PDBsum entry: 2vho

Ribosome

PDB id: 2vho

Contents

Protein chains

219 a.a. *

207 a.a. *

205 a.a. *

151 a.a. *

101 a.a. *

151 a.a. *

129 a.a. *

127 a.a. *

99 a.a. *

117 a.a. *

123 a.a. *

115 a.a. *

96 a.a. *

88 a.a. *

82 a.a. *

81 a.a. *

56 a.a. *

80 a.a. *

85 a.a. *

52 a.a. *

DNA/RNA

Metals

_MG ×60

Waters ×298

* Residue conservation analysis

PDB id:

2vho

Name:

Ribosome

Title:

Structure of pdf binding helix in complex with the ribosome (part 3 of 4)

Structure:

16s ribosomal RNA. Chain: a. 30s ribosomal protein s3. Chain: c. Fragment: residues 2-233. 30s ribosomal protein s4. Chain: d. Fragment: residues 2-206. 30s ribosomal protein s5.

Source:

Escherichia coli. Organism_taxid: 562. Strain: mre600. Strain: mre600

Resolution:

3.74Å R-factor: 0.259 R-free: 0.323

Authors:

R.Bingel-Erlenmeyer,R.Kohler,G.Kramer,A.Sandikci,S.Antolic, T.Maier,C.Schaffitzel,B.Wiedmann,B.Bukau,N.Ban

Key ref:

R.Bingel-Erlenmeyer et al. (2008). A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing. Nature, 452, 108-111. PubMed id: 18288106 DOI: 10.1038/nature06683

Date:

22-Nov-07 Release date: 26-Feb-08

Protein chain

P0A7V0  (RS2_ECOLI) -  30S ribosomal protein S2

Seq: 241 a.a.

Struc: 219 a.a.

Protein chain

P0A7V3  (RS3_ECOLI) -  30S ribosomal protein S3

Seq: 233 a.a.

Struc: 207 a.a.

Protein chain

Q0TCG5  (RS4_ECOL5) -  30S ribosomal protein S4

Seq: 206 a.a.

Struc: 205 a.a.

Protein chain

P0A7W1  (RS5_ECOLI) -  30S ribosomal protein S5

Seq: 167 a.a.

Struc: 151 a.a.

Protein chain

P02358  (RS6_ECOLI) -  30S ribosomal protein S6

Seq: 135 a.a.

Struc: 101 a.a.

Protein chain

P02359  (RS7_ECOLI) -  30S ribosomal protein S7

Seq: 179 a.a.

Struc: 151 a.a.

Protein chain

P0A7W7  (RS8_ECOLI) -  30S ribosomal protein S8

Seq: 130 a.a.

Struc: 129 a.a.

Protein chain

P0A7X3  (RS9_ECOLI) -  30S ribosomal protein S9

Seq: 130 a.a.

Struc: 127 a.a.

Protein chain

P0A7R5  (RS10_ECOLI) -  30S ribosomal protein S10

Seq: 103 a.a.

Struc: 99 a.a.

Protein chain

P0A7R9  (RS11_ECOLI) -  30S ribosomal protein S11

Seq: 129 a.a.

Struc: 117 a.a.

Protein chain

P0A7S3  (RS12_ECOLI) -  30S ribosomal protein S12

Seq: 124 a.a.

Struc: 123 a.a.

Protein chain

P0A7S9  (RS13_ECOLI) -  30S ribosomal protein S13

Seq: 118 a.a.

Struc: 115 a.a.

Protein chain

P0AG59  (RS14_ECOLI) -  30S ribosomal protein S14

Seq: 101 a.a.

Struc: 96 a.a.

Protein chain

Q8X9M2  (RS15_ECO57) -  30S ribosomal protein S15

Seq: 89 a.a.

Struc: 88 a.a.

Protein chain

P0A7T3  (RS16_ECOLI) -  30S ribosomal protein S16

Seq: 82 a.a.

Struc: 82 a.a.

Protein chain

Q1R616  (RS17_ECOUT) -  30S ribosomal protein S17

Seq: 84 a.a.

Struc: 81 a.a.

Protein chain

P0A7T7  (RS18_ECOLI) -  30S ribosomal protein S18

Seq: 75 a.a.

Struc: 56 a.a.

Protein chain

Q0TCE5  (RS19_ECOL5) -  30S ribosomal protein S19

Seq: 92 a.a.

