6o9v: Difference between revisions

Revision as of 07:06, 11 October 2023

KirBac3.1 mutant at a resolution of 3.1 Angstroms

Structural highlights

6o9v is a 2 chain structure with sequence from Magnetospirillum magnetotacticum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.094Å
Ligands:	DDQ, K, M1M, TMO
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IRK10_MAGMG Inward rectifier potassium channel that mediates potassium uptake into the cell. Inward rectifier potassium channels are characterized by a greater tendency to allow potassium to flow into the cell rather than out of it. The inward rectification may be achieved by the blockage of outward current by cytoplasmic divalent metal ions and polyamines. Complements an E.coli mutant that is defective in K(+) uptake.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The canonical mechanistic model explaining potassium channel gating is of a conformational change that alternately dilates and constricts a collar-like intracellular entrance to the pore. It is based on the premise that K(+) ions maintain a complete hydration shell while passing between the transmembrane cavity and cytosol, which must be accommodated. To put the canonical model to the test, we locked the conformation of a Kir K(+) channel to prevent widening of the narrow collar. Unexpectedly, conduction was unimpaired in the locked channels. In parallel, we employed all-atom molecular dynamics to simulate K(+) ions moving along the conduction pathway between the lower cavity and cytosol. During simulations, the constriction did not significantly widen. Instead, transient loss of some water molecules facilitated K(+) permeation through the collar. The low free energy barrier to partial dehydration in the absence of conformational change indicates Kir channels are not gated by the canonical mechanism.

A constricted opening in Kir channels does not impede potassium conduction.,Black KA, He S, Jin R, Miller DM, Bolla JR, Clarke OB, Johnson P, Windley M, Burns CJ, Hill AP, Laver D, Robinson CV, Smith BJ, Gulbis JM Nat Commun. 2020 Jun 15;11(1):3024. doi: 10.1038/s41467-020-16842-0. PMID:32541684^[4]

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

References

↑ Paynter JJ, Andres-Enguix I, Fowler PW, Tottey S, Cheng W, Enkvetchakul D, Bavro VN, Kusakabe Y, Sansom MS, Robinson NJ, Nichols CG, Tucker SJ. Functional complementation and genetic deletion studies of KirBac channels: activatory mutations highlight gating-sensitive domains. J Biol Chem. 2010 Dec 24;285(52):40754-61. doi: 10.1074/jbc.M110.175687. Epub, 2010 Sep 28. PMID:20876570 doi:https://dx.doi.org/10.1074/jbc.M110.175687
↑ Clarke OB, Caputo AT, Hill AP, Vandenberg JI, Smith BJ, Gulbis JM. Domain reorientation and rotation of an intracellular assembly regulate conduction in Kir potassium channels. Cell. 2010 Jun 11;141(6):1018-29. PMID:20564790
↑ Bavro VN, De Zorzi R, Schmidt MR, Muniz JR, Zubcevic L, Sansom MS, Venien-Bryan C, Tucker SJ. Structure of a KirBac potassium channel with an open bundle crossing indicates a mechanism of channel gating. Nat Struct Mol Biol. 2012 Jan 8;19(2):158-63. doi: 10.1038/nsmb.2208. PMID:22231399 doi:10.1038/nsmb.2208
↑ Black KA, He S, Jin R, Miller DM, Bolla JR, Clarke OB, Johnson P, Windley M, Burns CJ, Hill AP, Laver D, Robinson CV, Smith BJ, Gulbis JM. A constricted opening in Kir channels does not impede potassium conduction. Nat Commun. 2020 Jun 15;11(1):3024. doi: 10.1038/s41467-020-16842-0. PMID:32541684 doi:https://dx.doi.org/10.1038/s41467-020-16842-0

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Paynter JJ, Andres-Enguix I, Fowler PW, Tottey S, Cheng W, Enkvetchakul D, Bavro VN, Kusakabe Y, Sansom MS, Robinson NJ, Nichols CG, Tucker SJ. Functional complementation and genetic deletion studies of KirBac channels: activatory mutations highlight gating-sensitive domains. J Biol Chem. 2010 Dec 24;285(52):40754-61. doi: 10.1074/jbc.M110.175687. Epub, 2010 Sep 28. PMID:20876570 doi:https://dx.doi.org/10.1074/jbc.M110.175687

