapman, and O.C.Uhlenbeck (2009).
Understanding the sequence specificity of tRNA binding to elongation factor Tu using tRNA mutagenesis.
  J Mol Biol, 386, 1255-1264.  
20025795 X.Agirrezabala, and J.Frank (2009).
Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu.
  Q Rev Biophys, 42, 159-200.  
18221514 D.S.Kanibolotsky, O.V.Novosyl'na, C.M.Abbott, B.S.Negrutskii, and A.V.El'skaya (2008).
Multiple molecular dynamics simulation of the isoforms of human translation elongation factor 1A reveals reversible fluctuations between "open" and "closed" conformations and suggests specific for eEF1A1 affinity for Ca2+-calmodulin.
  BMC Struct Biol, 8, 4.  
18466919 M.Dupasquier, S.Kim, K.Halkidis, H.Gamper, and Y.M.Hou (2008).
tRNA integrity is a prerequisite for rapid CCA addition: implication for quality control.
  J Mol Biol, 379, 579-588.  
17897886 A.Fluitt, E.Pienaar, and H.Viljoen (2007).
Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis.
  Comput Biol Chem, 31, 335-346.  
17478519 H.Roy, H.D.Becker, M.H.Mazauric, and D.Kern (2007).
Structural elements defining elongation factor Tu mediated suppression of codon ambiguity.
  Nucleic Acids Res, 35, 3420-3430.  
17925388 K.B.Gromadski, T.Schümmer, A.Strømgaard, C.R.Knudsen, T.G.Kinzy, and M.V.Rodnina (2007).
Kinetics of the interactions between yeast elongation factors 1A and 1Balpha, guanine nucleotides, and aminoacyl-tRNA.
  J Biol Chem, 282, 35629-35637.  
17449728 L.E.Sanderson, and O.C.Uhlenbeck (2007).
The 51-63 base pair of tRNA confers specificity for binding by EF-Tu.
  RNA, 13, 835-840.  
17328911 L.E.Sanderson, and O.C.Uhlenbeck (2007).
Directed mutagenesis identifies amino acid residues involved in elongation factor Tu binding to yeast Phe-tRNAPhe.
  J Mol Biol, 368, 119-130.  
17351629 R.Fukunaga, and S.Yokoyama (2007).
Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea.
  Nat Struct Mol Biol, 14, 272-279.
PDB codes: 2du3 2du4 2du5 2du6 2du7
16556606 B.Wang, J.Zhou, M.Lodder, R.D.Anderson, and S.M.Hecht (2006).
Tandemly activated tRNAs as participants in protein synthesis.
  J Biol Chem, 281, 13865-13868.  
16415880 H.C.Losey, A.J.Ruthenburg, and G.L.Verdine (2006).
Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA.
  Nat Struct Mol Biol, 13, 153-159.
PDB code: 2b3j
16681365 J.S.Weinger, and S.A.Strobel (2006).
Participation of the tRNA A76 hydroxyl groups throughout translation.
  Biochemistry, 45, 5939-5948.  
17110926 K.Suto, Y.Shimizu, K.Watanabe, T.Ueda, S.Fukai, O.Nureki, and K.Tomita (2006).
Crystal structures of leucyl/phenylalanyl-tRNA-protein transferase and its complex with an aminoacyl-tRNA analog.
  EMBO J, 25, 5942-5950.
PDB codes: 2dps 2dpt
16717093 L.D.Dahl, H.J.Wieden, M.V.Rodnina, and C.R.Knudsen (2006).
The importance of P-loop and domain movements in EF-Tu for guanine nucleotide exchange.
  J Biol Chem, 281, 21139-21146.  
16407071 L.Yatime, Y.Mechulam, S.Blanquet, and E.Schmitt (2006).
Structural switch of the gamma subunit in an archaeal aIF2 alpha gamma heterodimer.
  Structure, 14, 119-128.
