2vdd: Difference between revisions

Latest revision as of 15:16, 13 December 2023

Crystal Structure of the Open State of TolC Outer Membrane Component of Mutlidrug Efflux Pumps

Structural highlights

2vdd is a 3 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.3Å
Ligands:	CL, K
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TOLC_ECOLI Outer membrane channel, which is required for the function of several efflux systems such as AcrAB-TolC, AcrEF-TolC, EmrAB-TolC and MacAB-TolC. These systems are involved in export of antibiotics and other toxic compounds from the cell. TolC is also involved in import of colicin E1 into the cells.^[1] ^[2] ^[3] ^[4] ^[5]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Drugs and certain proteins are transported across the membranes of Gram-negative bacteria by energy-activated pumps. The outer membrane component of these pumps is a channel that opens from a sealed resting state during the transport process. We describe two crystal structures of the Escherichia coli outer membrane protein TolC in its partially open state. Opening is accompanied by the exposure of three shallow intraprotomer grooves in the TolC trimer, where our mutagenesis data identify a contact point with the periplasmic component of a drug efflux pump, AcrA. We suggest that the assembly of multidrug efflux pumps is accompanied by induced fit of TolC driven mainly by accommodation of the periplasmic component.

Assembly and channel opening in a bacterial drug efflux machine.,Bavro VN, Pietras Z, Furnham N, Perez-Cano L, Fernandez-Recio J, Pei XY, Misra R, Luisi B Mol Cell. 2008 Apr 11;30(1):114-21. PMID:18406332^[6]

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

References

↑ Morona R, Manning PA, Reeves P. Identification and characterization of the TolC protein, an outer membrane protein from Escherichia coli. J Bacteriol. 1983 Feb;153(2):693-9. PMID:6337123
↑ Kobayashi K, Tsukagoshi N, Aono R. Suppression of hypersensitivity of Escherichia coli acrB mutant to organic solvents by integrational activation of the acrEF operon with the IS1 or IS2 element. J Bacteriol. 2001 Apr;183(8):2646-53. PMID:11274125 doi:https://dx.doi.org/10.1128/JB.183.8.2646-2653.2001
↑ Touze T, Eswaran J, Bokma E, Koronakis E, Hughes C, Koronakis V. Interactions underlying assembly of the Escherichia coli AcrAB-TolC multidrug efflux system. Mol Microbiol. 2004 Jul;53(2):697-706. PMID:15228545 doi:https://dx.doi.org/10.1111/j.1365-2958.2004.04158.x
↑ Lin HT, Bavro VN, Barrera NP, Frankish HM, Velamakanni S, van Veen HW, Robinson CV, Borges-Walmsley MI, Walmsley AR. MacB ABC transporter is a dimer whose ATPase activity and macrolide-binding capacity are regulated by the membrane fusion protein MacA. J Biol Chem. 2009 Jan 9;284(2):1145-54. doi: 10.1074/jbc.M806964200. Epub 2008, Oct 27. PMID:18955484 doi:https://dx.doi.org/10.1074/jbc.M806964200
↑ Zakharov SD, Sharma O, Zhalnina M, Yamashita E, Cramer WA. Pathways of colicin import: utilization of BtuB, OmpF porin and the TolC drug-export protein. Biochem Soc Trans. 2012 Dec 1;40(6):1463-8. doi: 10.1042/BST20120211. PMID:23176499 doi:https://dx.doi.org/10.1042/BST20120211
↑ Bavro VN, Pietras Z, Furnham N, Perez-Cano L, Fernandez-Recio J, Pei XY, Misra R, Luisi B. Assembly and channel opening in a bacterial drug efflux machine. Mol Cell. 2008 Apr 11;30(1):114-21. PMID:18406332 doi:10.1016/j.molcel.2008.02.015

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Morona R, Manning PA, Reeves P. Identification and characterization of the TolC protein, an outer membrane protein from Escherichia coli. J Bacteriol. 1983 Feb;153(2):693-9. PMID:6337123

[2] Kobayashi K, Tsukagoshi N, Aono R. Suppression of hypersensitivity of Escherichia coli acrB mutant to organic solvents by integrational activation of the acrEF operon with the IS1 or IS2 element. J Bacteriol. 2001 Apr;183(8):2646-53. PMID:11274125 doi:https://dx.doi.org/10.1128/JB.183.8.2646-2653.2001

