PDBsum entry 1vq5

Go to PDB code: 
protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
Protein chains
237 a.a. *
337 a.a. *
246 a.a. *
140 a.a. *
172 a.a. *
119 a.a. *
29 a.a. *
160 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. *
70 a.a. *
_CL ×22
_NA ×86
_MG ×118
_CD ×5
__K ×3
Waters ×7716
* Residue conservation analysis
PDB id:
Name: Ribosome
Title: The structure of the transition state analogue "raa" bound t large ribosomal subunit of haloarcula marismortui
Structure: 23s ribosomal RNA. Chain: 0. 5s ribosomal RNA. Chain: 9. 5'-d( (Dc)p (Dc)p (5Aa)p (2Op)p (Po2)p Ap C C)-3' chain: 4. Engineered: yes. 50s ribosomal protein l2p. Chain: a.
Source: Haloarcula marismortui. Organism_taxid: 2238. Synthetic: yes. Other_details: synthetic oligo dc-dc-hydroxyalanylpuromycin c. Organism_taxid: 2238
Biol. unit: 32mer (from PQS)
2.60Å     R-factor:   0.197     R-free:   0.237
Authors: T.M.Schmeing,T.A.Steitz
Key ref:
T.M.Schmeing et al. (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. PubMed id: 16285925 DOI: 10.1016/j.molcel.2005.09.006
16-Dec-04     Release date:   29-Nov-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P20276  (RL2_HALMA) -  50S ribosomal protein L2
240 a.a.
237 a.a.
Protein chain
Pfam   ArchSchema ?
P20279  (RL3_HALMA) -  50S ribosomal protein L3
338 a.a.
337 a.a.
Protein chain
Pfam   ArchSchema ?
P12735  (RL4_HALMA) -  50S ribosomal protein L4
246 a.a.
246 a.a.*
Protein chain
Pfam   ArchSchema ?
P14124  (RL5_HALMA) -  50S ribosomal protein L5
177 a.a.
140 a.a.
Protein chain
Pfam   ArchSchema ?
P14135  (RL6_HALMA) -  50S ribosomal protein L6
178 a.a.
172 a.a.
Protein chain
Pfam   ArchSchema ?
P12743  (RL7A_HALMA) -  50S ribosomal protein L7Ae
120 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P15825  (RLA0_HALMA) -  50S ribosomal protein L10
348 a.a.
29 a.a.*
Protein chain
Pfam   ArchSchema ?
P60617  (RL10_HALMA) -  50S ribosomal protein L10e
177 a.a.
160 a.a.*
Protein chain
Pfam   ArchSchema ?
P29198  (RL13_HALMA) -  50S ribosomal protein L13
145 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P22450  (RL14_HALMA) -  50S ribosomal protein L14
132 a.a.
132 a.a.*
Protein chain
Pfam   ArchSchema ?
P12737  (RL15_HALMA) -  50S ribosomal protein L15P
165 a.a.
145 a.a.
Protein chain
Pfam   ArchSchema ?
P60618  (RL15E_HALMA) -  50S ribosomal protein L15e
196 a.a.
194 a.a.*
Protein chain
Pfam   ArchSchema ?
P14123  (RL18_HALMA) -  50S ribosomal protein L18P
187 a.a.
186 a.a.
Protein chain
Pfam   ArchSchema ?
P12733  (RL18E_HALMA) -  50S ribosomal protein L18e
116 a.a.
115 a.a.
Protein chain
Pfam   ArchSchema ?
P14119  (RL19_HALMA) -  50S ribosomal protein L19e
149 a.a.
143 a.a.
Protein chain
Pfam   ArchSchema ?
P12734  (RL21_HALMA) -  50S ribosomal protein L21e
96 a.a.
95 a.a.
Protein chain
Pfam   ArchSchema ?
P10970  (RL22_HALMA) -  50S ribosomal protein L22P
155 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P12732  (RL23_HALMA) -  50S ribosomal protein L23P
85 a.a.
81 a.a.
Protein chain
Pfam   ArchSchema ?
P10972  (RL24_HALMA) -  50S ribosomal protein L24P
120 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P14116  (RL24E_HALMA) -  50S ribosomal protein L24e
67 a.a.
53 a.a.
Protein chain
Pfam   ArchSchema ?
P10971  (RL29_HALMA) -  50S ribosomal protein L29P
71 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P14121  (RL30_HALMA) -  50S ribosomal protein L30P
154 a.a.
154 a.a.
Protein chain
Pfam   ArchSchema ?
P18138  (RL31_HALMA) -  50S ribosomal protein L31e
92 a.a.
82 a.a.
