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PDBsum entry 1q7y
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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
1q7y

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
237 a.a. *
337 a.a. *
246 a.a. *
140 a.a. *
172 a.a. *
119 a.a. *
29 a.a. *
156 a.a. *
142 a.a. *
132 a.a. *
145 a.a. *
194 a.a. *
186 a.a. *
115 a.a. *
143 a.a. *
95 a.a. *
150 a.a. *
81 a.a. *
119 a.a. *
53 a.a. *
65 a.a. *
154 a.a. *
82 a.a. *
142 a.a. *
73 a.a. *
56 a.a. *
46 a.a. *
92 a.a. *
DNA/RNA
Ligands
PO4-PUY
Metals
_CL ×22
_NA ×86
_MG ×117
_CD ×5
__K ×2
Waters ×7871
* Residue conservation analysis
PDB id:
1q7y
Name: Ribosome
Title: Crystal structure of ccdap-puromycin bound at the peptidyl transferase center of the 50s ribosomal subunit
Structure: 23s ribosomal RNA. Chain: a. 5s ribosomal RNA. Chain: b. Ccda-p-puromycin. Chain: 5. Engineered: yes. Other_details: peptidyl transferase intermediate analogue contains puromycin.
Source: Haloarcula marismortui. Organism_taxid: 2238. Synthetic: yes. Other_details: ccda-p-puromycin synthesised by michael yarus lab, unviversity of colorado at boulder. Organism_taxid: 2238
Biol. unit: 31mer (from PQS)
Resolution:
3.20Å     R-factor:   0.225     R-free:   0.280
Authors: J.L.Hansen,T.M.Schmeing,P.B.Moore,T.A.Steitz
Key ref:
J.L.Hansen et al. (2002). Structural insights into peptide bond formation. Proc Natl Acad Sci U S A, 99, 11670-11675. PubMed id: 12185246 DOI: 10.1073/pnas.172404099
Date:
20-Aug-03     Release date:   07-Oct-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P20276  (RL2_HALMA) -  Large ribosomal subunit protein uL2 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		240 a.a.
237 a.a.*
Protein chain
Pfam   ArchSchema ?
P20279  (RL3_HALMA) -  Large ribosomal subunit protein uL3 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		338 a.a.
337 a.a.
Protein chain
Pfam   ArchSchema ?
P12735  (RL4_HALMA) -  Large ribosomal subunit protein uL4 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		246 a.a.
246 a.a.*
Protein chain
Pfam   ArchSchema ?
P14124  (RL5_HALMA) -  Large ribosomal subunit protein uL5 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		177 a.a.
140 a.a.
Protein chain
Pfam   ArchSchema ?
P14135  (RL6_HALMA) -  Large ribosomal subunit protein uL6 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		178 a.a.
172 a.a.
Protein chain
Pfam   ArchSchema ?
P12743  (RL7A_HALMA) -  Large ribosomal subunit protein eL8 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		120 a.a.
119 a.a.*
Protein chain
Pfam   ArchSchema ?
P15825  (RL10_HALMA) -  Large ribosomal subunit protein uL10 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		348 a.a.
29 a.a.*
Protein chain
Pfam   ArchSchema ?
P60617  (RL10E_HALMA) -  Large ribosomal subunit protein uL16 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		177 a.a.
156 a.a.*
Protein chain
Pfam   ArchSchema ?
P29198  (RL13_HALMA) -  Large ribosomal subunit protein uL13 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		145 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P22450  (RL14_HALMA) -  Large ribosomal subunit protein uL14 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		132 a.a.
132 a.a.
Protein chain
Pfam   ArchSchema ?
P12737  (RL15_HALMA) -  Large ribosomal subunit protein uL15 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		165 a.a.
145 a.a.
Protein chain
Pfam   ArchSchema ?
P60618  (RL15E_HALMA) -  Large ribosomal subunit protein eL15 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		196 a.a.
194 a.a.*
Protein chain
Pfam   ArchSchema ?
P14123  (RL18_HALMA) -  Large ribosomal subunit protein uL18 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		187 a.a.
186 a.a.
Protein chain
Pfam   ArchSchema ?
P12733  (RL18E_HALMA) -  Large ribosomal subunit protein eL18 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		116 a.a.
115 a.a.
Protein chain
Pfam   ArchSchema ?
P14119  (RL19E_HALMA) -  Large ribosomal subunit protein eL19 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		149 a.a.
