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PDBsum entry 1x18

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protein dna_rna links
Structural protein/RNA PDB id
1x18
Jmol
Contents
Protein chains
231 a.a.* *
154 a.a.* *
119 a.a.* *
73 a.a.* *
292 a.a.* *
DNA/RNA
* Residue conservation analysis
* C-alpha coords only
PDB id:
1x18
Name: Structural protein/RNA
Title: Contact sites of era gtpase on the thermus thermophilus 30s
Structure: 5'-r(p Cp Gp Ap Up Gp Gp Cp Gp Ap Ap G)-3'. Chain: a. RNA (31-mer). Chain: b. 5'-r(p Up Up Cp Cp Cp Gp Gp Gp Cp Cp Up Gp Gp Gp P Gp C)-3'. Chain: c. 5'-r(p Up Gp Up Up Gp Gp Gp Up Up Ap Ap Gp Up Cp P Ap Ap Cp Gp Ap G)-3'.
Source: Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Authors: M.R.Sharma,C.Barat,R.K.Agrawal
Key ref:
M.R.Sharma et al. (2005). Interaction of Era with the 30S ribosomal subunit implications for 30S subunit assembly. Mol Cell, 18, 319-329. PubMed id: 15866174 DOI: 10.1016/j.molcel.2005.03.028
Date:
02-Apr-05     Release date:   17-May-05    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P80371  (RS2_THET8) -  30S ribosomal protein S2
Seq:
Struc:
256 a.a.
231 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  30S ribosomal protein S7
Seq:
Struc:
156 a.a.
154 a.a.
Protein chain
Pfam   ArchSchema ?
P80376  (RS11_THET8) -  30S ribosomal protein S11
Seq:
Struc:
129 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLQ0  (RS18_THET8) -  30S ribosomal protein S18
Seq:
Struc:
88 a.a.
73 a.a.*
Protein chain
Pfam   ArchSchema ?
C9R153  (C9R153_ECOD1) -  GTPase Era
Seq:
Struc:
301 a.a.
292 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   7 terms 
  Biological process     ribosome biogenesis   4 terms 
  Biochemical function     structural constituent of ribosome     8 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.molcel.2005.03.028 Mol Cell 18:319-329 (2005)
PubMed id: 15866174  
 
 
Interaction of Era with the 30S ribosomal subunit implications for 30S subunit assembly.
M.R.Sharma, C.Barat, D.N.Wilson, T.M.Booth, M.Kawazoe, C.Hori-Takemoto, M.Shirouzu, S.Yokoyama, P.Fucini, R.K.Agrawal.
 
  ABSTRACT  
 
Era (E. coliRas-like protein) is a highly conserved and essential GTPase in bacteria. It binds to the 16S ribosomal RNA (rRNA) of the small (30S) ribosomal subunit, and its depletion leads to accumulation of an unprocessed precursor of the 16S rRNA. We have obtained a three-dimensional cryo-electron microscopic map of the Thermus thermophilus 30S-Era complex. Era binds in the cleft between the head and platform of the 30S subunit and locks the subunit in a conformation that is not favorable for association with the large (50S) ribosomal subunit. The RNA binding KH motif present within the C-terminal domain of Era interacts with the conserved nucleotides in the 3' region of the 16S rRNA. Furthermore, Era makes contact with several assembly elements of the 30S subunit. These observations suggest a direct involvement of Era in the assembly and maturation of the 30S subunit.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Conformational Differences between Era bound and Unbound 30S Subunits and Effect of Era Binding on the Association with the 50S Subunit
Figure 4.
Figure 4. Interactions between the Helix-Turn-Helix Motif of the KH Domain of Era’s CTD and the 3′ Segment of the 16S rRNA
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2005, 18, 319-329) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21102555 S.Goto, S.Kato, T.Kimura, A.Muto, and H.Himeno (2011).
RsgA releases RbfA from 30S ribosome during a late stage of ribosome biosynthesis.
  EMBO J, 30, 104-114.  
20188109 A.E.Bunner, S.Nord, P.M.Wikström, and J.R.Williamson (2010).
The effect of ribosome assembly cofactors on in vitro 30S subunit reconstitution.
  J Mol Biol, 398, 1-7.  
21124459 A.H.Ratje, J.Loerke, A.Mikolajka, M.Brünner, P.W.Hildebrand, A.L.Starosta, A.Dönhöfer, S.R.Connell, P.Fucini, T.Mielke, P.C.Whitford, J.N.Onuchic, Y.Yu, K.Y.Sanbonmatsu, R.K.Hartmann, P.A.Penczek, D.N.Wilson, and C.M.Spahn (2010).
Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites.
  Nature, 468, 713-716.
PDB codes: 2xsy 2xtg 2xux 2xuy
21030658 A.M.Mulder, C.Yoshioka, A.H.Beck, A.E.Bunner, R.A.Milligan, C.S.Potter, B.Carragher, and J.R.Williamson (2010).
Visualizing ribosome biogenesis: parallel assembly pathways for the 30S subunit.
