2nwx

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of GltPh in complex with L-aspartate and sodium ions

Structural highlights

2nwx is a 3 chain structure with sequence from Pyrococcus horikoshii. The March 2014 RCSB PDB Molecule of the Month feature on Neurotransmitter Transporters by David Goodsell is 10.2210/rcsb_pdb/mom_2014_3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.29Å
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]

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

Secondary transporters are integral membrane proteins that catalyse the movement of substrate molecules across the lipid bilayer by coupling substrate transport to one or more ion gradients, thereby providing a mechanism for the concentrative uptake of substrates. Here we describe crystallographic and thermodynamic studies of Glt(Ph), a sodium (Na+)-coupled aspartate transporter, defining sites for aspartate, two sodium ions and d,l-threo-beta-benzyloxyaspartate, an inhibitor. We further show that helical hairpin 2 is the extracellular gate that controls access of substrate and ions to the internal binding sites. At least two sodium ions bind in close proximity to the substrate and these sodium-binding sites, together with the sodium-binding sites in another sodium-coupled transporter, LeuT, define an unwound alpha-helix as the central element of the ion-binding motif, a motif well suited to the binding of sodium and to participation in conformational changes that accompany ion binding and unbinding during the transport cycle.

Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter.,Boudker O, Ryan RM, Yernool D, Shimamoto K, Gouaux E Nature. 2007 Jan 25;445(7126):387-93. Epub 2007 Jan 17. PMID:17230192^[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
↑ 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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2nwx"

@@ Line 3: / Line 3: @@
 <StructureSection load='2nwx' size='340' side='right'caption='[[2nwx]], [[Resolution|resolution]] 3.29&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2nwx]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. The March 2014 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Neurotransmitter Transporters''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2014_3 10.2210/rcsb_pdb/mom_2014_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NWX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NWX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2nwx]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. The March 2014 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Neurotransmitter Transporters''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2014_3 10.2210/rcsb_pdb/mom_2014_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NWX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NWX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</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]] 3.29&#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;'>[[1xhf|1xhf]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</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=2nwx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nwx OCA], [https://pdbe.org/2nwx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nwx RCSB], [https://www.ebi.ac.uk/pdbsum/2nwx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nwx ProSAT]</span></td></tr>
 </table>
+== Function ==
+[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]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Pyrococcus shinkaii]]
 [[Category: Large Structures]]
 [[Category: Neurotransmitter Transporters]]
+[[Category: Pyrococcus horikoshii]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Boudker, O]]
+[[Category: Boudker O]]
-[[Category: Gouaux, E]]
+[[Category: Gouaux E]]
-[[Category: Ryan, R]]
+[[Category: Ryan R]]
-[[Category: Shimamoto, K]]
+[[Category: Shimamoto K]]
-[[Category: Yernool, D]]
+[[Category: Yernool D]]
-[[Category: Amino acid transporter]]
-[[Category: Aspartate transporter]]
-[[Category: Binding site]]
-[[Category: Sodium binding]]
-[[Category: Substrate binding]]
-[[Category: Transmembrane transporter]]
-[[Category: Transport protein]]

2nwx

From Proteopedia

Current revision

Crystal structure of GltPh in complex with L-aspartate and sodium ions

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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