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PDBsum entry 3kit

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protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
3kit
Jmol
Contents
Protein chains
120 a.a. *
271 a.a. *
204 a.a. *
207 a.a. *
181 a.a. *
164 a.a. *
145 a.a. *
130 a.a. *
138 a.a. *
122 a.a. *
146 a.a. *
140 a.a. *
117 a.a. *
98 a.a. *
135 a.a. *
117 a.a. *
101 a.a. *
113 a.a. *
92 a.a. *
100 a.a. *
184 a.a. *
84 a.a. *
93 a.a. *
71 a.a. *
59 a.a. *
57 a.a. *
55 a.a. *
50 a.a. *
47 a.a. *
63 a.a. *
37 a.a. *
DNA/RNA
Metals
_MG ×300
_ZN
* Residue conservation analysis
PDB id:
3kit
Name: Ribosome
Title: Structure of rele nuclease bound to the 70s ribosome (precleavage state; part 4 of 4)
Structure: 50s ribosomal protein l1. Chain: c. 50s ribosomal protein l2. Chain: d. 50s ribosomal protein l3. Chain: e. 50s ribosomal protein l4. Chain: f. Synonym: l1e.
Source: Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8 / atcc 27634 / dsm 579. Strain: hb8 / atcc 27634 / dsm 579
Resolution:
3.30Å     R-factor:   0.219     R-free:   0.247
Authors: C.Neubauer,Y.-G.Gao,K.R.Andersen,C.M.Dunham,A.C.Kelley, J.Hentschel,K.Gerdes,V.Ramakrishnan,D.E.Brodersen
Key ref:
C.Neubauer et al. (2009). The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE. Cell, 139, 1084-1095. PubMed id: 20005802 DOI: 10.1016/j.cell.2009.11.015
Date:
02-Nov-09     Release date:   15-Dec-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5SLP7  (RL1_THET8) -  50S ribosomal protein L1
Seq:
Struc:
229 a.a.
120 a.a.
Protein chain
Pfam   ArchSchema ?
P60405  (RL2_THET8) -  50S ribosomal protein L2
Seq:
Struc:
276 a.a.
271 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN8  (RL3_THET8) -  50S ribosomal protein L3
Seq:
Struc:
206 a.a.
204 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN9  (RL4_THET8) -  50S ribosomal protein L4
Seq:
Struc:
210 a.a.
207 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ0  (RL5_THET8) -  50S ribosomal protein L5
Seq:
Struc:
182 a.a.
181 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ3  (RL6_THET8) -  50S ribosomal protein L6
Seq:
Struc:
180 a.a.
164 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLQ1  (RL9_THET8) -  50S ribosomal protein L9
Seq:
Struc:
148 a.a.
145 a.a.
Protein chain
Pfam   ArchSchema ?
Q8VVE3  (RL10_THET8) -  50S ribosomal protein L10
Seq:
Struc:
173 a.a.
130 a.a.
Protein chain
Pfam   ArchSchema ?
P60488  (RL13_THET8) -  50S ribosomal protein L13
Seq:
Struc:
140 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP8  (RL14_THET8) -  50S ribosomal protein L14
Seq:
Struc:
122 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ7  (RL15_THET8) -  50S ribosomal protein L15
Seq:
Struc:
150 a.a.
146 a.a.
Protein chain
Pfam   ArchSchema ?
P60489  (RL16_THET8) -  50S ribosomal protein L16
Seq:
Struc:
141 a.a.
140 a.a.
Protein chain
Pfam   ArchSchema ?
Q9Z9H5  (RL17_THET8) -  50S ribosomal protein L17
Seq:
Struc:
118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ4  (RL18_THET8) -  50S ribosomal protein L18
Seq:
Struc:
112 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P60490  (RL19_THET8) -  50S ribosomal protein L19
Seq:
Struc:
146 a.a.
135 a.a.
Protein chain
Pfam   ArchSchema ?
P60491  (RL20_THET8) -  50S ribosomal protein L20
Seq:
Struc:
118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P60492  (RL21_THET8) -  50S ribosomal protein L21
Seq:
Struc:
101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP3  (RL22_THET8) -  50S ribosomal protein L22
Seq:
Struc:
113 a.a.
113 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP0  (RL23_THET8) -  50S ribosomal protein L23
Seq:
Struc:
96 a.a.
92 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP9  (RL24_THET8) -  50S ribosomal protein L24
Seq:
Struc:
110 a.a.
100 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHZ1  (RL25_THET8) -  50S ribosomal protein L25
Seq:
Struc:
206 a.a.
184 a.a.
Protein chain
Pfam   ArchSchema ?
P60493  (RL27_THET8) -  50S ribosomal protein L27
Seq:
Struc:
85 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P60494  (RL28_THET8) -  50S ribosomal protein L28
Seq:
Struc:
98 a.a.
93 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP6  (RL29_THET8) -  50S ribosomal protein L29
Seq:
Struc:
72 a.a.
71 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ6  (RL30_THET8) -  50S ribosomal protein L30
Seq:
Struc:
60 a.a.
59 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJE1  (RL31_THET8) -  50S ribosomal protein L31
Seq:
Struc:
71 a.a.
57 a.a.
Protein chain
Pfam   ArchSchema ?
P80339  (RL32_THET8) -  50S ribosomal protein L32
Seq:
Struc:
60 a.a.
55 a.a.
Protein chain
Pfam   ArchSchema ?
P35871  (RL33_THET8) -  50S ribosomal protein L33
Seq:
Struc:
54 a.a.
50 a.a.
Protein chain
Pfam   ArchSchema ?
P80340  (RL34_THET8) -  50S ribosomal protein L34
Seq:
Struc:
49 a.a.
47 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SKU1  (RL35_THET8) -  50S ribosomal protein L35
Seq:
Struc:
65 a.a.
63 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHR2  (RL36_THET8) -  50S ribosomal protein L36
Seq:
Struc:
37 a.a.
37 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     ribosome biogenesis   3 terms 
  Biochemical function     structural constituent of ribosome     9 terms  

