3zeb: Difference between revisions

Revision as of 05:44, 10 August 2022

A complex of GlpG with isocoumarin inhibitor covalently bonded to serine 201 and histidine 150

Structural highlights

3zeb is a 1 chain structure with sequence from Ecobd. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	BNG, CL, SV1
Activity:	Rhomboid protease, with EC number 3.4.21.105
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Publication Abstract from PubMed

Rhomboid proteases are evolutionary conserved intramembrane serine proteases. Because of their emerging role in many important biological pathways, rhomboids are potential drug targets. Unfortunately, few chemical tools are available for their study. Here, we describe a mass spectrometry-based assay to measure rhomboid substrate cleavage and inhibition. We have identified isocoumarin inhibitors and developed activity-based probes for rhomboid proteases. The probes can distinguish between active and inactive rhomboids due to covalent, reversible binding of the active-site serine and stable modification of a histidine residue. Finally, the structure of an isocoumarin-based inhibitor with Escherichia coli rhomboid GlpG uncovers an unusual mode of binding at the active site and suggests that the interactions between the 3-substituent on the isocoumarin inhibitor and hydrophobic residues on the protease reflect S' subsite binding. Overall, these probes represent valuable tools for rhomboid study, and the structural insights may facilitate future inhibitor design.

Activity-based probes for rhomboid proteases discovered in a mass spectrometry-based assay.,Vosyka O, Vinothkumar KR, Wolf EV, Brouwer AJ, Liskamp RM, Verhelst SH Proc Natl Acad Sci U S A. 2013 Jan 28. PMID:23359682^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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
↑ Vosyka O, Vinothkumar KR, Wolf EV, Brouwer AJ, Liskamp RM, Verhelst SH. Activity-based probes for rhomboid proteases discovered in a mass spectrometry-based assay. Proc Natl Acad Sci U S A. 2013 Jan 28. PMID:23359682 doi:https://dx.doi.org/10.1073/pnas.1215076110

Proteopedia Page Contributors and Editors (what is this?)

OCA

[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

[3] Vosyka O, Vinothkumar KR, Wolf EV, Brouwer AJ, Liskamp RM, Verhelst SH. Activity-based probes for rhomboid proteases discovered in a mass spectrometry-based assay. Proc Natl Acad Sci U S A. 2013 Jan 28. PMID:23359682 doi:https://dx.doi.org/10.1073/pnas.1215076110

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==A complex of GlpG with isocoumarin inhibitor covalently bonded to serine 201 and histidine 150==
-<StructureSection load='3zeb' size='340' side='right' caption='[[3zeb]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='3zeb' size='340' side='right'caption='[[3zeb]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3zeb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecobd Ecobd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZEB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZEB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3zeb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecobd Ecobd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZEB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SV1:2-PHENYLETHYL+2-(4-AZANYL-2-METHANOYL-PHENYL)ETHANOATE'>SV1</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SV1:2-PHENYLETHYL+2-(4-AZANYL-2-METHANOYL-PHENYL)ETHANOATE'>SV1</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Rhomboid_protease Rhomboid protease], with EC number [https://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=3zeb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zeb OCA], [http://pdbe.org/3zeb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3zeb RCSB], [http://www.ebi.ac.uk/pdbsum/3zeb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3zeb 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=3zeb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zeb OCA], [https://pdbe.org/3zeb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zeb RCSB], [https://www.ebi.ac.uk/pdbsum/3zeb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zeb ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GLPG_ECOLI GLPG_ECOLI]] Rhomboid-type serine protease that catalyzes intramembrane proteolysis.<ref>PMID:17099694</ref> <ref>PMID:16216077</ref>
+[[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 ==
@@ Line 27: / Line 27: @@
 </StructureSection>
 [[Category: Ecobd]]
+[[Category: Large Structures]]
 [[Category: Rhomboid protease]]
 [[Category: Brouwer, A J]]

3zeb: Difference between revisions

Revision as of 05:44, 10 August 2022

A complex of GlpG with isocoumarin inhibitor covalently bonded to serine 201 and histidine 150

Structural highlights

Function

Publication Abstract from PubMed

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References

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