7ahk

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the outward-facing state of the substrate-free Na+-only bound glutamate transporter homolog GltPh

Structural highlights

7ahk is a 1 chain structure with sequence from Pyrococcus horikoshii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GLT_PYRHO Sodium-dependent, high-affinity amino acid transporter that mediates aspartate uptake (PubMed:17435767, PubMed:19380583, PubMed:17230192, Ref.11). Has only very low glutamate transport activity (PubMed:19380583, PubMed:17230192). Functions as a symporter that transports one amino acid molecule together with two or three Na(+) ions, resulting in electrogenic transport (PubMed:17435767, PubMed:19380583, Ref.11). Na(+) binding enhances the affinity for aspartate (PubMed:19380583, Ref.11). Mediates Cl(-) flux that is not coupled to amino acid transport; this avoids the accumulation of negative charges due to aspartate and Na(+) symport (PubMed:17435767). In contrast to mammalian homologs, transport does not depend on pH or K(+) ions (PubMed:19380583).^[1] ^[2] ^[3] [PDB:4P19]

Publication Abstract from PubMed

Excitatory amino acid transporters (EAATs) harness [Na(+)], [K(+)], and [H(+)] gradients for fast and efficient glutamate removal from the synaptic cleft. Since each glutamate is cotransported with three Na(+) ions, [Na(+)] gradients are the predominant driving force for glutamate uptake. We combined all-atom molecular dynamics simulations, fluorescence spectroscopy, and x-ray crystallography to study Na(+):substrate coupling in the EAAT homolog Glt(Ph) A lipidic cubic phase x-ray crystal structure of wild-type, Na(+)-only bound Glt(Ph) at 2.5-A resolution revealed the fully open, outward-facing state primed for subsequent substrate binding. Simulations and kinetic experiments established that only the binding of two Na(+) ions to the Na1 and Na3 sites ensures complete HP2 gate opening via a conformational selection-like mechanism and enables high-affinity substrate binding via electrostatic attraction. The combination of Na(+)-stabilized gate opening and electrostatic coupling of aspartate to Na(+) binding provides a constant Na(+):substrate transport stoichiometry over a broad range of neurotransmitter concentrations.

Na(+)-dependent gate dynamics and electrostatic attraction ensure substrate coupling in glutamate transporters.,Alleva C, Kovalev K, Astashkin R, Berndt MI, Baeken C, Balandin T, Gordeliy V, Fahlke C, Machtens JP Sci Adv. 2020 Nov 18;6(47):eaba9854. doi: 10.1126/sciadv.aba9854. Print 2020 Nov. PMID:33208356^[4]

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

References

↑ Boudker O, Ryan RM, Yernool D, Shimamoto K, Gouaux E. Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter. Nature. 2007 Jan 25;445(7126):387-93. Epub 2007 Jan 17. PMID:17230192 doi:10.1038/nature05455
↑ Ryan RM, Mindell JA. The uncoupled chloride conductance of a bacterial glutamate transporter homolog. Nat Struct Mol Biol. 2007 May;14(5):365-71. doi: 10.1038/nsmb1230. Epub 2007 Apr , 15. PMID:17435767 doi:http://dx.doi.org/10.1038/nsmb1230
↑ Ryan RM, Compton EL, Mindell JA. Functional characterization of a Na+-dependent aspartate transporter from Pyrococcus horikoshii. J Biol Chem. 2009 Jun 26;284(26):17540-8. doi: 10.1074/jbc.M109.005926. Epub 2009, Apr 20. PMID:19380583 doi:http://dx.doi.org/10.1074/jbc.M109.005926
↑ Alleva C, Kovalev K, Astashkin R, Berndt MI, Baeken C, Balandin T, Gordeliy V, Fahlke C, Machtens JP. Na(+)-dependent gate dynamics and electrostatic attraction ensure substrate coupling in glutamate transporters. Sci Adv. 2020 Nov 18;6(47):eaba9854. PMID:33208356 doi:10.1126/sciadv.aba9854

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7ahk"

