5ylu: Difference between revisions

Latest revision as of 08:33, 22 November 2023

Crystal structure of the gastric proton pump complexed with vonoprazan

Structural highlights

5ylu is a 2 chain structure with sequence from Sus scrofa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7998896Å
Ligands:	BFD, CE1, HKT, MG, NAG, PCW
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ATP4A_PIG Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.

Publication Abstract from PubMed

The gastric proton pump-the H(+), K(+)-ATPase-is a P-type ATPase responsible for acidifying the gastric juice down to pH 1. This corresponds to a million-fold proton gradient across the membrane of the parietal cell, the steepest known cation gradient of any mammalian tissue. The H(+), K(+)-ATPase is an important target for drugs that treat gastric acid-related diseases. Here we present crystal structures of the H(+), K(+)-ATPase in complex with two blockers, vonoprazan and SCH28080, in the luminal-open state, at 2.8 A resolution. The drugs have partially overlapping but clearly distinct binding modes in the middle of a conduit running from the gastric lumen to the cation-binding site. The crystal structures suggest that the tight configuration at the cation-binding site lowers the pK a value of Glu820 sufficiently to enable the release of a proton even into the pH 1 environment of the stomach.

Crystal structures of the gastric proton pump.,Abe K, Irie K, Nakanishi H, Suzuki H, Fujiyoshi Y Nature. 2018 Apr;556(7700):214-218. doi: 10.1038/s41586-018-0003-8. Epub 2018 Apr, 4. PMID:29618813^[1]

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

References

↑ Abe K, Irie K, Nakanishi H, Suzuki H, Fujiyoshi Y. Crystal structures of the gastric proton pump. Nature. 2018 Apr;556(7700):214-218. doi: 10.1038/s41586-018-0003-8. Epub 2018 Apr, 4. PMID:29618813 doi:https://dx.doi.org/10.1038/s41586-018-0003-8

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Abe K, Irie K, Nakanishi H, Suzuki H, Fujiyoshi Y. Crystal structures of the gastric proton pump. Nature. 2018 Apr;556(7700):214-218. doi: 10.1038/s41586-018-0003-8. Epub 2018 Apr, 4. PMID:29618813 doi:https://dx.doi.org/10.1038/s41586-018-0003-8

[1]

@@ Line 1: / Line 1: @@
 ==Crystal structure of the gastric proton pump complexed with vonoprazan==
-<StructureSection load='5ylu' size='340' side='right' caption='[[5ylu]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='5ylu' size='340' side='right'caption='[[5ylu]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ylu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YLU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YLU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ylu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YLU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YLU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CE1:O-DODECANYL+OCTAETHYLENE+GLYCOL'>CE1</scene>, <scene name='pdbligand=HKT:1-[5-(2-fluorophenyl)-1-pyridin-3-ylsulfonyl-pyrrol-3-yl]-~{N}-methyl-methanamine'>HKT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</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]] 2.7998896&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BFD:ASPARTATE+BERYLLIUM+TRIFLUORIDE'>BFD</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BFD:ASPARTATE+BERYLLIUM+TRIFLUORIDE'>BFD</scene>, <scene name='pdbligand=CE1:O-DODECANYL+OCTAETHYLENE+GLYCOL'>CE1</scene>, <scene name='pdbligand=HKT:1-[5-(2-fluorophenyl)-1-pyridin-3-ylsulfonyl-pyrrol-3-yl]-~{N}-methyl-methanamine'>HKT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCW:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PCW</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ATP4A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG]), ATP4B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</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=5ylu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ylu OCA], [https://pdbe.org/5ylu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ylu RCSB], [https://www.ebi.ac.uk/pdbsum/5ylu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ylu ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydrogen/potassium-exchanging_ATPase Hydrogen/potassium-exchanging ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.10 3.6.3.10] </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=5ylu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ylu OCA], [http://pdbe.org/5ylu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ylu RCSB], [http://www.ebi.ac.uk/pdbsum/5ylu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ylu ProSAT]</span></td></tr>
 </table>
-== Disease ==
-[[http://www.uniprot.org/uniprot/ATP4B_PIG ATP4B_PIG]] Note=Parietal cell autoantigen associated with autoimmune gastritis.
 == Function ==
-[[http://www.uniprot.org/uniprot/ATP4A_PIG ATP4A_PIG]] Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.
+[https://www.uniprot.org/uniprot/ATP4A_PIG ATP4A_PIG] Catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. Responsible for acid production in the stomach.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 19: @@
 </div>
 <div class="pdbe-citations 5ylu" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[ATPase 3D structures|ATPase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Hydrogen/potassium-exchanging ATPase]]
+[[Category: Large Structures]]
-[[Category: Pig]]
+[[Category: Sus scrofa]]
-[[Category: Abe, K]]
+[[Category: Abe K]]
-[[Category: Fujiyoshi, Y]]
+[[Category: Fujiyoshi Y]]
-[[Category: Irie, K]]
+[[Category: Irie K]]
-[[Category: Nakanishi, H]]
+[[Category: Nakanishi H]]
-[[Category: Gastric]]
-[[Category: H+]]
-[[Category: K+-atpase]]
-[[Category: Membrane protein]]
-[[Category: P-type atpase]]
-[[Category: Proton pump]]
-[[Category: Transporter]]

5ylu: Difference between revisions

Latest revision as of 08:33, 22 November 2023

Crystal structure of the gastric proton pump complexed with vonoprazan

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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