2xtv: Difference between revisions

Latest revision as of 08:03, 23 August 2023

Structure of E.coli rhomboid protease GlpG, active site mutant, S201T, orthorhombic crystal form

Structural highlights

2xtv is a 1 chain structure with sequence from Escherichia coli BL21(DE3). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:	MC3
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Publication Abstract from PubMed

Structures of the prokaryotic homologue of rhomboid proteases reveal a core of six transmembrane helices, with the active-site residues residing in a hydrophilic cavity. The native environment of rhomboid protease is a lipid bilayer, yet all the structures determined thus far are in a nonnative detergent environment. There remains a possibility of structural artefacts arising from the use of detergents. In an attempt to address the effect of detergents on the structure of rhomboid protease, crystals of GlpG, an Escherichia coli rhomboid protease in a lipid environment, were obtained using two alternative approaches. The structure of GlpG refined to 1. 7-A resolution was obtained from crystals grown in the presence of lipid bicelles. This structure reveals well-ordered and partly ordered lipid molecules forming an annulus around the protein. Lipid molecules adapt to the surface features of protein and arrange such that they match the hydrophobic thickness of GlpG. Virtually identical two-dimensional crystals were also obtained after detergent removal by dialysis. A comparison of an equivalent structure determined in a completely delipidated detergent environment provides insights on how detergent substitutes for lipid. A detergent molecule is also observed close to the active site, helping to postulate a model for substrate binding and hydrolysis in rhomboids.

Structure of rhomboid protease in a lipid environment.,Vinothkumar KR J Mol Biol. 2011 Mar 25;407(2):232-47. Epub 2011 Jan 19. PMID:21256137^[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
↑ Vinothkumar KR. Structure of rhomboid protease in a lipid environment. J Mol Biol. 2011 Mar 25;407(2):232-47. Epub 2011 Jan 19. PMID:21256137 doi:10.1016/j.jmb.2011.01.029

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] Vinothkumar KR. Structure of rhomboid protease in a lipid environment. J Mol Biol. 2011 Mar 25;407(2):232-47. Epub 2011 Jan 19. PMID:21256137 doi:10.1016/j.jmb.2011.01.029

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='2xtv' size='340' side='right'caption='[[2xtv]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2xtv]] 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=2XTV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XTV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2xtv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XTV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XTV FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MC3:1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE'>MC3</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]] 1.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ic8|2ic8]], [[2xov|2xov]], [[2xtu|2xtu]], [[2xow|2xow]], [[2irv|2irv]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MC3:1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE'>MC3</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=2xtv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xtv OCA], [https://pdbe.org/2xtv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xtv RCSB], [https://www.ebi.ac.uk/pdbsum/2xtv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xtv ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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>
+[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 26: @@
 __TOC__
 </StructureSection>
-[[Category: Ecobd]]
 [[Category: Large Structures]]
-[[Category: Rhomboid protease]]
+[[Category: Vinothkumar KR]]
-[[Category: Vinothkumar, K R]]
-[[Category: Hydrolase]]
-[[Category: Membrane protein]]

2xtv: Difference between revisions

Latest revision as of 08:03, 23 August 2023

Structure of E.coli rhomboid protease GlpG, active site mutant, S201T, orthorhombic crystal form

Structural highlights

Function

Publication Abstract from PubMed

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References

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