PDB code: 2aho
17012285 M.Arita, T.Suematsu, A.Osanai, T.Inaba, H.Kamiya, K.Kita, M.Sisido, Y.Watanabe, and T.Ohtsuki (2006).
An evolutionary 'intermediate state' of mitochondrial translation systems found in Trichinella species of parasitic nematodes: co-evolution of tRNA and EF-Tu.
  Nucleic Acids Res, 34, 5291-5299.  
16601123 Y.Shimizu, and T.Ueda (2006).
SmpB triggers GTP hydrolysis of elongation factor Tu on ribosomes by compensating for the lack of codon-anticodon interaction during trans-translation initiation.
  J Biol Chem, 281, 15987-15996.  
15817565 E.Kikovska, M.Brännvall, J.Kufel, and L.A.Kirsebom (2005).
Substrate discrimination in RNase P RNA-mediated cleavage: importance of the structural environment of the RNase P cleavage site.
  Nucleic Acids Res, 33, 2012-2021.  
16377777 J.Cabello-Villegas, and E.P.Nikonowicz (2005).
Solution structure of psi32-modified anticodon stem-loop of Escherichia coli tRNAPhe.
  Nucleic Acids Res, 33, 6961-6971.
PDB code: 2awq
16098189 T.Rathinavelan, and N.Yathindra (2005).
Molecular dynamics structures of peptide nucleic acid x DNA hybrid in the wild-type and mutated alleles of Ki-ras proto-oncogene--stereochemical rationale for the low affinity of PNA in the presence of an AC mismatch.
  FEBS J, 272, 4055-4070.  
16113240 T.Suematsu, A.Sato, M.Sakurai, K.Watanabe, and T.Ohtsuki (2005).
A unique tRNA recognition mechanism of Caenorhabditis elegans mitochondrial EF-Tu2.
  Nucleic Acids Res, 33, 4683-4691.  
14872064 A.Théobald-Dietrich, M.Frugier, R.Giegé, and J.Rudinger-Thirion (2004).
Atypical archaeal tRNA pyrrolysine transcript behaves towards EF-Tu as a typical elongator tRNA.
  Nucleic Acids Res, 32, 1091-1096.  
14767080 L.S.Harlow, A.Kadziola, K.F.Jensen, and S.Larsen (2004).
Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding.
  Protein Sci, 13, 668-677.
PDB codes: 1oyp 1oyr 1oys
15385567 M.Steiner-Mosonyi, C.Creuzenet, R.A.Keates, B.R.Strub, and D.Mangroo (2004).
The Pseudomonas aeruginosa initiation factor IF-2 is responsible for formylation-independent protein initiation in P. aeruginosa.
  J Biol Chem, 279, 52262-52269.  
15016354 P.Auffinger, L.Bielecki, and E.Westhof (2004).
Anion binding to nucleic acids.
  Structure, 12, 379-388.  
15489861 S.Hauenstein, C.M.Zhang, Y.M.Hou, and J.J.Perona (2004).
Shape-selective RNA recognition by cysteinyl-tRNA synthetase.
  Nat Struct Mol Biol, 11, 1134-1141.
PDB code: 1u0b
15653432 T.Brodegger, A.Stockmann, J.Oberstrass, W.Nellen, and H.Follmann (2004).
Novel thioredoxin targets in Dictyostelium discoideum identified by two-hybrid analysis: interactions of thioredoxin with elongation factor 1alpha and yeast alcohol dehydrogenase.
  Biol Chem, 385, 1185-1192.  
12810913 C.Evilia, X.Ming, S.Dassarma, and Y.M.Hou (2003).
Aminoacylation of an unusual tRNA(Cys) from an extreme halophile.
  RNA, 9, 794-801.  
12932732 G.R.Andersen, P.Nissen, and J.Nyborg (2003).
Elongation factors in protein biosynthesis.
  Trends Biochem Sci, 28, 434-441.  
12824344 H.Yang, F.Jossinet, N.Leontis, L.Chen, J.Westbrook, H.Berman, and E.Westhof (2003).
Tools for the automatic identification and classification of RNA base pairs.
