4hdd: Difference between revisions

Revision as of 08:11, 3 November 2022

Domain swapping in the cytoplasmic domain of the Escherichia coli rhomboid protease

Structural highlights

4hdd is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	ACT, MSE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Publication Abstract from PubMed

Rhomboids are membrane-embedded serine proteases that cleave membrane protein substrates. Escherichia coli rhomboid GlpG (ecGlpG) consists of an N-terminal cytoplasmic domain and a membrane domain containing the active site. We determined the crystal structure of the soluble cytoplasmic domain of ecGlpG at 1.35A resolution and examined whether this domain affected the catalytic activity of the enzyme. The structure revealed that the ecGlpG cytoplasmic domain exists as a dimer with extensive domain swapping between the two monomers. Domain-swapped dimers can be isolated from the full-length protein, suggesting that this is a physiologically relevant structure. An extensive steady-state kinetic analysis of the full-length ecGlpG and its membrane domain using soluble and transmembrane model protein substrates resulted in an unexpected conclusion: removal of the cytoplasmic domain does not alter the catalytic parameters for detergent-solubilized rhomboid for both substrates.

Domain swapping in the cytoplasmic domain of the Escherichia coli rhomboid protease.,Lazareno-Saez C, Arutyunova E, Coquelle N, Lemieux MJ J Mol Biol. 2013 Apr 12;425(7):1127-42. doi: 10.1016/j.jmb.2013.01.019. Epub 2013, Jan 23. PMID:23353827^[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
↑ Lazareno-Saez C, Arutyunova E, Coquelle N, Lemieux MJ. Domain swapping in the cytoplasmic domain of the Escherichia coli rhomboid protease. J Mol Biol. 2013 Apr 12;425(7):1127-42. doi: 10.1016/j.jmb.2013.01.019. Epub 2013, Jan 23. PMID:23353827 doi:10.1016/j.jmb.2013.01.019

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] Lazareno-Saez C, Arutyunova E, Coquelle N, Lemieux MJ. Domain swapping in the cytoplasmic domain of the Escherichia coli rhomboid protease. J Mol Biol. 2013 Apr 12;425(7):1127-42. doi: 10.1016/j.jmb.2013.01.019. Epub 2013, Jan 23. PMID:23353827 doi:10.1016/j.jmb.2013.01.019

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Domain swapping in the cytoplasmic domain of the Escherichia coli rhomboid protease==
-<StructureSection load='4hdd' size='340' side='right' caption='[[4hdd]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
+<StructureSection load='4hdd' size='340' side='right'caption='[[4hdd]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4hdd]] is a 1 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=4HDD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HDD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4hdd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HDD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4hdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hdd OCA], [https://pdbe.org/4hdd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hdd RCSB], [https://www.ebi.ac.uk/pdbsum/4hdd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hdd ProSAT]</span></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2lep|2lep]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b3424, glpG, JW5687 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=4hdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hdd OCA], [http://pdbe.org/4hdd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4hdd RCSB], [http://www.ebi.ac.uk/pdbsum/4hdd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4hdd 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 29: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Rhomboid protease]]
+[[Category: Large Structures]]
-[[Category: Arutyunova, E]]
+[[Category: Arutyunova E]]
-[[Category: Coquelle, N]]
+[[Category: Coquelle N]]
-[[Category: Lazareno-Saez, C]]
+[[Category: Lazareno-Saez C]]
-[[Category: Lemieux, M J]]
+[[Category: Lemieux MJ]]
-[[Category: Domain swapping]]
-[[Category: Hydrolase]]
-[[Category: Intramembrane protease]]
-[[Category: Membrane]]
-[[Category: Peptidase]]

4hdd: Difference between revisions

Revision as of 08:11, 3 November 2022

Domain swapping in the cytoplasmic domain of the Escherichia coli rhomboid protease

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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