Protein chain
Pfam   ArchSchema ?
P12736  (RL32_HALMA) -  50S ribosomal protein L32e
241 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P60619  (RL37A_HALMA) -  50S ribosomal protein L37Ae
92 a.a.
73 a.a.*
Protein chain
Pfam   ArchSchema ?
P32410  (RL37_HALMA) -  50S ribosomal protein L37e
57 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P22452  (RL39_HALMA) -  50S ribosomal protein L39e
50 a.a.
46 a.a.
Protein chain
Pfam   ArchSchema ?
P32411  (RL44_HALMA) -  50S ribosomal protein L44e
92 a.a.
92 a.a.
Protein chain
Pfam   ArchSchema ?
P14122  (RL11_HALMA) -  50S ribosomal protein L11
162 a.a.
70 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 24 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   5 terms 
  Biological process     ribosome biogenesis   6 terms 
  Biochemical function     structural constituent of ribosome     11 terms  


DOI no: 10.1016/j.molcel.2005.09.006 Mol Cell 20:437-448 (2005)
PubMed id: 16285925  
Structural insights into the roles of water and the 2' hydroxyl of the P site tRNA in the peptidyl transferase reaction.
T.M.Schmeing, K.S.Huang, D.E.Kitchen, S.A.Strobel, T.A.Steitz.
Peptide bond formation is catalyzed at the peptidyl transferase center (PTC) of the large ribosomal subunit. Crystal structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with several analogs that represent either the substrates or the transition state intermediate of the peptidyl transferase reaction show that this reaction proceeds through a tetrahedral intermediate with S chirality. The oxyanion of the tetrahedral intermediate interacts with a water molecule that is positioned by nucleotides A2637 (E. coli numbering, 2602) and (methyl)U2619(2584). There are no Mg2+ ions or monovalent metal ions observed in the PTC that could directly promote catalysis. The A76 2' hydroxyl of the peptidyl-tRNA is hydrogen bonded to the alpha-amino group and could facilitate peptide bond formation by substrate positioning and by acting as a proton shuttle between the alpha-amino group and the A76 3' hydroxyl of the peptidyl-tRNA.
  Selected figure(s)  
Figure 1.
Figure 1. Unbiased F[o] − F[c] Electron Density Maps for Some of the Complexes of the 50S Subunit Bound with Peptidyl Transferase Ligands, All Contoured at 3 σ
Figure 6.
Figure 6. The Reaction Pathway for Peptide Bond Formation
  The above figures are reprinted by permission from Cell Press: Mol Cell (2005, 20, 437-448) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21055949 H.J.Kang, and E.N.Baker (2011).
Intramolecular isopeptide bonds: protein crosslinks built for stress?
  Trends Biochem Sci, 36, 229-237.  
21292164 H.Ramu, N.Vázquez-Laslop, D.Klepacki, Q.Dai, J.Piccirilli, R.Micura, and A.S.Mankin (2011).
Nascent peptide in the ribosome exit tunnel affects functional properties of the A-site of the peptidyl transferase center.
  Mol Cell, 41, 321-330.  
21286631 K.S.Krishnakumar, B.Y.Michel, N.Q.Nguyen-Trung, B.Fenet, and P.Strazewski (2011).
Intrinsic pK(a) values of 3'-N-α-l-aminoacyl-3'-aminodeoxyadenosines determined by pH dependent (1)H NMR in H(2)O.
  Chem Commun (Camb), 47, 3290-3292.  
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.  
21804565 S.Kuhlenkoetter, W.Wintermeyer, and M.V.Rodnina (2011).
Different substrate-dependent transition states in the active site of the ribosome.
  Nature, 476, 351-354.  
20375101 A.Chirkova, M.D.Erlacher, N.Clementi, M.Zywicki, M.Aigner, and N.Polacek (2010).
The role of the universally conserved A2450-C2063 base pair in the ribosomal peptidyl transferase center.
  Nucleic Acids Res, 38, 4844-4855.  
20359191 D.A.Hiller, M.Zhong, V.Singh, and S.A.Strobel (2010).
Transition states of uncatalyzed hydrolysis and aminolysis reactions of a ribosomal P-site substrate determined by kinetic isotope effects.
  Biochemistry, 49, 3868-3878.  
20385807 D.B.Johnson, and L.Wang (2010).
Imprints of the genetic code in the ribosome.
  Proc Natl Acad Sci U S A, 107, 8298-8303.  
20080677 G.Wallin, and J.Aqvist (2010).
The transition state for peptide bond formation reveals the ribosome as a water trap.
  Proc Natl Acad Sci U S A, 107, 1888-1893.  
