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| | <SX load='6izi' size='340' side='right' viewer='molstar' caption='[[6izi]], [[Resolution|resolution]] 11.80Å' scene=''> | | <SX load='6izi' size='340' side='right' viewer='molstar' caption='[[6izi]], [[Resolution|resolution]] 11.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6izi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IZI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6IZI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6izi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IZI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IZI FirstGlance]. <br> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 11.8Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6izi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6izi OCA], [http://pdbe.org/6izi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6izi RCSB], [http://www.ebi.ac.uk/pdbsum/6izi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6izi 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=6izi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6izi OCA], [https://pdbe.org/6izi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6izi RCSB], [https://www.ebi.ac.uk/pdbsum/6izi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6izi ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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/MAP1_ECOLI MAP1_ECOLI]] Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed.[HAMAP-Rule:MF_01974]<ref>PMID:20521764</ref> <ref>PMID:3027045</ref> | + | [https://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] |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | 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.
| + | |
| | | | |
| - | 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>
| + | ==See Also== |
| - | | + | *[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]] |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 6izi" style="background-color:#fffaf0;"></div>
| + | |
| - | == References == | + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </SX> | | </SX> |
| | + | [[Category: Escherichia coli K-12]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Peptide deformylase]]
| + | [[Category: Akbar S]] |
| - | [[Category: Akbar, S]] | + | [[Category: Bhakta S]] |
| - | [[Category: Bhakta, S]] | + | [[Category: Sengupta J]] |
| - | [[Category: Sengupta, J]] | + | |
| - | [[Category: E. coli 70s ribosome]]
| + | |
| - | [[Category: Methionine aminopeptidase]]
| + | |
| - | [[Category: Polypeptide exit tunnel]]
| + | |
| - | [[Category: Protein biogenesis]]
| + | |
| - | [[Category: Ribosome]]
| + | |