143 a.a.*
Protein chain
Pfam   ArchSchema ?
P12734  (RL21_HALMA) -  Large ribosomal subunit protein eL21 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		96 a.a.
95 a.a.
Protein chain
Pfam   ArchSchema ?
P10970  (RL22_HALMA) -  Large ribosomal subunit protein uL22 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		155 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P12732  (RL23_HALMA) -  Large ribosomal subunit protein uL23 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		85 a.a.
81 a.a.
Protein chain
Pfam   ArchSchema ?
P10972  (RL24_HALMA) -  Large ribosomal subunit protein uL24 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		120 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P14116  (RL24E_HALMA) -  Large ribosomal subunit protein eL24 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		67 a.a.
53 a.a.
Protein chain
Pfam   ArchSchema ?
P10971  (RL29_HALMA) -  Large ribosomal subunit protein uL29 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		71 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P14121  (RL30_HALMA) -  Large ribosomal subunit protein uL30 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		154 a.a.
154 a.a.
Protein chain
Pfam   ArchSchema ?
P18138  (RL31_HALMA) -  Large ribosomal subunit protein eL31 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		92 a.a.
82 a.a.
Protein chain
Pfam   ArchSchema ?
P12736  (RL32_HALMA) -  Large ribosomal subunit protein eL32 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		241 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P60619  (RL37A_HALMA) -  Large ribosomal subunit protein eL43 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		92 a.a.
73 a.a.*
Protein chain
Pfam   ArchSchema ?
P32410  (RL37_HALMA) -  Large ribosomal subunit protein eL37 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		57 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P22452  (RL39_HALMA) -  Large ribosomal subunit protein eL39 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		50 a.a.
46 a.a.*
Protein chain
Pfam   ArchSchema ?
P32411  (RL44E_HALMA) -  Large ribosomal subunit protein eL42 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		92 a.a.
92 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 185 residue positions (black crosses)

DNA/RNA chains
  U-A-U-G-C-C-A-G-C-U-G-G-U-G-G-A-U-U-G-C-U-C-G-G-C-U-C-A-G-G-C-G-C-U-G-A-U-G-A- ... 2754 bases
  U-U-A-G-G-C-G-G-C-C-A-C-A-G-C-G-G-U-G-G-G-G-U-U-G-C-C-U-C-C-C-G-U-A-C-C-C-A-U- 122 bases
  C-C-A 3 bases

 Enzyme reactions 
   Enzyme class: Chains C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2, 3, 4: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1073/pnas.172404099 Proc Natl Acad Sci U S A 99:11670-11675 (2002)
PubMed id: 12185246  
 
 
Structural insights into peptide bond formation.
J.L.Hansen, T.M.Schmeing, P.B.Moore, T.A.Steitz.
 
  ABSTRACT  
 
The large ribosomal subunit catalyzes peptide bond formation and will do so by using small aminoacyl- and peptidyl-RNA fragments of tRNA. We have refined at 3-A resolution the structures of both A and P site substrate and product analogues, as well as an intermediate analogue, bound to the Haloarcula marismortui 50S ribosomal subunit. A P site substrate, CCA-Phe-caproic acid-biotin, binds equally to both sites, but in the presence of sparsomycin binds only to the P site. The CCA portions of these analogues are bound identically by either the A or P loop of the 23S rRNA. Combining the separate P and A site substrate complexes into one model reveals interactions that may occur when both are present simultaneously. The alpha-NH(2) group of an aminoacylated fragment in the A site forms one hydrogen bond with the N3 of A2486 (2451) and may form a second hydrogen bond either with the 2' OH of the A-76 ribose in the P site or with the 2' OH of A2486 (2451). These interactions position the alpha amino group adjacent to the carbonyl carbon of esterified P site substrate in an orientation suitable for a nucleophilic attack.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Chemical structures of peptidyl transferase substrate analogues. (A) CCA-pcb is active as a P site substrate and binds to only the P site in the presence of the antibiotic, sparsomycin. (B) An aminoacylated RNA minihelix binds to the A site. (C) CCdA-phosphate-puromycin is an intermediate analogue containing A and P site-binding components. (D) CC-puromycin-phenylalanine-caproic acid-biotin and deacylated CCA are products of the peptidyl transferase reaction. 		Figure 2.