20421507 H.Jin, A.C.Kelley, D.Loakes, and V.Ramakrishnan (2010).
Structure of the 70S ribosome bound to release factor 2 and a substrate analog provides insights into catalysis of peptide release.
  Proc Natl Acad Sci U S A, 107, 8593-8598.
PDB codes: 2x9r 2x9s 2x9t 2x9u
20631789 M.Ehrenberg (2010).
Protein synthesis: Translocation in slow motion.
  Nature, 466, 325-326.  
19962317 M.V.Rodnina, and W.Wintermeyer (2010).
The ribosome goes Nobel.
  Trends Biochem Sci, 35, 1-5.  
20689681 N.B.Ulyanov, and T.L.James (2010).
RNA structural motifs that entail hydrogen bonds involving sugar-phosphate backbone atoms of RNA.
  New J Chem, 34, 910-917.  
20141197 R.E.Watts, and A.C.Forster (2010).
Chemical models of peptide formation in translation.
  Biochemistry, 49, 2177-2185.  
20932481 S.Bhushan, H.Meyer, A.L.Starosta, T.Becker, T.Mielke, O.Berninghausen, M.Sattler, D.N.Wilson, and R.Beckmann (2010).
Structural basis for translational stalling by human cytomegalovirus and fungal arginine attenuator peptide.
  Mol Cell, 40, 138-146.
PDB code: 2xl1
20139981 S.Bhushan, M.Gartmann, M.Halic, J.P.Armache, A.Jarasch, T.Mielke, O.Berninghausen, D.N.Wilson, and R.Beckmann (2010).
alpha-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel.
  Nat Struct Mol Biol, 17, 313-317.  
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.
  J Mol Recognit, 23, 128-141.  
19656820 A.Yonath (2009).
Large facilities and the evolving ribosome, the cellular machine for genetic-code translation.
  J R Soc Interface, 6, S575-S585.  
19933110 B.Seidelt, C.A.Innis, D.N.Wilson, M.Gartmann, J.P.Armache, E.Villa, L.G.Trabuco, T.Becker, T.Mielke, K.Schulten, T.A.Steitz, and R.Beckmann (2009).
Structural insight into nascent polypeptide chain-mediated translational stalling.
  Science, 326, 1412-1415.
PDB codes: 2wwl 2wwq
19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
  Crit Rev Biochem Mol Biol, 44, 393-433.  
19089882 E.Zimmerman, and A.Yonath (2009).
Biological implications of the ribosome's stunning stereochemistry.
  Chembiochem, 10, 63-72.  
19362093 G.Gürel, G.Blaha, P.B.Moore, and T.A.Steitz (2009).
U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.
  J Mol Biol, 389, 146-156.
PDB codes: 3g4s 3g6e 3g71
19738021 G.Gürel, G.Blaha, T.A.Steitz, and P.B.Moore (2009).
Structures of triacetyloleandomycin and mycalamide A bind to the large ribosomal subunit of Haloarcula marismortui.
  Antimicrob Agents Chemother, 53, 5010-5014.
PDB codes: 3i55 3i56
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.  
19363482 R.M.Voorhees, A.Weixlbaumer, D.Loakes, A.C.Kelley, and V.Ramakrishnan (2009).
Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome.
  Nat Struct Mol Biol, 16, 528-533.
PDB codes: 2wdg 2wdh 2wdi 2wdj 2wdk 2wdl 2wdm 2wdn
19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.
  Nature, 461, 1234-1242.  
19150407 W.K.Olson, M.Esguerra, Y.Xin, and X.J.Lu (2009).
New information content in RNA base pairing deduced from quantitative analysis of high-resolution structures.
  Methods, 47, 177-186.  
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.  
19915655 A.Bashan, and A.Yonath (2008).
The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility.
  J Mol Struct, 890, 289-294.  
18997014 A.Minajigi, and C.S.Francklyn (2008).
RNA-assisted catalysis in a protein enzyme: The 2'-hydroxyl of tRNA(Thr) A76 promotes aminoacylation by threonyl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 105, 17748-17753.  
18482701 D.A.Kingery, E.Pfund, R.M.Voorhees, K.Okuda, I.Wohlgemuth, D.E.Kitchen, M.V.Rodnina, and S.A.Strobel (2008).
An uncharged amine in the transition state of the ribosomal peptidyl transfer reaction.
  Chem Biol, 15, 493-500.  
18544041 E.M.Youngman, M.E.McDonald, and R.Green (2008).
Peptide release on the ribosome: mechanism and implications for translational control.
  Annu Rev Microbiol, 62, 353-373.  