[3] Touze T, Eswaran J, Bokma E, Koronakis E, Hughes C, Koronakis V. Interactions underlying assembly of the Escherichia coli AcrAB-TolC multidrug efflux system. Mol Microbiol. 2004 Jul;53(2):697-706. PMID:15228545 doi:https://dx.doi.org/10.1111/j.1365-2958.2004.04158.x

[4] Lin HT, Bavro VN, Barrera NP, Frankish HM, Velamakanni S, van Veen HW, Robinson CV, Borges-Walmsley MI, Walmsley AR. MacB ABC transporter is a dimer whose ATPase activity and macrolide-binding capacity are regulated by the membrane fusion protein MacA. J Biol Chem. 2009 Jan 9;284(2):1145-54. doi: 10.1074/jbc.M806964200. Epub 2008, Oct 27. PMID:18955484 doi:https://dx.doi.org/10.1074/jbc.M806964200

[5] Zakharov SD, Sharma O, Zhalnina M, Yamashita E, Cramer WA. Pathways of colicin import: utilization of BtuB, OmpF porin and the TolC drug-export protein. Biochem Soc Trans. 2012 Dec 1;40(6):1463-8. doi: 10.1042/BST20120211. PMID:23176499 doi:https://dx.doi.org/10.1042/BST20120211

[6] Bavro VN, Pietras Z, Furnham N, Perez-Cano L, Fernandez-Recio J, Pei XY, Misra R, Luisi B. Assembly and channel opening in a bacterial drug efflux machine. Mol Cell. 2008 Apr 11;30(1):114-21. PMID:18406332 doi:10.1016/j.molcel.2008.02.015

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@@ Line 3: / Line 3: @@
 <StructureSection load='2vdd' size='340' side='right'caption='[[2vdd]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vdd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VDD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vdd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VDD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 3.3&#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;'>[[1ek9|1ek9]], [[1ttq|1ttq]], [[1tqq|1tqq]], [[2vde|2vde]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=2vdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vdd OCA], [https://pdbe.org/2vdd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vdd RCSB], [https://www.ebi.ac.uk/pdbsum/2vdd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vdd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/TOLC_ECOLI TOLC_ECOLI]] Outer membrane channel, which is required for the function of several efflux systems such as AcrAB-TolC, AcrEF-TolC, EmrAB-TolC and MacAB-TolC. These systems are involved in export of antibiotics and other toxic compounds from the cell. TolC is also involved in import of colicin E1 into the cells.<ref>PMID:6337123</ref> <ref>PMID:11274125</ref> <ref>PMID:15228545</ref> <ref>PMID:18955484</ref> <ref>PMID:23176499</ref>
+[https://www.uniprot.org/uniprot/TOLC_ECOLI TOLC_ECOLI] Outer membrane channel, which is required for the function of several efflux systems such as AcrAB-TolC, AcrEF-TolC, EmrAB-TolC and MacAB-TolC. These systems are involved in export of antibiotics and other toxic compounds from the cell. TolC is also involved in import of colicin E1 into the cells.<ref>PMID:6337123</ref> <ref>PMID:11274125</ref> <ref>PMID:15228545</ref> <ref>PMID:18955484</ref> <ref>PMID:23176499</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Bavro, V N]]
+[[Category: Bavro VN]]
-[[Category: Fernandez-Recio, J]]
+[[Category: Fernandez-Recio J]]
-[[Category: Furnham, N]]
+[[Category: Furnham N]]
-[[Category: Luisi, B]]
+[[Category: Luisi B]]
-[[Category: Misra, R]]
+[[Category: Misra R]]
-[[Category: Pei, X Y]]
+[[Category: Pei XY]]
-[[Category: Perez-Cano, L]]
+[[Category: Perez-Cano L]]
-[[Category: Pietras, Z]]
+[[Category: Pietras Z]]
-[[Category: Truer, R]]
+[[Category: Truer R]]
-[[Category: Alpha helical barrel]]
-[[Category: Beta barrel]]
-[[Category: Integral membrane protein]]
-[[Category: Membrane]]
-[[Category: Multidrug efflux pump]]
-[[Category: Outer membrane]]
-[[Category: Transmembrane]]
-[[Category: Transport]]
-[[Category: Transport protein]]

2vdd: Difference between revisions

Latest revision as of 15:16, 13 December 2023

Crystal Structure of the Open State of TolC Outer Membrane Component of Mutlidrug Efflux Pumps

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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