Fig. 2. Experimental electron density maps. (A) An F[o] F[o] electron density map (blue net) contoured at 4.0 shows density corresponding to CCA-pcb (green) in the P site and sparsomycin (yellow). Additional density corresponds to altered conformations of nucleotides such as A2637 (orange). (B) F[o] F[o] electron density map of CCA-pcb shows that in the absence of sparsomycin, the P site substrate is bound equally between the P site (green) and the A site (red).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22525755 M.Selmer, Y.G.Gao, A.Weixlbaumer, and V.Ramakrishnan (2012).
Ribosome engineering to promote new crystal forms.
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21539788 C.Y.Liu, M.T.Qureshi, and T.H.Lee (2011).
Interaction Strengths between the Ribosome and tRNA at Various Steps of Translocation.
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21055949 H.J.Kang, and E.N.Baker (2011).
Intramolecular isopeptide bonds: protein crosslinks built for stress?
  Trends Biochem Sci, 36, 229-237.  
21169502 M.Johansson, K.W.Ieong, S.Trobro, P.Strazewski, J.Åqvist, M.Y.Pavlov, and M.Ehrenberg (2011).
pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA.
  Proc Natl Acad Sci U S A, 108, 79-84.  
21267063 S.Bhushan, T.Hoffmann, B.Seidelt, J.Frauenfeld, T.Mielke, O.Berninghausen, D.N.Wilson, and R.Beckmann (2011).
SecM-stalled ribosomes adopt an altered geometry at the peptidyl transferase center.
  PLoS Biol, 9, e1000581.  
20494981 H.David-Eden, A.S.Mankin, and Y.Mandel-Gutfreund (2010).
Structural signatures of antibiotic binding sites on the ribosome.
  Nucleic Acids Res, 38, 5982-5994.  
20676057 N.Vázquez-Laslop, H.Ramu, D.Klepacki, K.Kannan, and A.S.Mankin (2010).
The key function of a conserved and modified rRNA residue in the ribosomal response to the nascent peptide.
  EMBO J, 29, 3108-3117.  
20151411 X.Ge, and B.Roux (2010).
Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials.
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19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
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19089882 E.Zimmerman, and A.Yonath (2009).
Biological implications of the ribosome's stunning stereochemistry.
  Chembiochem, 10, 63-72.  
19258537 J.F.Atkins, and G.R.Björk (2009).
A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment.
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19225518 K.Bokov, and S.V.Steinberg (2009).
A hierarchical model for evolution of 23S ribosomal RNA.
  Nature, 457, 977-980.  
19595805 M.Simonović, and T.A.Steitz (2009).
A structural view on the mechanism of the ribosome-catalyzed peptide bond formation.
  Biochim Biophys Acta, 1789, 612-623.  
19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.
  Nature, 461, 1234-1242.  
18845572 Y.Xin, and W.K.Olson (2009).
BPS: a database of RNA base-pair structures.
  Nucleic Acids Res, 37, D83-D88.  
18824514 D.Rodriguez-Correa, and A.E.Dahlberg (2008).
Kinetic and thermodynamic studies of peptidyltransferase in ribosomes from the extreme thermophile Thermus thermophilus.
  RNA, 14, 2314-2318.  
18455733 G.Blaha, G.Gürel, S.J.Schroeder, P.B.Moore, and T.A.Steitz (2008).
Mutations outside the anisomycin-binding site can make ribosomes drug-resistant.
  J Mol Biol, 379, 505-519.
PDB codes: 3cc2 3cc4 3cc7 3cce 3ccj 3ccl 3ccm 3ccq 3ccr 3ccs 3ccu 3ccv 3cd6
18672893 K.S.Huang, N.Carrasco, E.Pfund, and S.A.Strobel (2008).
Transition state chirality and role of the vicinal hydroxyl in the ribosomal peptidyl transferase reaction.
  Biochemistry, 47, 8822-8827.  
18369182 M.Beringer (2008).
Modulating the activity of the peptidyl transferase center of the ribosome.
  RNA, 14, 795-801.  
18802635 M.Duca, S.Chen, and S.M.Hecht (2008).
Modeling the reactive properties of tandemly activated tRNAs.
  Org Biomol Chem, 6, 3292-3299.  
18538657 M.Johansson, E.Bouakaz, M.Lovmar, and M.Ehrenberg (2008).
The kinetics of ribosomal peptidyl transfer revisited.
