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PDBsum entry 4kfk

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protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
4kfk
Jmol
Contents
Protein chains
362 a.a.
234 a.a.
206 a.a.
208 a.a.
151 a.a.
101 a.a.
155 a.a.
138 a.a.
127 a.a.
98 a.a.
114 a.a.
122 a.a.
117 a.a.
60 a.a.
88 a.a.
83 a.a.
99 a.a.
70 a.a.
78 a.a.
99 a.a.
24 a.a.
DNA/RNA
Metals
_MG
_ZN
PDB id:
4kfk
Name: Ribosome
Title: Crystal structure of the 70s ribosome bound with the q253p m release factor rf2. 30s of the b subunit
Structure: 16s rrna (1504-mer). Chain: a. Messenger RNA (5'-r( Ap Ap Up Gp Up Ap G)-3'). Chain: v. P-site tRNA-fmet. Chain: w. Mutation: yes. Bacterial peptide chain release factor 2 (rf-2). Chain: y.
Source: Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Gene: tt_c1852. Expressed in: escherichia coli. Expression_system_taxid: 469008. Strain: hb27
Resolution:
3.40Å     R-factor:   0.235     R-free:   0.268
Authors: N.Santos,J.Zhu,J.P.Donohue,A.A.Korostelev,H.F.Noller
Key ref: N.Santos et al. (2013). Crystal structure of the 70S ribosome bound with the Q253P mutant form of release factor RF2. Structure, 21, 1258-1263. PubMed id: 23769667 DOI: 10.1016/j.str.2013.04.028
Date:
26-Apr-13     Release date:   03-Jul-13    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q72GJ6  (Q72GJ6_THET2) -  Bacterial peptide chain release factor 2 (RF-2)
Seq:
Struc:
378 a.a.
362 a.a.*
Protein chain
Pfam   ArchSchema ?
P62662  (RS2_THET2) -  30S ribosomal protein S2
Seq:
Struc:
256 a.a.
234 a.a.
Protein chain
Pfam   ArchSchema ?
P62663  (RS3_THET2) -  30S ribosomal protein S3
Seq:
Struc:
239 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P62664  (RS4_THET2) -  30S ribosomal protein S4
Seq:
Struc:
209 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
P62665  (RS5_THET2) -  30S ribosomal protein S5
Seq:
Struc:
162 a.a.
151 a.a.
Protein chain
Pfam   ArchSchema ?
P62666  (RS6_THET2) -  30S ribosomal protein S6
Seq:
Struc:
101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P62667  (RS7_THET2) -  30S ribosomal protein S7
Seq:
Struc:
156 a.a.
155 a.a.
Protein chain
Pfam   ArchSchema ?
P62668  (RS8_THET2) -  30S ribosomal protein S8
Seq:
Struc:
138 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
P62669  (RS9_THET2) -  30S ribosomal protein S9
Seq:
Struc:
128 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
P62653  (RS10_THET2) -  30S ribosomal protein S10
Seq:
Struc:
105 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P62654  (RS11_THET2) -  30S ribosomal protein S11
Seq:
Struc:
129 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P61941  (RS12_THET2) -  30S ribosomal protein S12
Seq:
Struc:
132 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
P62655  (RS13_THET2) -  30S ribosomal protein S13
Seq:
Struc:
126 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P62656  (RS14Z_THET2) -  30S ribosomal protein S14 type Z
Seq:
Struc:
61 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
P62657  (RS15_THET2) -  30S ribosomal protein S15
Seq:
Struc:
89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
P62238  (RS16_THET2) -  30S ribosomal protein S16
Seq:
Struc:
88 a.a.
83 a.a.
Protein chain
Pfam   ArchSchema ?
P62658  (RS17_THET2) -  30S ribosomal protein S17
Seq:
Struc:
105 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P62659  (RS18_THET2) -  30S ribosomal protein S18
Seq:
Struc:
88 a.a.
70 a.a.
Protein chain
Pfam   ArchSchema ?
P62660  (RS19_THET2) -  30S ribosomal protein S19
Seq:
Struc:
93 a.a.
78 a.a.
Protein chain
Pfam   ArchSchema ?
P62661  (RS20_THET2) -  30S ribosomal protein S20
Seq:
Struc:
106 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P62613  (RSHX_THET2) -  30S ribosomal protein Thx
Seq:
Struc:
27 a.a.
24 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   5 terms 
  Biological process     translation   2 terms 
  Biochemical function     structural constituent of ribosome     9 terms  

 

 
DOI no: 10.1016/j.str.2013.04.028 Structure 21:1258-1263 (2013)
PubMed id: 23769667  
 
 
Crystal structure of the 70S ribosome bound with the Q253P mutant form of release factor RF2.
N.Santos, J.Zhu, J.P.Donohue, A.A.Korostelev, H.F.Noller.
 
  ABSTRACT  
 
Bacterial translation termination is mediated by release factors RF1 and RF2, which recognize stop codons and catalyze hydrolysis of the peptidyl-tRNA ester bond. The catalytic mechanism has been debated. We proposed that the backbone amide NH group, rather than the side chain, of the glutamine of the universally conserved GGQ motif participates in catalysis by H-bonding to the tetrahedral transition-state intermediate and by product stabilization. This was supported by complete loss of RF1 catalytic activity when glutamine is replaced by proline, the only residue that lacks a backbone NH group. Here, we present the 3.4 Å crystal structure of the ribosome complex containing the RF2 Q253P mutant and find that its fold, including the GGP sequence, is virtually identical to that of wild-type RF2. This rules out proline-induced misfolding and further supports the proposal that catalytic activity requires interaction of the Gln-253 backbone amide with the 3' end of peptidyl-tRNA.