  Science, 330, 673-677.  
20419091 A.Neueder, S.Jakob, G.Pöll, J.Linnemann, R.Deutzmann, H.Tschochner, and P.Milkereit (2010).
A local role for the small ribosomal subunit primary binder rpS5 in final 18S rRNA processing in yeast.
  PLoS One, 5, e10194.  
20172997 J.Hwang, and M.Inouye (2010).
Interaction of an essential Escherichia coli GTPase, Der, with the 50S ribosome via the KH-like domain.
  J Bacteriol, 192, 2277-2283.  
20123128 K.W.Hung, Y.W.Chang, E.T.Eng, J.H.Chen, Y.C.Chen, Y.J.Sun, C.D.Hsiao, G.Dong, K.A.Spasov, V.M.Unger, and T.H.Huang (2010).
Structural fold, conservation and Fe(II) binding of the intracellular domain of prokaryote FeoB.
  J Struct Biol, 170, 501-512.
PDB codes: 2wia 2wib 2wic 3k53
19965869 M.R.Sharma, A.Dönhöfer, C.Barat, V.Marquez, P.P.Datta, P.Fucini, D.N.Wilson, and R.K.Agrawal (2010).
PSRP1 is not a ribosomal protein, but a ribosome-binding factor that is recycled by the ribosome-recycling factor (RRF) and elongation factor G (EF-G).
  J Biol Chem, 285, 4006-4014.  
20604745 S.Dennerlein, A.Rozanska, M.Wydro, Z.M.Chrzanowska-Lightowlers, and R.N.Lightowlers (2010).
Human ERAL1 is a mitochondrial RNA chaperone involved in the assembly of the 28S small mitochondrial ribosomal subunit.
  Biochem J, 430, 551-558.  
20453830 S.Granneman, E.Petfalski, A.Swiatkowska, and D.Tollervey (2010).
Cracking pre-40S ribosomal subunit structure by systematic analyses of RNA-protein cross-linking.
  EMBO J, 29, 2026-2036.  
20430825 T.Uchiumi, K.Ohgaki, M.Yagi, Y.Aoki, A.Sakai, S.Matsumoto, and D.Kang (2010).
ERAL1 is associated with mitochondrial ribosome and elimination of ERAL1 leads to mitochondrial dysfunction and growth retardation.
  Nucleic Acids Res, 38, 5554-5568.  
19258531 B.A.Maguire (2009).
Inhibition of bacterial ribosome assembly: a suitable drug target?
  Microbiol Mol Biol Rev, 73, 22-35.  
19706445 C.Tu, X.Zhou, J.E.Tropea, B.P.Austin, D.S.Waugh, D.L.Court, and X.Ji (2009).
Structure of ERA in complex with the 3' end of 16S rRNA: implications for ribosome biogenesis.
  Proc Natl Acad Sci U S A, 106, 14843-14848.
PDB codes: 3ieu 3iev
20021644 E.L.Cooper, J.García-Lara, and S.J.Foster (2009).
YsxC, an essential protein in Staphylococcus aureus crucial for ribosome assembly/stability.
  BMC Microbiol, 9, 266.  
19285505 H.Demirci, R.Belardinelli, E.Seri, S.T.Gregory, C.Gualerzi, A.E.Dahlberg, and G.Jogl (2009).
Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine.
  J Mol Biol, 388, 271-282.
PDB codes: 3fut 3fuu 3fuv 3fuw 3fux
19376708 K.Connolly, and G.Culver (2009).
Deconstructing ribosome construction.
  Trends Biochem Sci, 34, 256-263.  
19109926 N.Jain, N.Dhimole, A.R.Khan, D.De, S.K.Tomar, M.Sajish, D.Dutta, P.Parrack, and B.Prakash (2009).
E. coli HflX interacts with 50S ribosomal subunits in presence of nucleotides.
  Biochem Biophys Res Commun, 379, 201-205.  
19575570 R.A.Britton (2009).
Role of GTPases in bacterial ribosome assembly.
  Annu Rev Microbiol, 63, 155-176.  
18466225 B.Roy-Chaudhuri, N.Kirthi, T.Kelley, and G.M.Culver (2008).
Suppression of a cold-sensitive mutation in ribosomal protein S5 reveals a role for RimJ in ribosome biogenesis.
  Mol Microbiol, 68, 1547-1559.  
18223068 T.L.Campbell, and E.D.Brown (2008).
Genetic interaction screens with ordered overexpression and deletion clone sets implicate the Escherichia coli GTPase YjeQ in late ribosome biogenesis.
  J Bacteriol, 190, 2537-2545.  
18723622 Y.Feng, M.Li, H.Zhang, B.Zheng, H.Han, C.Wang, J.Yan, J.Tang, and G.F.Gao (2008).
Functional definition and global regulation of Zur, a zinc uptake regulator in a Streptococcus suis serotype 2 strain causing streptococcal toxic shock syndrome.
