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6j45

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Current revision (10:36, 27 March 2024) (edit) (undo)
 
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<SX load='6j45' size='340' side='right' viewer='molstar' caption='[[6j45]], [[Resolution|resolution]] 12.20&Aring;' scene=''>
<SX load='6j45' size='340' side='right' viewer='molstar' caption='[[6j45]], [[Resolution|resolution]] 12.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6j45]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J45 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6J45 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6j45]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_H591 Escherichia coli H591]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J45 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6J45 FirstGlance]. <br>
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</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 12.2&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6j45 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j45 OCA], [http://pdbe.org/6j45 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j45 RCSB], [http://www.ebi.ac.uk/pdbsum/6j45 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j45 ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6j45 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j45 OCA], [https://pdbe.org/6j45 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6j45 RCSB], [https://www.ebi.ac.uk/pdbsum/6j45 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6j45 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/F4VJS7_ECOLX F4VJS7_ECOLX]] 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/F4VAM2_ECOLX F4VAM2_ECOLX]] Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase.[HAMAP-Rule:MF_00303]
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[https://www.uniprot.org/uniprot/F4VJS7_ECOLX F4VJS7_ECOLX] 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]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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During protein biosynthesis in bacteria, one of the earliest events that a nascent polypeptide chain goes through is the co-translational enzymatic processing. The event includes two enzymatic pathways: deformylation of the N-terminal methionine by the enzyme peptide deformylase (PDF), followed by methionine excision catalyzed by methionine aminopeptidase (MetAP). During the enzymatic processing, the emerging nascent protein likely remains shielded by the ribosome-associated chaperone trigger factor. The ribosome tunnel exit serves as a stage for recruiting proteins involved in maturation processes of the nascent chain. Co-translational processing of nascent chains is a critical step for subsequent folding and functioning of mature proteins. Here, we present cryo-electron microscopy structures of Escherichia coli (E. coli) ribosome in complex with the nascent chain processing proteins. The structures reveal overlapping binding sites for PDF and MetAP when they bind individually at the tunnel exit site, where L22-L32 protein region provides primary anchoring sites for both proteins. In the absence of PDF, trigger factor can access ribosomal tunnel exit when MetAP occupies its primary binding site. Interestingly, however, in the presence of PDF, when MetAP's primary binding site is already engaged, MetAP has a remarkable ability to occupy an alternative binding site adjacent to PDF. Our study, thus, discloses an unexpected mechanism that MetAP adopts for context-specific ribosome association.
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Cryo-EM Structures Reveal Relocalization of MetAP in the Presence of Other Protein Biogenesis Factors at the Ribosomal Tunnel Exit.,Bhakta S, Akbar S, Sengupta J J Mol Biol. 2019 Mar 29;431(7):1426-1439. doi: 10.1016/j.jmb.2019.02.002. Epub, 2019 Feb 10. PMID:30753870<ref>PMID:30753870</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6j45" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</SX>
</SX>
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[[Category: Escherichia coli H591]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Peptide deformylase]]
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[[Category: Akbar S]]
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[[Category: Akbar, S]]
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[[Category: Bhakta S]]
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[[Category: Bhakta, S]]
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[[Category: Sengupta J]]
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[[Category: Sengupta, J]]
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[[Category: Chaperone]]
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[[Category: E. coli 70s ribosome]]
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[[Category: Polypeptide exit tunnel]]
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[[Category: Ppiase]]
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[[Category: Protein biogenesis]]
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[[Category: Ribosome]]
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[[Category: Trigger factor]]
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Current revision

Crystal structure of E. coli peptide deformylase enzyme and chaperone trigger factor fitted into the cryo-EM density map of the complex

6j45, resolution 12.20Å

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