@@ Line 3: / Line 3: @@
 <StructureSection load='7ahk' size='340' side='right'caption='[[7ahk]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7ahk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AHK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7AHK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7ahk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AHK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AHK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.5&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PH1295 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 'Pyrococcus shinkaii'])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=7ahk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ahk OCA], [http://pdbe.org/7ahk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7ahk RCSB], [http://www.ebi.ac.uk/pdbsum/7ahk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7ahk ProSAT]</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=7ahk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ahk OCA], [https://pdbe.org/7ahk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ahk RCSB], [https://www.ebi.ac.uk/pdbsum/7ahk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ahk ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GLT_PYRHO GLT_PYRHO]] Sodium-dependent, high-affinity amino acid transporter that mediates aspartate uptake (PubMed:17435767, PubMed:19380583, PubMed:17230192, Ref.11). Has only very low glutamate transport activity (PubMed:19380583, PubMed:17230192). Functions as a symporter that transports one amino acid molecule together with two or three Na(+) ions, resulting in electrogenic transport (PubMed:17435767, PubMed:19380583, Ref.11). Na(+) binding enhances the affinity for aspartate (PubMed:19380583, Ref.11). Mediates Cl(-) flux that is not coupled to amino acid transport; this avoids the accumulation of negative charges due to aspartate and Na(+) symport (PubMed:17435767). In contrast to mammalian homologs, transport does not depend on pH or K(+) ions (PubMed:19380583).<ref>PMID:17230192</ref> <ref>PMID:17435767</ref> <ref>PMID:19380583</ref> [PDB:4P19]
+[https://www.uniprot.org/uniprot/GLT_PYRHO GLT_PYRHO] Sodium-dependent, high-affinity amino acid transporter that mediates aspartate uptake (PubMed:17435767, PubMed:19380583, PubMed:17230192, Ref.11). Has only very low glutamate transport activity (PubMed:19380583, PubMed:17230192). Functions as a symporter that transports one amino acid molecule together with two or three Na(+) ions, resulting in electrogenic transport (PubMed:17435767, PubMed:19380583, Ref.11). Na(+) binding enhances the affinity for aspartate (PubMed:19380583, Ref.11). Mediates Cl(-) flux that is not coupled to amino acid transport; this avoids the accumulation of negative charges due to aspartate and Na(+) symport (PubMed:17435767). In contrast to mammalian homologs, transport does not depend on pH or K(+) ions (PubMed:19380583).<ref>PMID:17230192</ref> <ref>PMID:17435767</ref> <ref>PMID:19380583</ref> [PDB:4P19]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Excitatory amino acid transporters (EAATs) harness [Na(+)], [K(+)], and [H(+)] gradients for fast and efficient glutamate removal from the synaptic cleft. Since each glutamate is cotransported with three Na(+) ions, [Na(+)] gradients are the predominant driving force for glutamate uptake. We combined all-atom molecular dynamics simulations, fluorescence spectroscopy, and x-ray crystallography to study Na(+):substrate coupling in the EAAT homolog Glt(Ph) A lipidic cubic phase x-ray crystal structure of wild-type, Na(+)-only bound Glt(Ph) at 2.5-A resolution revealed the fully open, outward-facing state primed for subsequent substrate binding. Simulations and kinetic experiments established that only the binding of two Na(+) ions to the Na1 and Na3 sites ensures complete HP2 gate opening via a conformational selection-like mechanism and enables high-affinity substrate binding via electrostatic attraction. The combination of Na(+)-stabilized gate opening and electrostatic coupling of aspartate to Na(+) binding provides a constant Na(+):substrate transport stoichiometry over a broad range of neurotransmitter concentrations.
+Na(+)-dependent gate dynamics and electrostatic attraction ensure substrate coupling in glutamate transporters.,Alleva C, Kovalev K, Astashkin R, Berndt MI, Baeken C, Balandin T, Gordeliy V, Fahlke C, Machtens JP Sci Adv. 2020 Nov 18;6(47):eaba9854. doi: 10.1126/sciadv.aba9854. Print 2020 Nov. PMID:33208356<ref>PMID:33208356</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 7ahk" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Symporter 3D structures|Symporter 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Pyrococcus shinkaii]]
 [[Category: Large Structures]]
-[[Category: Alleva, C]]
+[[Category: Pyrococcus horikoshii]]
-[[Category: Astashkin, A]]
+[[Category: Alleva C]]
-[[Category: Fahlke, C]]
+[[Category: Astashkin A]]
-[[Category: Gordeliy, V]]
+[[Category: Fahlke C]]
-[[Category: Kovalev, K]]
+[[Category: Gordeliy V]]
-[[Category: Machtens, J P]]
+[[Category: Kovalev K]]
-[[Category: Aminoacid transport]]
+[[Category: Machtens J-P]]
-[[Category: Glutamate transporter]]
-[[Category: Homologue]]
-[[Category: Membrane protein]]

7ahk

From Proteopedia

Current revision

Crystal structure of the outward-facing state of the substrate-free Na+-only bound glutamate transporter homolog GltPh

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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