  Mol Cell, 30, 589-598.  
18187576 M.Simonović, and T.A.Steitz (2008).
Cross-crystal averaging reveals that the structure of the peptidyl-transferase center is the same in the 70S ribosome and the 50S subunit.
  Proc Natl Acad Sci U S A, 105, 500-505.  
18818369 M.Simonović, and T.A.Steitz (2008).
Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA.
  RNA, 14, 2372-2378.
PDB codes: 3cma 3cme
18292779 T.A.Steitz (2008).
A structural understanding of the dynamic ribosome machine.
  Nat Rev Mol Cell Biol, 9, 242-253.  
17369838 A.L.Konevega, N.Fischer, Y.P.Semenkov, H.Stark, W.Wintermeyer, and M.V.Rodnina (2007).
Spontaneous reverse movement of mRNA-bound tRNA through the ribosome.
  Nat Struct Mol Biol, 14, 318-324.  
17693476 H.D.Kim, J.D.Puglisi, and S.Chu (2007).
Fluctuations of transfer RNAs between classical and hybrid states.
  Biophys J, 93, 3575-3582.  
17188006 J.S.Weinger, and S.A.Strobel (2007).
Exploring the mechanism of protein synthesis with modified substrates and novel intermediate mimics.
  Blood Cells Mol Dis, 38, 110-116.  
17499045 K.L.Leach, S.M.Swaney, J.R.Colca, W.G.McDonald, J.R.Blinn, L.M.Thomasco, R.C.Gadwood, D.Shinabarger, L.Xiong, and A.S.Mankin (2007).
The site of action of oxazolidinone antibiotics in living bacteria and in human mitochondria.
  Mol Cell, 26, 393-402.  
17187988 K.Y.Sanbonmatsu, and C.S.Tung (2007).
High performance computing in biology: multimillion atom simulations of nanoscale systems.
  J Struct Biol, 157, 470-480.  
17570820 M.Beringer, and M.V.Rodnina (2007).
Importance of tRNA interactions with 23S rRNA for peptide bond formation on the ribosome: studies with substrate analogs.
  Biol Chem, 388, 687-691.  
17499039 M.Beringer, and M.V.Rodnina (2007).
The ribosomal peptidyl transferase.
  Mol Cell, 26, 311-321.  
17157507 M.V.Rodnina, M.Beringer, and W.Wintermeyer (2007).
How ribosomes make peptide bonds.
  Trends Biochem Sci, 32, 20-26.  
17956547 S.Zaman, M.Fitzpatrick, L.Lindahl, and J.Zengel (2007).
Novel mutations in ribosomal proteins L4 and L22 that confer erythromycin resistance in Escherichia coli.
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17135184 A.Lescoute, and E.Westhof (2006).
The interaction networks of structured RNAs.
  Nucleic Acids Res, 34, 6587-6604.  
16522645 A.Mokdad, M.V.Krasovska, J.Sponer, and N.B.Leontis (2006).
Structural and evolutionary classification of G/U wobble basepairs in the ribosome.
  Nucleic Acids Res, 34, 1326-1341.  
16566836 A.V.Uzilov, J.M.Keegan, and D.H.Mathews (2006).
Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change.
  BMC Bioinformatics, 7, 173.  
17188037 F.J.LaRiviere, S.E.Cole, D.J.Ferullo, and M.J.Moore (2006).
A late-acting quality control process for mature eukaryotic rRNAs.
  Mol Cell, 24, 619-626.  
16681365 J.S.Weinger, and S.A.Strobel (2006).
Participation of the tRNA A76 hydroxyl groups throughout translation.
  Biochemistry, 45, 5939-5948.  
16648860 P.Bieling, M.Beringer, S.Adio, and M.V.Rodnina (2006).
Peptide bond formation does not involve acid-base catalysis by ribosomal residues.
  Nat Struct Mol Biol, 13, 423-428.  
16501572 S.Dorner, J.L.Brunelle, D.Sharma, and R.Green (2006).
The hybrid state of tRNA binding is an authentic translation elongation intermediate.
  Nat Struct Mol Biol, 13, 234-241.  
17189194 S.Shoji, S.E.Walker, and K.Fredrick (2006).
Reverse translocation of tRNA in the ribosome.
  Mol Cell, 24, 931-942.  
15731207 D.H.Mathews (2005).
Predicting a set of minimal free energy RNA secondary structures common to two sequences.