[2] Clarke OB, Caputo AT, Hill AP, Vandenberg JI, Smith BJ, Gulbis JM. Domain reorientation and rotation of an intracellular assembly regulate conduction in Kir potassium channels. Cell. 2010 Jun 11;141(6):1018-29. PMID:20564790

[3] Bavro VN, De Zorzi R, Schmidt MR, Muniz JR, Zubcevic L, Sansom MS, Venien-Bryan C, Tucker SJ. Structure of a KirBac potassium channel with an open bundle crossing indicates a mechanism of channel gating. Nat Struct Mol Biol. 2012 Jan 8;19(2):158-63. doi: 10.1038/nsmb.2208. PMID:22231399 doi:10.1038/nsmb.2208

[4] Black KA, He S, Jin R, Miller DM, Bolla JR, Clarke OB, Johnson P, Windley M, Burns CJ, Hill AP, Laver D, Robinson CV, Smith BJ, Gulbis JM. A constricted opening in Kir channels does not impede potassium conduction. Nat Commun. 2020 Jun 15;11(1):3024. doi: 10.1038/s41467-020-16842-0. PMID:32541684 doi:https://dx.doi.org/10.1038/s41467-020-16842-0

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[2]

[3]

[4]

@@ Line 3: / Line 3: @@
 <StructureSection load='6o9v' size='340' side='right'caption='[[6o9v]], [[Resolution|resolution]] 3.09&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6o9v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_31632 Atcc 31632]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O9V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6O9V FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6o9v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Magnetospirillum_magnetotacticum Magnetospirillum magnetotacticum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6O9V FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DDQ:DECYLAMINE-N,N-DIMETHYL-N-OXIDE'>DDQ</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=M1M:1,1-Methanediyl+Bismethanethiosulfonate'>M1M</scene>, <scene name='pdbligand=TMO:TRIMETHYLAMINE+OXIDE'>TMO</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]] 3.094&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6o9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o9v OCA], [http://pdbe.org/6o9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o9v RCSB], [http://www.ebi.ac.uk/pdbsum/6o9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o9v ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DDQ:DECYLAMINE-N,N-DIMETHYL-N-OXIDE'>DDQ</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=M1M:1,1-Methanediyl+Bismethanethiosulfonate'>M1M</scene>, <scene name='pdbligand=TMO:TRIMETHYLAMINE+OXIDE'>TMO</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=6o9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o9v OCA], [https://pdbe.org/6o9v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6o9v RCSB], [https://www.ebi.ac.uk/pdbsum/6o9v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6o9v ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/IRK10_MAGMG IRK10_MAGMG]] Inward rectifier potassium channel that mediates potassium uptake into the cell. Inward rectifier potassium channels are characterized by a greater tendency to allow potassium to flow into the cell rather than out of it. The inward rectification may be achieved by the blockage of outward current by cytoplasmic divalent metal ions and polyamines. Complements an E.coli mutant that is defective in K(+) uptake.<ref>PMID:20876570</ref> <ref>PMID:20564790</ref> <ref>PMID:22231399</ref>
+[https://www.uniprot.org/uniprot/IRK10_MAGMG IRK10_MAGMG] Inward rectifier potassium channel that mediates potassium uptake into the cell. Inward rectifier potassium channels are characterized by a greater tendency to allow potassium to flow into the cell rather than out of it. The inward rectification may be achieved by the blockage of outward current by cytoplasmic divalent metal ions and polyamines. Complements an E.coli mutant that is defective in K(+) uptake.<ref>PMID:20876570</ref> <ref>PMID:20564790</ref> <ref>PMID:22231399</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 31632]]
 [[Category: Large Structures]]
-[[Category: Black, K A]]
+[[Category: Magnetospirillum magnetotacticum]]
-[[Category: Gulbis, J M]]
+[[Category: Black KA]]
-[[Category: Miller, D M]]
+[[Category: Gulbis JM]]
-[[Category: Membrane protein]]
+[[Category: Miller DM]]

6o9v: Difference between revisions

Revision as of 07:06, 11 October 2023

KirBac3.1 mutant at a resolution of 3.1 Angstroms

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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