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| | ==Structure of the SecA-SecY complex with a translocating polypeptide substrate== | | ==Structure of the SecA-SecY complex with a translocating polypeptide substrate== |
| - | <StructureSection load='5eul' size='340' side='right' caption='[[5eul]], [[Resolution|resolution]] 3.70Å' scene=''> | + | <StructureSection load='5eul' size='340' side='right'caption='[[5eul]], [[Resolution|resolution]] 3.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5eul]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EUL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EUL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5eul]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168], [https://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans_NG80-2 Geobacillus thermodenitrificans NG80-2], [https://en.wikipedia.org/wiki/Vicugna_pacos Vicugna pacos] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EUL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EUL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TBR:HEXATANTALUM+DODECABROMIDE'>TBR</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]] 3.7Å</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=5eul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eul OCA], [http://pdbe.org/5eul PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eul RCSB], [http://www.ebi.ac.uk/pdbsum/5eul PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5eul ProSAT]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <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=5eul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eul OCA], [https://pdbe.org/5eul PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5eul RCSB], [https://www.ebi.ac.uk/pdbsum/5eul PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5eul ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SECA_BACSU SECA_BACSU]] Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane (By similarity).[HAMAP-Rule:MF_01382] [[http://www.uniprot.org/uniprot/A4IJK8_GEOTN A4IJK8_GEOTN]] The central subunit of the protein translocation channel SecYEG. Consists of two halves formed by TMs 1-5 and 6-10. These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7, and are clamped together by SecE at the back. The channel is closed by both a pore ring composed of hydrophobic SecY resides and a short helix (helix 2A) on the extracellular side of the membrane which forms a plug. The plug probably moves laterally to allow the channel to open. The ring and the pore may move independently.[HAMAP-Rule:MF_01465][RuleBase:RU000537] | + | [https://www.uniprot.org/uniprot/SECA_BACSU SECA_BACSU] Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane (By similarity).[HAMAP-Rule:MF_01382] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 5eul" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5eul" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Preprotein translocase 3D structures|Preprotein translocase 3D structures]] |
| | + | *[[SecA|SecA]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ingram, J]] | + | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| - | [[Category: Li, L]] | + | [[Category: Geobacillus thermodenitrificans NG80-2]] |
| - | [[Category: Ling, J]] | + | [[Category: Large Structures]] |
| - | [[Category: Park, E]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Ploegh, H]] | + | [[Category: Vicugna pacos]] |
| - | [[Category: Rapoport, T A]] | + | [[Category: Ingram J]] |
| - | [[Category: Atpase]] | + | [[Category: Li L]] |
| - | [[Category: Channel]] | + | [[Category: Ling J]] |
| - | [[Category: Protein transport]] | + | [[Category: Park E]] |
| - | [[Category: Seca]] | + | [[Category: Ploegh H]] |
| - | [[Category: Secy]] | + | [[Category: Rapoport TA]] |
| Structural highlights
5eul is a 4 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168, Geobacillus thermodenitrificans NG80-2, Vicugna pacos and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 3.7Å |
| Ligands: | , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
SECA_BACSU Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane (By similarity).[HAMAP-Rule:MF_01382]
Publication Abstract from PubMed
Hydrophobic signal sequences target secretory polypeptides to a protein-conducting channel formed by a heterotrimeric membrane protein complex, the prokaryotic SecY or eukaryotic Sec61 complex. How signal sequences are recognized is poorly understood, particularly because they are diverse in sequence and length. Structures of the inactive channel show that the largest subunit, SecY or Sec61alpha, consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membrane and a lateral gate that faces lipid. The cytoplasmic funnel is empty, while the extracellular funnel is filled with a plug domain. In bacteria, the SecY channel associates with the translating ribosome in co-translational translocation, and with the SecA ATPase in post-translational translocation. How a translocating polypeptide inserts into the channel is uncertain, as cryo-electron microscopy structures of the active channel have a relatively low resolution (~10 A) or are of insufficient quality. Here we report a crystal structure of the active channel, assembled from SecY complex, the SecA ATPase, and a segment of a secretory protein fused into SecA. The translocating protein segment inserts into the channel as a loop, displacing the plug domain. The hydrophobic core of the signal sequence forms a helix that sits in a groove outside the lateral gate, while the following polypeptide segment intercalates into the gate. The carboxy (C)-terminal section of the polypeptide loop is located in the channel, surrounded by residues of the pore ring. Thus, during translocation, the hydrophobic segments of signal sequences, and probably bilayer-spanning domains of nascent membrane proteins, exit the lateral gate and dock at a specific site that faces the lipid phase.
Crystal structure of a substrate-engaged SecY protein-translocation channel.,Li L, Park E, Ling J, Ingram J, Ploegh H, Rapoport TA Nature. 2016 Mar 17;531(7594):395-9. doi: 10.1038/nature17163. Epub 2016 Mar 7. PMID:26950603[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Li L, Park E, Ling J, Ingram J, Ploegh H, Rapoport TA. Crystal structure of a substrate-engaged SecY protein-translocation channel. Nature. 2016 Mar 17;531(7594):395-9. doi: 10.1038/nature17163. Epub 2016 Mar 7. PMID:26950603 doi:http://dx.doi.org/10.1038/nature17163
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