  Bioinformatics, 21, 2246-2253.  
15851032 D.Tu, G.Blaha, P.B.Moore, and T.A.Steitz (2005).
Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance.
  Cell, 121, 257-270.
PDB codes: 1yhq 1yi2 1yij 1yit 1yj9 1yjn 1yjw
16164408 I.Agmon, A.Bashan, R.Zarivach, and A.Yonath (2005).
Symmetry at the active site of the ribosome: structural and functional implications.
  Biol Chem, 386, 833-844.  
15980485 J.Kleinjung, and F.Fraternali (2005).
POPSCOMP: an automated interaction analysis of biomolecular complexes.
  Nucleic Acids Res, 33, W342-W346.  
15922593 J.Nilsson, and P.Nissen (2005).
Elongation factors on the ribosome.
  Curr Opin Struct Biol, 15, 349-354.  
16253545 J.Soppa (2005).
From replication to cultivation: hot news from Haloarchaea.
  Curr Opin Microbiol, 8, 737-744.  
16249344 K.Y.Sanbonmatsu, S.Joseph, and C.S.Tung (2005).
Simulating movement of tRNA into the ribosome during decoding.
  Proc Natl Acad Sci U S A, 102, 15854-15859.  
15767286 M.D.Erlacher, K.Lang, N.Shankaran, B.Wotzel, A.Hüttenhofer, R.Micura, A.S.Mankin, and N.Polacek (2005).
Chemical engineering of the peptidyl transferase center reveals an important role of the 2'-hydroxyl group of A2451.
  Nucleic Acids Res, 33, 1618-1627.  
15956979 M.J.Fedor, and J.R.Williamson (2005).
The catalytic diversity of RNAs.
  Nat Rev Mol Cell Biol, 6, 399-412.  
16257828 N.Polacek, and A.S.Mankin (2005).
The ribosomal peptidyl transferase center: structure, function, evolution, inhibition.
  Crit Rev Biochem Mol Biol, 40, 285-311.  
15950868 P.B.Moore, and T.A.Steitz (2005).
The ribosome revealed.
  Trends Biochem Sci, 30, 281-283.  
15795375 P.Pfister, N.Corti, S.Hobbie, C.Bruell, R.Zarivach, A.Yonath, and E.C.Böttger (2005).
23S rRNA base pair 2057-2611 determines ketolide susceptibility and fitness cost of the macrolide resistance mutation 2058A-->G.
  Proc Natl Acad Sci U S A, 102, 5180-5185.  
15917438 S.Dorner, W.Schmid, and A.Barta (2005).
Activity of 3'-thioAMP derivatives as ribosomal P-site substrates.
  Nucleic Acids Res, 33, 3065-3071.  
16116099 S.Trobro, and J.Aqvist (2005).
Mechanism of peptide bond synthesis on the ribosome.
  Proc Natl Acad Sci U S A, 102, 12395-12400.  
16244128 T.Dale, and O.C.Uhlenbeck (2005).
Binding of misacylated tRNAs to the ribosomal A site.
  RNA, 11, 1610-1615.  
16285925 T.M.Schmeing, K.S.Huang, D.E.Kitchen, S.A.Strobel, and T.A.Steitz (2005).
Structural insights into the roles of water and the 2' hydroxyl of the P site tRNA in the peptidyl transferase reaction.
  Mol Cell, 20, 437-448.
PDB codes: 1vq4 1vq5 1vq8 1vq9 1vqk 1vql 1vqm 1vqo 1vqp
16306996 T.M.Schmeing, K.S.Huang, S.A.Strobel, and T.A.Steitz (2005).
An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA.
  Nature, 438, 520-524.
PDB codes: 1vq6 1vq7 1vqn
15141076 A.Sievers, M.Beringer, M.V.Rodnina, and R.Wolfenden (2004).
The ribosome as an entropy trap.
  Proc Natl Acad Sci U S A, 101, 7897-7901.  
15487937 A.Yonath, and A.Bashan (2004).
Ribosomal crystallography: initiation, peptide bond formation, and amino acid polymerization are hampered by antibiotics.
  Annu Rev Microbiol, 58, 233-251.  
15272121 D.E.Ryan, C.H.Kim, J.B.Murray, C.J.Adams, P.G.Stockley, and J.Abelson (2004).
New tertiary constraints between the RNA components of active yeast spliceosomes: a photo-crosslinking study.