  Nucleic Acids Res, 31, 3450-3460.  
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.  
14622005 T.Navratil, and L.L.Spremulli (2003).
Effects of mutagenesis of Gln97 in the switch II region of Escherichia coli elongation factor Tu on its interaction with guanine nucleotides, elongation factor Ts, and aminoacyl-tRNA.
  Biochemistry, 42, 13587-13595.  
14654688 Y.Pan, and A.D.MacKerell (2003).
Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening.
  Nucleic Acids Res, 31, 7131-7140.  
11891293 H.Asahara, and O.C.Uhlenbeck (2002).
The tRNA specificity of Thermus thermophilus EF-Tu.
  Proc Natl Acad Sci U S A, 99, 3499-3504.  
12145639 T.Ohtsuki, A.Sato, Y.Watanabe, and K.Watanabe (2002).
A unique serine-specific elongation factor Tu found in nematode mitochondria.
  Nat Struct Biol, 9, 669-673.  
12762022 C.Mayer, A.Stortchevoi, C.Köhrer, U.Varshney, and U.L.RajBhandary (2001).
Initiator tRNA and its role in initiation of protein synthesis.
  Cold Spring Harb Symp Quant Biol, 66, 195-206.  
11588263 F.J.LaRiviere, A.D.Wolfson, and O.C.Uhlenbeck (2001).
Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation.
  Science, 294, 165-168.  
12762045 G.R.Andersen, and J.Nyborg (2001).
Structural studies of eukaryotic elongation factors.
  Cold Spring Harb Symp Quant Biol, 66, 425-437.  
11574461 L.Vitagliano, M.Masullo, F.Sica, A.Zagari, and V.Bocchini (2001).
The crystal structure of Sulfolobus solfataricus elongation factor 1alpha in complex with GDP reveals novel features in nucleotide binding and exchange.
  EMBO J, 20, 5305-5311.
PDB code: 1jny
11588242 M.Ibba (2001).
Protein synthesis. Discriminating right from wrong.
  Science, 294, 70-71.  
10851193 A.D.Frankel (2000).
Fitting peptides into the RNA world.
  Curr Opin Struct Biol, 10, 332-340.  
10970870 D.Fagegaltier, N.Hubert, K.Yamada, T.Mizutani, P.Carbon, and A.Krol (2000).
Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation.
  EMBO J, 19, 4796-4805.  
10998062 G.Raimo, M.Masullo, B.Lombardo, and V.Bocchini (2000).
The archaeal elongation factor 1alpha bound to GTP forms a ternary complex with eubacterial and eukaryal aminoacyl-tRNA.
  Eur J Biochem, 267, 6012-6018.  
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.  
10644698 R.Spurio, L.Brandi, E.Caserta, C.L.Pon, C.O.Gualerzi, R.Misselwitz, C.Krafft, K.Welfle, and H.Welfle (2000).
The C-terminal subdomain (IF2 C-2) contains the entire fMet-tRNA binding site of initiation factor IF2.
  J Biol Chem, 275, 2447-2454.  
10679458 S.Blanquet, Y.Mechulam, and E.Schmitt (2000).
The many routes of bacterial transfer RNAs after aminoacylation.
  Curr Opin Struct Biol, 10, 95.  
10775275 S.Meunier, R.Spurio, M.Czisch, R.Wechselberger, M.Guenneugues, C.O.Gualerzi, and R.Boelens (2000).
Structure of the fMet-tRNA(fMet)-binding domain of B. stearothermophilus initiation factor IF2.
  EMBO J, 19, 1918-1926.
PDB code: 1d1n
11105758 T.A.Nissan, and J.J.Perona (2000).
Alternative designs for construction of the class II transfer RNA tertiary core.
  RNA, 6, 1585-1596.  
10737860 P.J.Beuning, and K.Musier-Forsyth (1999).
Transfer RNA recognition by aminoacyl-tRNA synthetases.
  Biopolymers, 52, 1.  
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 codes are shown on the right.

 

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