 

 
DOI no: 10.1016/j.cell.2009.11.015 Cell 139:1084-1095 (2009)
PubMed id: 20005802  
 
 
The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE.
C.Neubauer, Y.G.Gao, K.R.Andersen, C.M.Dunham, A.C.Kelley, J.Hentschel, K.Gerdes, V.Ramakrishnan, D.E.Brodersen.
 
  ABSTRACT  
 
Translational control is widely used to adjust gene expression levels. During the stringent response in bacteria, mRNA is degraded on the ribosome by the ribosome-dependent endonuclease, RelE. The molecular basis for recognition of the ribosome and mRNA by RelE and the mechanism of cleavage are unknown. Here, we present crystal structures of E. coli RelE in isolation (2.5 A) and bound to programmed Thermus thermophilus 70S ribosomes before (3.3 A) and after (3.6 A) cleavage. RelE occupies the A site and causes cleavage of mRNA after the second nucleotide of the codon by reorienting and activating the mRNA for 2'-OH-induced hydrolysis. Stacking of A site codon bases with conserved residues in RelE and 16S rRNA explains the requirement for the ribosome in catalysis and the subtle sequence specificity of the reaction. These structures provide detailed insight into the translational regulation on the bacterial ribosome by mRNA cleavage.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Overview of the RelE-Bound 70S Ribosome
(A) Top view of the 70S ribosome with the 50S (blue) and 30S (wheat) subunits surrounding RelE (A site, blue), tRNA^fMet (P site, green), a noncognate tRNA^fMet (E site, red), and mRNA (magenta). (A)–(C) are based on the precleavage structure.
(B) Close-up of the A and P sites of the 30S subunit viewed from the interface to the 50S. RelE (blue cartoon) spans the 16S rRNA from the head (helix 31 region, green) to the body (helix 18, pink). The mRNA is shown in purple sticks, and the P and E site tRNAs colored as in (A).
(C) Close-up view of the A and P sites showing RelE (blue Cα trace), mRNA (purple sticks), and P site tRNA (green cartoon) along with the DF[o]-mF[c] electron density of the precleavage structure contoured at 1.5 σ. The mRNA sequence is indicated.
(D) The postcleavage structure showing the position of the 2′-3′ cyclic phosphate generated upon cleavage (2′-3′ cP). The map is contoured at 1.2 σ.
See also Figure S1.
Figure 3.
Figure 3. In Vitro mRNA Cleavage Assay on the 70S Ribosome
(A) Sequence of E. coli RelE with the conservation among homologs indicated as increasing strength of red color and the conserved tyrosine at the C terminus in light blue. The secondary structure is shown above the sequence and the interactions to rRNA and mRNA below (all numbers correspond to the E. coli 16S sequence). Residues in the P. horikoshii RelE homolog that affect the activity are indicated with black boxes (Takagi et al., 2005).
(B) Overview of the mRNAs used for the in vitro cleavage assays. The 25 nt mRNA consists of a Shine-Dalgarno element (SD) followed by a spacer and the P site (AUG) and A site (UAG) codons. “Trunc Asite” ends after the P site codon with a 3′-OH. The table shows predicted masses of full length mRNA and fragments that would result from cleavage after position 1 or 2 of the A site codon leaving either a 3′-OH, 3′-phosphate (3′-P), or 2′-3′ cyclic phosphate (2′,3′-cP).
(C) MALDI mass spectrometry spectra and masses of RNA fragments isolated from complexes in the absence (blue) or presence (red) of RelE.
(D) In vitro cleavage assay using 5′ ^32P-labeled mRNA substrates. • is the 25 nt unmodified mRNA; MAP has phosphorothioate linkages after A site codon positions 1 and 2; MAO, MAO2, and MAO3 are 2′-O-methylated at position 1, positions 1 + 2, or all three positions, respectively; and MAD contains a deoxyribose at position 1. The mRNAs were incubated with either T. thermophilus (T.th.) or E. coli (E.co.) 70S ribosomes, tRNA^fMet, and either RelE^wt or RelE^R81A/R45A (RelE^dm) as indicated for either 1 hr (lanes 1–16) or overnight (lanes 17 and 18). The size markers indicate the positions of the full-length (25 nt 3′-OH) and Trunc Asite (18 nt 3′-OH) RNAs and the 20 nt 2′-3′ cyclic phosphate cleavage product, which runs approximately 1 nt faster than the corresponding 3′-OH species.
See also Figure S3.
 