  RNA, 10, 1251-1265.  
15123812 D.H.Mathews, M.D.Disney, J.L.Childs, S.J.Schroeder, M.Zuker, and D.H.Turner (2004).
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.
  Proc Natl Acad Sci U S A, 101, 7287-7292.  
15272118 D.H.Mathews (2004).
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization.
  RNA, 10, 1178-1190.  
15554968 F.Schlünzen, E.Pyetan, P.Fucini, A.Yonath, and J.M.Harms (2004).
Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin.
  Mol Microbiol, 54, 1287-1294.
PDB code: 1xbp
15059283 J.M.Harms, F.Schlünzen, P.Fucini, H.Bartels, and A.Yonath (2004).
Alterations at the peptidyl transferase centre of the ribosome induced by the synergistic action of the streptogramins dalfopristin and quinupristin.
  BMC Biol, 2, 4.
PDB code: 1sm1
14999092 J.S.Weinger, D.Kitchen, S.A.Scaringe, S.A.Strobel, and G.W.Muth (2004).
Solid phase synthesis and binding affinity of peptidyl transferase transition state mimics containing 2'-OH at P-site position A76.
  Nucleic Acids Res, 32, 1502-1511.  
15475967 J.S.Weinger, K.M.Parnell, S.Dorner, R.Green, and S.A.Strobel (2004).
Substrate-assisted catalysis of peptide bond formation by the ribosome.
  Nat Struct Mol Biol, 11, 1101-1106.  
14691943 P.C.Bevilacqua, T.S.Brown, S.Nakano, and R.Yajima (2004).
Catalytic roles for proton transfer and protonation in ribozymes.
  Biopolymers, 73, 90.  
15574334 R.P.Fahlman, T.Dale, and O.C.Uhlenbeck (2004).
Uniform binding of aminoacylated transfer RNAs to the ribosomal A and P sites.
  Mol Cell, 16, 799-805.  
12535524 A.Bashan, I.Agmon, R.Zarivach, F.Schluenzen, J.Harms, R.Berisio, H.Bartels, F.Franceschi, T.Auerbach, H.A.Hansen, E.Kossoy, M.Kessler, and A.Yonath (2003).
Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression.
  Mol Cell, 11, 91.
PDB codes: 1njm 1njn 1njo 1njp
14669983 A.Yonath (2003).
Ribosomal tolerance and peptide bond formation.
  Biol Chem, 384, 1411-1419.  
12932345 D.R.Southworth, and R.Green (2003).
Ribosomal translocation: sparsomycin pushes the button.
  Curr Biol, 13, R652-R654.  
12787020 I.Agmon, T.Auerbach, D.Baram, H.Bartels, A.Bashan, R.Berisio, P.Fucini, H.A.Hansen, J.Harms, M.Kessler, M.Peretz, F.Schluenzen, A.Yonath, and R.Zarivach (2003).
On peptide bond formation, translocation, nascent protein progression and the regulatory properties of ribosomes. Derived on 20 October 2002 at the 28th FEBS Meeting in Istanbul.
  Eur J Biochem, 270, 2543-2556.  
12869702 M.Beringer, S.Adio, W.Wintermeyer, and M.Rodnina (2003).
The G2447A mutation does not affect ionization of a ribosomal group taking part in peptide bond formation.
  RNA, 9, 919-922.  
12831884 M.V.Rodnina, and W.Wintermeyer (2003).
Peptide bond formation on the ribosome: structure and mechanism.
  Curr Opin Struct Biol, 13, 334-340.  
12554855 P.B.Moore, and T.A.Steitz (2003).
After the ribosome structures: how does peptidyl transferase work?
  RNA, 9, 155-159.  
14527328 P.B.Moore, and T.A.Steitz (2003).
The structural basis of large ribosomal subunit function.
  Annu Rev Biochem, 72, 813-850.  
12932729 T.A.Steitz, and P.B.Moore (2003).
RNA, the first macromolecular catalyst: the ribosome is a ribozyme.
  Trends Biochem Sci, 28, 411-418.  
12925990 T.Hermann (2003).
Chemical and functional diversity of small molecule ligands for RNA.
  Biopolymers, 70, 4.  
14561884 T.M.Schmeing, P.B.Moore, and T.A.Steitz (2003).
Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit.
  RNA, 9, 1345-1352.
PDB codes: 1qvf 1qvg
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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