Struc: 80 a.a.

Protein chain

Q0TLW7  (RS20_ECOL5) -  30S ribosomal protein S20

Seq: 87 a.a.

Struc: 85 a.a.

Protein chain

P68679  (RS21_ECOLI) -  30S ribosomal protein S21

Seq: 71 a.a.

Struc: 52 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (5 terms)
• Biological process: response to antibiotic (7 terms)
• Biochemical function: structural constituent of ribosome (12 terms)

DOI no: 10.1038/nature06683

Nature 452:108-111 (2008)

PubMed id: 18288106

A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing.

R.Bingel-Erlenmeyer, R.Kohler, G.Kramer, A.Sandikci, S.Antolić, T.Maier, C.Schaffitzel, B.Wiedmann, B.Bukau, N.Ban.

ABSTRACT

Messenger-RNA-directed protein synthesis is accomplished by the ribosome. In eubacteria, this complex process is initiated by a specialized transfer RNA charged with formylmethionine (tRNA(fMet)). The amino-terminal formylated methionine of all bacterial nascent polypeptides blocks the reactive amino group to prevent unfavourable side-reactions and to enhance the efficiency of translation initiation. The first enzymatic factor that processes nascent chains is peptide deformylase (PDF); it removes this formyl group as polypeptides emerge from the ribosomal tunnel and before the newly synthesized proteins can adopt their native fold, which may bury the N terminus. Next, the N-terminal methionine is excised by methionine aminopeptidase. Bacterial PDFs are metalloproteases sharing a conserved N-terminal catalytic domain. All Gram-negative bacteria, including Escherichia coli, possess class-1 PDFs characterized by a carboxy-terminal alpha-helical extension. Studies focusing on PDF as a target for antibacterial drugs have not revealed the mechanism of its co-translational mode of action despite indications in early work that it co-purifies with ribosomes. Here we provide biochemical evidence that E. coli PDF interacts directly with the ribosome via its C-terminal extension. Crystallographic analysis of the complex between the ribosome-interacting helix of PDF and the ribosome at 3.7 A resolution reveals that the enzyme orients its active site towards the ribosomal tunnel exit for efficient co-translational processing of emerging nascent chains. Furthermore, we have found that the interaction of PDF with the ribosome enhances cell viability. These results provide the structural basis for understanding the coupling between protein synthesis and enzymatic processing of nascent chains, and offer insights into the interplay of PDF with the ribosome-associated chaperone trigger factor.

Selected figure(s)

Figure 1.
Figure 1: PDF specifically binds to the 50S ribosomal subunit via its C-terminal helix. a, 50S ribosome sedimentation assay containing 1 M of non-translating E. coli 50S ribosomes and different concentrations of Strep-tagged PDF. A positive control (pos.) was loaded as a reference (for details see Methods). b, Comparison of the interaction of 5 M Strep-PDF with 1 M of 30S, 50S and 70S, respectively, using the same method as in a. c, PDF constructs used in the ribosome sedimentation assays to determine the ribosome-binding region of PDF. d, Ribosome sedimentation assay as in a, using different Strep-tagged PDF constructs to dissect the two PDF domains for ribosome binding.

Figure 4.
Figure 4: Model for the concerted mechanism of PDF and trigger factor. a, PDF (catalytic domain in dark red, C-terminal helix in red, substrate shown as yellow spheres) superimposed onto the ribosome-bound helix. A star marks the exit tunnel. b, View through the cradle of the trigger factor (in blue, TF, active site residues of the peptidyl-prolyl-cis/trans-isomerase (PPIase) in orange spheres) across the exit tunnel towards the active site of PDF (colouring as in a). An arrow indicates the route from the exit tunnel to the active site of PDF. c, Footprints of PDF (red) and trigger factor (blue, TF) on the ribosome, from crystallographic data. Filled areas indicate binding sites for PDF and trigger factor, projections are shown as outlines in the same colours (view onto the exit tunnel). d, A schematic of the trigger factor (blue, TF) with its two arms and ribosome-binding domain (contact point) forming a hydrophobic nascent chain folding and processing chamber and functioning as a router, viewed from the ribosomal tunnel. Methionine-aminopeptidase (MAP) and PDF close the lateral openings of the trigger factor.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 452, 108-111) copyright 2008.

Figures were selected by the author.