6pj4: Difference between revisions

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<StructureSection load='6pj4' size='340' side='right'caption='[[6pj4]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='6pj4' size='340' side='right'caption='[[6pj4]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6pj4]] 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=6PJ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PJ4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[6pj4]] 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=6PJ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PJ4 FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5f5d|5f5d]]</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]] 2.3&#8491;</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6pj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pj4 OCA], [https://pdbe.org/6pj4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pj4 RCSB], [https://www.ebi.ac.uk/pdbsum/6pj4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pj4 ProSAT]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6pj4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pj4 OCA], [http://pdbe.org/6pj4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pj4 RCSB], [http://www.ebi.ac.uk/pdbsum/6pj4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pj4 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;">
== 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<ref>PMID:31570873</ref>
==See Also==
 
*[[Rhomboid protease|Rhomboid protease]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6pj4" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__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: Inhibitor complex]]
[[Category: Membrane protein]]
[[Category: Membrane protein-inhibitor complex]]

Latest revision as of 17:55, 13 March 2024

Time-resolved structural snapshot of proteolysis by GlpG inside the membraneTime-resolved structural snapshot of proteolysis by GlpG inside the membrane

Structural highlights

6pj4 is a 2 chain structure with sequence from Drosophila melanogaster and Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GLPG_ECOLI Rhomboid-type serine protease that catalyzes intramembrane proteolysis.[1] [2]

See Also

References

  1. ↑ 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
  2. ↑ 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

6pj4, resolution 2.30Å

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