4v5b: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<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>
<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" id="ligandDat"><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]] 3.74&#8491;</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>
<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>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/RL34_ECOLI RL34_ECOLI]  
[https://www.uniprot.org/uniprot/RL34_ECOLI RL34_ECOLI]  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4v5b" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ribosome 3D structures|Ribosome 3D structures]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
== References ==
<references/>
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