  The above figures are reprinted by permission from Cell Press: Cell (2009, 139, 1084-1095) copyright 2009.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23072885 M.Graille, and B.Séraphin (2012).
Surveillance pathways rescuing eukaryotic ribosomes lost in translation.
  Nat Rev Mol Cell Biol, 13, 727-735.  
  21253384 D.Kurita, A.Muto, and H.Himeno (2011).
tRNA/mRNA Mimicry by tmRNA and SmpB in Trans-Translation.
  J Nucleic Acids, 2011, 130581.  
21502523 K.S.Winther, and K.Gerdes (2011).
Enteric virulence associated protein VapC inhibits translation by cleavage of initiator tRNA.
  Proc Natl Acad Sci U S A, 108, 7403-7407.  
21166897 Q.Tan, N.Awano, and M.Inouye (2011).
YeeV is an Escherichia coli toxin that inhibits cell division by targeting the cytoskeleton proteins, FtsZ and MreB.
  Mol Microbiol, 79, 109-118.  
21315267 T.R.Blower, G.P.Salmond, and B.F.Luisi (2011).
Balancing at survival's edge: the structure and adaptive benefits of prokaryotic toxin-antitoxin partners.
  Curr Opin Struct Biol, 21, 109-118.  
21240270 T.R.Blower, X.Y.Pei, F.L.Short, P.C.Fineran, D.P.Humphreys, B.F.Luisi, and G.P.Salmond (2011).
A processed noncoding RNA regulates an altruistic bacterial antiviral system.
  Nat Struct Mol Biol, 18, 185-190.
PDB codes: 2xd0 2xdb
21448132 V.P.Pisareva, M.A.Skabkin, C.U.Hellen, T.V.Pestova, and A.V.Pisarev (2011).
Dissociation by Pelota, Hbs1 and ABCE1 of mammalian vacant 80S ribosomes and stalled elongation complexes.
  EMBO J, 30, 1804-1817.  
21323758 Y.Zhang, and M.Inouye (2011).
RatA (YfjG), an Escherichia coli toxin, inhibits 70S ribosome association to block translation initiation.
  Mol Microbiol, 79, 1418-1429.  
20487277 A.Fiebig, C.M.Castro Rojas, D.Siegal-Gaskins, and S.Crosson (2010).
Interaction specificity, toxicity and regulation of a paralogous set of ParE/RelE-family toxin-antitoxin systems.
  Mol Microbiol, 77, 236-251.  
20677831 C.Göbl, S.Kosol, T.Stockner, H.M.Rückert, and K.Zangger (2010).
Solution structure and membrane binding of the toxin fst of the par addiction module.
  Biochemistry, 49, 6567-6575.
PDB code: 2kv5
20852642 C.L.Ng, K.Lang, N.A.Meenan, A.Sharma, A.C.Kelley, C.Kleanthous, and V.Ramakrishnan (2010).
Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3.
  Nat Struct Mol Biol, 17, 1241-1246.
PDB codes: 2xfz 2xg0 2xg1 2xg2
20585658 C.Nieto, E.Sadowy, A.G.de la Campa, W.Hryniewicz, and M.Espinosa (2010).
The relBE2Spn toxin-antitoxin system of Streptococcus pneumoniae: role in antibiotic tolerance and functional conservation in clinical isolates.
  PLoS One, 5, e11289.  
20569269 E.Diago-Navarro, A.M.Hernandez-Arriaga, J.López-Villarejo, A.J.Muñoz-Gómez, M.B.Kamphuis, R.Boelens, M.Lemonnier, and R.Díaz-Orejas (2010).
parD toxin-antitoxin system of plasmid R1--basic contributions, biotechnological applications and relationships with closely-related toxin-antitoxin systems.
  FEBS J, 277, 3097-3117.  
20143871 K.M.Dalton, and S.Crosson (2010).
A conserved mode of protein recognition and binding in a ParD-ParE toxin-antitoxin complex.
  Biochemistry, 49, 2205-2215.
PDB code: 3kxe
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.