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| {{Large structure}}
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| ==Structure of PDF binding helix in complex with the ribosome== | | ==Structure of PDF binding helix in complex with the ribosome.== |
| <StructureSection load='4v5b' size='340' side='right' caption='[[4v5b]], [[Resolution|resolution]] 3.74Å' scene=''> | | <StructureSection load='4v5b' size='340' side='right'caption='[[4v5b]], [[Resolution|resolution]] 3.74Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[4v5b]] is a 105 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes and combines the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vhm 2vhm], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vhn 2vhn], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vho 2vho] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vhp 2vhp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V5B FirstGlance]. <br> | | <table><tr><td colspan='2'>[[4v5b]] is a 19 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vhm 2vhm], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vhn 2vhn], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vho 2vho] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vhp 2vhp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V5B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V5B FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.74Å</td></tr> |
| <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4v5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v5b OCA], [http://pdbe.org/4v5b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v5b RCSB], [http://www.ebi.ac.uk/pdbsum/4v5b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v5b ProSAT]</span></td></tr> | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4v5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v5b OCA], [https://pdbe.org/4v5b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v5b RCSB], [https://www.ebi.ac.uk/pdbsum/4v5b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v5b ProSAT]</span></td></tr> |
| </table> | | </table> |
| {{Large structure}}
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| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/RL31_ECO57 RL31_ECO57]] Binds the 23S rRNA. [[http://www.uniprot.org/uniprot/RL18_ECOLI RL18_ECOLI]] This is one of the proteins that mediates the attachment of the 5S rRNA subcomplex onto the large ribosomal subunit where it forms part of the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.<ref>PMID:353728</ref> [[http://www.uniprot.org/uniprot/RL23_ECOUT RL23_ECOUT]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RL15_ECOLI RL15_ECOLI]] This protein binds the 5S rRNA. It is required for the late stages of subunit assembly, and is essential for 5S rRNA assembly onto the ribosome.[HAMAP-Rule:MF_01341_B] [[http://www.uniprot.org/uniprot/RL13_ECOUT RL13_ECOUT]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly (By similarity). [[http://www.uniprot.org/uniprot/RS12_ECOLI RS12_ECOLI]] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403_B] Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_00403_B] Cryo-EM studies suggest that S12 contacts the EF-Tu bound tRNA in the A-site during codon-recognition. This contact is most likely broken as the aminoacyl-tRNA moves into the peptidyl transferase center in the 50S subunit.[HAMAP-Rule:MF_00403_B] [[http://www.uniprot.org/uniprot/RL24_ECO57 RL24_ECO57]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01326] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/RL3_ECOL6 RL3_ECOL6]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit. [[http://www.uniprot.org/uniprot/RS3_ECOL6 RS3_ECOL6]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity). [[http://www.uniprot.org/uniprot/RL4_ECO57 RL4_ECO57]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01328] Protein L4 is a both a transcriptional repressor and a translational repressor protein. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader. L4 controls the translation of the S10 operon by binding to its mRNA (By similarity). Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/RS16_ECOLI RS16_ECOLI]] In addition to being a ribosomal protein, S16 also has a cation-dependent endonuclease activity.<ref>PMID:8730873</ref> In-frame fusions with the ribosome maturation factor rimM suppress mutations in the latter (probably due to increased rimM expression) and are found in translationally active 70S ribosomes.<ref>PMID:8730873</ref> [[http://www.uniprot.org/uniprot/RS18_ECOLI RS18_ECOLI]] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit.[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/RS7_ECOL6 RS7_ECOL6]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA.[HAMAP-Rule:MF_00480] [[http://www.uniprot.org/uniprot/RS9_ECOLI RS9_ECOLI]] The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs. Mutations that decrease this affinity are suppressed in the 70S ribosome.<ref>PMID:15308780</ref> [[http://www.uniprot.org/uniprot/RL5_ECO57 RL5_ECO57]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333] [[http://www.uniprot.org/uniprot/RL11_ECOL6 RL11_ECOL6]] Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors.[HAMAP-Rule:MF_00736] [[http://www.uniprot.org/uniprot/RS20_ECOL5 RS20_ECOL5]] Binds directly to 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS13_ECO57 RS13_ECO57]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the E.coli 70S ribosome in the initiation state it has been modeled to contact the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; bridge B1a is broken in the model with bound EF-G, while the protein-protein contacts between S13 and L5 in B1b change. Contacts the tRNAs in the A and P sites (By similarity). [[http://www.uniprot.org/uniprot/RL16_ECOLI RL16_ECOLI]] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/RL14_ECOUT RL14_ECOUT]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome (By similarity). [[http://www.uniprot.org/uniprot/RL29_ECOL6 RL29_ECOL6]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. [[http://www.uniprot.org/uniprot/RL22_ECOL6 RL22_ECOL6]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome. [[http://www.uniprot.org/uniprot/RL25_ECOLI RL25_ECOLI]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [[http://www.uniprot.org/uniprot/RS8_ECOK1 RS8_ECOK1]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RL9_ECOLI RL9_ECOLI]] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/RS17_ECOUT RS17_ECOUT]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RL21_ECOL5 RL21_ECOL5]] This protein binds to 23S rRNA in the presence of protein L20 (By similarity). [[http://www.uniprot.org/uniprot/RL19_ECOLI RL19_ECOLI]] This protein is located at the 30S-50S ribosomal subunit interface. In the 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit forming part of bridges B6 and B8. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA. The protein conformation is quite different between the 50S and 70S structures, which may be necessary for translocation.[HAMAP-Rule:MF_00402] [[http://www.uniprot.org/uniprot/RS10_ECOLI RS10_ECOLI]] Involved in the binding of tRNA to the ribosomes.[HAMAP-Rule:MF_00508] [[http://www.uniprot.org/uniprot/RS14_ECOLI RS14_ECOLI]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site.[HAMAP-Rule:MF_00537] [[http://www.uniprot.org/uniprot/RL20_ECOLI RL20_ECOLI]] One of the primary rRNA binding proteins, it binds close to the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/RL6_ECO57 RL6_ECO57]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center (By similarity). [[http://www.uniprot.org/uniprot/DEF_ECOLI DEF_ECOLI]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163] [[http://www.uniprot.org/uniprot/RS4_ECOL5 RS4_ECOL5]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit (By similarity). With S5 and S12 plays an important role in translational accuracy (By similarity). [[http://www.uniprot.org/uniprot/RL2_ECO57 RL2_ECO57]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.[HAMAP-Rule:MF_01320] [[http://www.uniprot.org/uniprot/RS19_ECOL5 RS19_ECOL5]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS15_ECO57 RS15_ECO57]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA (By similarity). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS6_ECOL6 RS6_ECOL6]] Binds together with S18 to 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RS5_ECOLI RS5_ECOLI]] With S4 and S12 plays an important role in translational accuracy. Many suppressors of streptomycin-dependent mutants of protein S12 are found in this protein, some but not all of which decrease translational accuracy (ram, ribosomal ambiguity mutations).<ref>PMID:15652481</ref> Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.<ref>PMID:15652481</ref> The physical location of this protein suggests it may also play a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp.<ref>PMID:15652481</ref> [[http://www.uniprot.org/uniprot/RS11_ECOK1 RS11_ECOK1]] Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome (By similarity). | | [https://www.uniprot.org/uniprot/RL34_ECOLI RL34_ECOLI] |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| 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.
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| A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing.,Bingel-Erlenmeyer R, Kohler R, Kramer G, Sandikci A, Antolic S, Maier T, Schaffitzel C, Wiedmann B, Bukau B, Ban N Nature. 2008 Mar 6;452(7183):108-11. Epub 2008 Feb 20. PMID:18288106<ref>PMID:18288106</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 4v5b" style="background-color:#fffaf0;"></div>
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| ==See Also== | | ==See Also== |
| *[[Ribosome 3D structures|Ribosome 3D structures]] | | *[[Ribosome 3D structures|Ribosome 3D structures]] |
| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| [[Category: Antolic, S]] | | [[Category: Large Structures]] |
| [[Category: Ban, N]] | | [[Category: Antolic S]] |
| [[Category: Bingel-Erlenmeyer, R]] | | [[Category: Ban N]] |
| [[Category: Bukau, B]] | | [[Category: Bingel-Erlenmeyer R]] |
| [[Category: Kohler, R]] | | [[Category: Bukau B]] |
| [[Category: Kramer, G]] | | [[Category: Kohler R]] |
| [[Category: Maier, T]] | | [[Category: Kramer G]] |
| [[Category: Sandikci, A]] | | [[Category: Maier T]] |
| [[Category: Schaffitzel, C]] | | [[Category: Sandikci A]] |
| [[Category: Wiedmann, B]] | | [[Category: Schaffitzel C]] |
| [[Category: 50s ribosomal subunit]]
| | [[Category: Wiedmann B]] |
| [[Category: Antibiotic resistance]]
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| [[Category: Nascent chain processing]]
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| [[Category: Peptide deformylase]]
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| [[Category: Protein biosynthesis]]
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| [[Category: Ribonucleoprotein]]
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| [[Category: Ribosomal protein]]
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| [[Category: Ribosome]]
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| [[Category: Rna-binding]]
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| [[Category: Rna-protein complex]]
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| [[Category: Translation]]
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| [[Category: Translation regulation]]
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| [[Category: Trna binding]]
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