18809677 I.Wohlgemuth, S.Brenner, M.Beringer, and M.V.Rodnina (2008).
Modulation of the rate of peptidyl transfer on the ribosome by the nature of substrates.
  J Biol Chem, 283, 32229-32235.  
18567817 J.L.Brunelle, J.J.Shaw, E.M.Youngman, and R.Green (2008).
Peptide release on the ribosome depends critically on the 2' OH of the peptidyl-tRNA substrate.
  RNA, 14, 1526-1531.  
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.  
18538657 M.Johansson, E.Bouakaz, M.Lovmar, and M.Ehrenberg (2008).
The kinetics of ribosomal peptidyl transfer revisited.
  Mol Cell, 30, 589-598.  
18596689 M.Laurberg, H.Asahara, A.Korostelev, J.Zhu, S.Trakhanov, and H.F.Noller (2008).
Structural basis for translation termination on the 70S ribosome.
  Nature, 454, 852-857.
PDB codes: 3d5a 3d5b 3d5c 3d5d
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.  
18382121 T.A.Steitz (2008).
Structural insights into the functions of the large ribosomal subunit, a major antibiotic target.
  Keio J Med, 57, 1.  
17488874 A.T.Torelli, J.Krucinska, and J.E.Wedekind (2007).
A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization.
  RNA, 13, 1052-1070.
PDB codes: 2p7d 2p7e 2p7f
17379815 A.V.Manuilov, S.S.Hixson, and R.A.Zimmermann (2007).
New photoreactive tRNA derivatives for probing the peptidyl transferase center of the ribosome.
  RNA, 13, 793-800.  
17621307 E.S.Poole, D.J.Young, M.E.Askarian-Amiri, D.J.Scarlett, and W.P.Tate (2007).
Accommodating the bacterial decoding release factor as an alien protein among the RNAs at the active site of the ribosome.
  Cell Res, 17, 591-607.  
17284455 H.Tjong, and H.X.Zhou (2007).
DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces.
  Nucleic Acids Res, 35, 1465-1477.  
17456564 J.F.Atkins, N.M.Wills, G.Loughran, C.Y.Wu, K.Parsawar, M.D.Ryan, C.H.Wang, and C.C.Nelson (2007).
A case for "StopGo": reprogramming translation to augment codon meaning of GGN by promoting unconventional termination (Stop) after addition of glycine and then allowing continued translation (Go).
  RNA, 13, 803-810.  
17996709 J.J.Shaw, and R.Green (2007).
Two distinct components of release factor function uncovered by nucleophile partitioning analysis.
  Mol Cell, 28, 458-467.  
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.  
17891155 K.Watanabe, Y.Toh, K.Suto, Y.Shimizu, N.Oka, T.Wada, and K.Tomita (2007).
Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase.
  Nature, 449, 867-871.
PDB codes: 2z3k 2z3l 2z3m 2z3n 2z3o 2z3p
17660192 M.Amort, B.Wotzel, K.Bakowska-Zywicka, M.D.Erlacher, R.Micura, and N.Polacek (2007).
An intact ribose moiety at A2602 of 23S rRNA is key to trigger peptidyl-tRNA hydrolysis during translation termination.
  Nucleic Acids Res, 35, 5130-5140.  
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.  
18158891 N.G.Walter (2007).
Ribozyme catalysis revisited: is water involved?
  Mol Cell, 28, 923-929.  
17981494 S.A.Strobel, and J.C.Cochrane (2007).
RNA catalysis: ribozymes, ribosomes, and riboswitches.
  Curr Opin Chem Biol, 11, 636-643.  
17574829 V.Berk, and J.H.Cate (2007).
Insights into protein biosynthesis from structures of bacterial ribosomes.
  Curr Opin Struct Biol, 17, 302-309.  
16962654 A.Korostelev, S.Trakhanov, M.Laurberg, and H.F.Noller (2006).
Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements.
  Cell, 126, 1065-1077.
PDB codes: 1vsa 2ow8
16799464 I.Wohlgemuth, M.Beringer, and M.V.Rodnina (2006).
Rapid peptide bond formation on isolated 50S ribosomal subunits.
  EMBO Rep, 7, 699-703.  
16681365 J.S.Weinger, and S.A.Strobel (2006).
Participation of the tRNA A76 hydroxyl groups throughout translation.
  Biochemistry, 45, 5939-5948.  
16411744 J.Salter, J.Krucinska, S.Alam, V.Grum-Tokars, and J.E.Wedekind (2006).
Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer.
  Biochemistry, 45, 686-700.
PDB codes: 1zfr 1zft 1zfv 1zfx 2bcy 2bcz 2fgp 2oue
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.  
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.