  J Bacteriol, 190, 7567-7578.  
17889642 D.Boehringer, and N.Ban (2007).
Trapping the ribosome to control gene expression.
  Cell, 130, 983-985.  
17890303 K.Inoue, S.Basu, and M.Inouye (2007).
Dissection of 16S rRNA methyltransferase (KsgA) function in Escherichia coli.
  J Bacteriol, 189, 8510-8518.  
17804668 M.Kaczanowska, and M.Rydén-Aulin (2007).
Ribosome biogenesis and the translation process in Escherichia coli.
  Microbiol Mol Biol Rev, 71, 477-494.  
17895579 P.C.Loh, T.Morimoto, Y.Matsuo, T.Oshima, and N.Ogasawara (2007).
The GTP-binding protein YqeH participates in biogenesis of the 30S ribosome subunit in Bacillus subtilis.
  Genes Genet Syst, 82, 281-289.  
17996707 P.P.Datta, D.N.Wilson, M.Kawazoe, N.K.Swami, T.Kaminishi, M.R.Sharma, T.M.Booth, C.Takemoto, P.Fucini, S.Yokoyama, and R.K.Agrawal (2007).
Structural aspects of RbfA action during small ribosomal subunit assembly.
  Mol Cell, 28, 434-445.
PDB codes: 2dyj 2r1c 2r1g
17349960 S.R.Connell, C.Takemoto, D.N.Wilson, H.Wang, K.Murayama, T.Terada, M.Shirouzu, M.Rost, M.Schüler, J.Giesebrecht, M.Dabrowski, T.Mielke, P.Fucini, S.Yokoyama, and C.M.Spahn (2007).
Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.
  Mol Cell, 25, 751-764.
PDB code: 2om7
17355865 T.Kaminishi, D.N.Wilson, C.Takemoto, J.M.Harms, M.Kawazoe, F.Schluenzen, K.Hanawa-Suetsugu, M.Shirouzu, P.Fucini, and S.Yokoyama (2007).
A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction.
  Structure, 15, 289-297.
PDB code: 2e5l
17651431 Y.Huang, B.Zhang, K.Dong, X.Zhang, L.Hou, T.Wang, N.Chen, and S.Chen (2007).
Up-regulation of yggG promotes the survival of Escherichia coli cells containing Era-1 mutant protein.
  FEMS Microbiol Lett, 275, 8.  
17613524 Y.Matsuo, T.Oshima, P.C.Loh, T.Morimoto, and N.Ogasawara (2007).
Isolation and characterization of a dominant negative mutant of Bacillus subtilis GTP-binding protein, YlqF, essential for biogenesis and maintenance of the 50 S ribosomal subunit.
  J Biol Chem, 282, 25270-25277.  
16998488 F.Schluenzen, C.Takemoto, D.N.Wilson, T.Kaminishi, J.M.Harms, K.Hanawa-Suetsugu, W.Szaflarski, M.Kawazoe, M.Shirouzu, M.Shirouzo, K.H.Nierhaus, S.Yokoyama, and P.Fucini (2006).
The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation.
  Nat Struct Mol Biol, 13, 871-878.
PDB code: 2hhh
16930151 J.Hwang, and M.Inouye (2006).
The tandem GTPase, Der, is essential for the biogenesis of 50S ribosomal subunits in Escherichia coli.
  Mol Microbiol, 61, 1660-1672.  
16997968 L.Schaefer, W.C.Uicker, C.Wicker-Planquart, A.E.Foucher, J.M.Jault, and R.A.Britton (2006).
Multiple GTPases participate in the assembly of the large ribosomal subunit in Bacillus subtilis.
  J Bacteriol, 188, 8252-8258.  
16894162 S.P.Muench, L.Xu, S.E.Sedelnikova, and D.W.Rice (2006).
The essential GTPase YphC displays a major domain rearrangement associated with nucleotide binding.
  Proc Natl Acad Sci U S A, 103, 12359-12364.
PDB code: 2hjg
16390447 W.C.Uicker, L.Schaefer, and R.A.Britton (2006).
The essential GTPase RbgA (YlqF) is required for 50S ribosome assembly in Bacillus subtilis.
  Mol Microbiol, 59, 528-540.  
16333325 E.D.Brown (2005).
Conserved P-loop GTPases of unknown function in bacteria: an emerging and vital ensemble in bacterial physiology.
  Biochem Cell Biol, 83, 738-746.  
16337596 P.P.Datta, M.R.Sharma, L.Qi, J.Frank, and R.K.Agrawal (2005).
Interaction of the G' domain of elongation factor G and the C-terminal domain of ribosomal protein L7/L12 during translocation as revealed by cryo-EM.
  Mol Cell, 20, 723-731.
PDB code: 2bcw
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.