3zot: Difference between revisions

Latest revision as of 11:08, 20 December 2023

Structure of E.coli rhomboid protease GlpG in complex with monobactam L29 (data set 2)

Structural highlights

3zot 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 2.399Å
Ligands:	BNG, CL, L6C
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 evolutionarily conserved serine proteases that cleave transmembrane proteins within the membrane. The increasing number of known rhomboid functions in prokaryotes and eukaryotes makes them attractive drug targets. Here, we describe structures of the Escherichia coli rhomboid GlpG in complex with beta-lactam inhibitors. The inhibitors form a single bond to the catalytic serine and the carbonyl oxygen of the inhibitor faces away from the oxyanion hole. The hydrophobic N-substituent of beta-lactam inhibitors points into a cavity within the enzyme, providing a structural explanation for the specificity of beta-lactams on rhomboid proteases. This same cavity probably represents the S2' substrate binding site of GlpG. We suggest that the structural changes in beta-lactam inhibitor binding reflect the state of the enzyme at an initial stage of substrate binding to the active site. The structural insights from these enzyme-inhibitor complexes provide a starting point for structure-based design for rhomboid inhibitors.

Structure of Rhomboid Protease in Complex with beta-Lactam Inhibitors Defines the S2' Cavity.,Vinothkumar KR, Pierrat OA, Large JM, Freeman M Structure. 2013 May 7. pii: S0969-2126(13)00117-2. doi:, 10.1016/j.str.2013.03.013. PMID:23665170^[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, Pierrat OA, Large JM, Freeman M. Structure of Rhomboid Protease in Complex with beta-Lactam Inhibitors Defines the S2' Cavity. Structure. 2013 May 7. pii: S0969-2126(13)00117-2. doi:, 10.1016/j.str.2013.03.013. PMID:23665170 doi:10.1016/j.str.2013.03.013

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, Pierrat OA, Large JM, Freeman M. Structure of Rhomboid Protease in Complex with beta-Lactam Inhibitors Defines the S2' Cavity. Structure. 2013 May 7. pii: S0969-2126(13)00117-2. doi:, 10.1016/j.str.2013.03.013. PMID:23665170 doi:10.1016/j.str.2013.03.013

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Structure of E.coli rhomboid protease GlpG in complex with monobactam L29 (data set 2)==
-<StructureSection load='3zot' size='340' side='right' caption='[[3zot]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='3zot' size='340' side='right'caption='[[3zot]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3zot]] 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=3ZOT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZOT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3zot]] 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=3ZOT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZOT 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=L6C:PHENYL+N-[(1R)-3-OXIDANYLIDENE-1-PHENYL-PROPYL]CARBAMATE'>L6C</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]] 2.399&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3zmh|3zmh]], [[3zmi|3zmi]], [[3zmj|3zmj]]</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=L6C:PHENYL+N-[(1R)-3-OXIDANYLIDENE-1-PHENYL-PROPYL]CARBAMATE'>L6C</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=3zot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zot OCA], [https://pdbe.org/3zot PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zot RCSB], [https://www.ebi.ac.uk/pdbsum/3zot PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zot 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=3zot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zot OCA], [http://pdbe.org/3zot PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3zot RCSB], [http://www.ebi.ac.uk/pdbsum/3zot PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3zot 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 26: @@
 __TOC__
 </StructureSection>
-[[Category: Ecobd]]
+[[Category: Large Structures]]
-[[Category: Rhomboid protease]]
+[[Category: Freeman M]]
-[[Category: Freeman, M]]
+[[Category: Large JM]]
-[[Category: Large, J M]]
+[[Category: Pierrat OA]]
-[[Category: Pierrat, O A]]
+[[Category: Vinothkumar KR]]
-[[Category: Vinothkumar, K R]]
-[[Category: Acyl enzyme]]
-[[Category: Antibiotic]]
-[[Category: Beta lactam]]
-[[Category: Hydrolase]]
-[[Category: Intra-membrane protease]]

3zot: Difference between revisions

Latest revision as of 11:08, 20 December 2023

Structure of E.coli rhomboid protease GlpG in complex with monobactam L29 (data set 2)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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