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| | <StructureSection load='6pjr' size='340' side='right'caption='[[6pjr]], [[Resolution|resolution]] 2.40Å' scene=''> | | <StructureSection load='6pjr' size='340' side='right'caption='[[6pjr]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6pjr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PJR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PJR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6pjr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster] and [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PJR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PJR FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2.4Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">glpG, APT88_21985, SK83_00858 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Rhomboid_protease Rhomboid protease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.105 3.4.21.105] </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=6pjr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pjr OCA], [https://pdbe.org/6pjr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pjr RCSB], [https://www.ebi.ac.uk/pdbsum/6pjr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pjr ProSAT]</span></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=6pjr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pjr OCA], [http://pdbe.org/6pjr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pjr RCSB], [http://www.ebi.ac.uk/pdbsum/6pjr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pjr ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A0A0J2E248_ECOLX A0A0J2E248_ECOLX]] Rhomboid-type serine protease that catalyzes intramembrane proteolysis.[HAMAP-Rule:MF_01594] | + | [https://www.uniprot.org/uniprot/GLPG_ECOLI GLPG_ECOLI] Rhomboid-type serine protease that catalyzes intramembrane proteolysis.<ref>PMID:17099694</ref> <ref>PMID:16216077</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Drosophila melanogaster]] |
| | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Rhomboid protease]]
| + | [[Category: Cho S]] |
| - | [[Category: Cho, S]] | + | [[Category: Urban S]] |
| - | [[Category: Urban, S]] | + | |
| - | [[Category: Membrane protein]]
| + | |
| - | [[Category: Membrane protein-inhibitor complex]]
| + | |
| - | [[Category: Substrate complex]]
| + | |
| Structural highlights
Function
GLPG_ECOLI Rhomboid-type serine protease that catalyzes intramembrane proteolysis.[1] [2]
Publication Abstract from PubMed
Protein cleavage inside the cell membrane triggers various pathophysiological signaling pathways, but the mechanism of catalysis is poorly understood. We solved ten structures of the Escherichia coli rhomboid protease in a bicelle membrane undergoing time-resolved steps that encompass the entire proteolytic reaction on a transmembrane substrate and an aldehyde inhibitor. Extensive gate opening accompanied substrate, but not inhibitor, binding, revealing that substrates and inhibitors take different paths to the active site. Catalysis unexpectedly commenced with, and was guided through subsequent catalytic steps by, motions of an extracellular loop, with local contributions from active site residues. We even captured the elusive tetrahedral intermediate that is uncleaved but covalently attached to the catalytic serine, about which the substrate was forced to bend dramatically. This unexpectedly stable intermediate indicates rhomboid catalysis uses an unprecedented reaction coordinate that may involve mechanically stressing the peptide bond, and could be selectively targeted by inhibitors.
Ten catalytic snapshots of rhomboid intramembrane proteolysis from gate opening to peptide release.,Cho S, Baker RP, Ji M, Urban S Nat Struct Mol Biol. 2019 Sep 30. pii: 10.1038/s41594-019-0296-9. doi:, 10.1038/s41594-019-0296-9. PMID:31570873[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Wu Z, Yan N, Feng L, Oberstein A, Yan H, Baker RP, Gu L, Jeffrey PD, Urban S, Shi Y. Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry. Nat Struct Mol Biol. 2006 Dec;13(12):1084-91. Epub 2006 Nov 10. PMID:17099694 doi:10.1038/nsmb1179
- ↑ Maegawa S, Ito K, Akiyama Y. Proteolytic action of GlpG, a rhomboid protease in the Escherichia coli cytoplasmic membrane. Biochemistry. 2005 Oct 18;44(41):13543-52. PMID:16216077 doi:10.1021/bi051363k
- ↑ Cho S, Baker RP, Ji M, Urban S. Ten catalytic snapshots of rhomboid intramembrane proteolysis from gate opening to peptide release. Nat Struct Mol Biol. 2019 Sep 30. pii: 10.1038/s41594-019-0296-9. doi:, 10.1038/s41594-019-0296-9. PMID:31570873 doi:http://dx.doi.org/10.1038/s41594-019-0296-9
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