5gpj: Difference between revisions

Latest revision as of 11:38, 2 August 2023

Crystal Structure of Proton-Pumping Pyrophosphatase

Structural highlights

5gpj is a 4 chain structure with sequence from Vigna radiata var. radiata. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.5Å
Ligands:	MG, PO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AVP_VIGRR Proton-translocating inorganic pyrophosphatase that contributes to the transtonoplast (from cytosol to vacuole lumen) H(+)-electrochemical potential difference. It establishes a proton gradient of similar and often greater magnitude than the H(+)-ATPase on the same membrane.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Membrane-bound pyrophosphatases (M-PPases), which couple proton/sodium ion transport to pyrophosphate synthesis/hydrolysis, are important in abiotic stress resistance and in the infectivity of protozoan parasites. Here, three M-PPase structures in different catalytic states show that closure of the substrate-binding pocket by helices 5-6 affects helix 13 in the dimer interface and causes helix 12 to move down. This springs a 'molecular mousetrap', repositioning a conserved aspartate and activating the nucleophilic water. Corkscrew motion at helices 6 and 16 rearranges the key ionic gate residues and leads to ion pumping. The pumped ion is above the ion gate in one of the ion-bound structures, but below it in the other. Electrometric measurements show a single-turnover event with a non-hydrolysable inhibitor, supporting our model that ion pumping precedes hydrolysis. We propose a complete catalytic cycle for both proton and sodium-pumping M-PPases, and one that also explains the basis for ion specificity.

Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism.,Li KM, Wilkinson C, Kellosalo J, Tsai JY, Kajander T, Jeuken LJ, Sun YJ, Goldman A Nat Commun. 2016 Dec 6;7:13596. doi: 10.1038/ncomms13596. PMID:27922000^[5]

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

References

↑ Yang SJ, Jiang SS, Kuo SY, Hung SH, Tam MF, Pan RL. Localization of a carboxylic residue possibly involved in the inhibition of vacuolar H+-pyrophosphatase by N, N'-dicyclohexylcarbodi-imide. Biochem J. 1999 Sep 15;342 Pt 3:641-6. PMID:10477275
↑ Lin SM, Tsai JY, Hsiao CD, Huang YT, Chiu CL, Liu MH, Tung JY, Liu TH, Pan RL, Sun YJ. Crystal structure of a membrane-embedded H+-translocating pyrophosphatase. Nature. 2012 Mar 28;484(7394):399-403. doi: 10.1038/nature10963. PMID:22456709 doi:10.1038/nature10963
↑ Maeshima M, Yoshida S. Purification and properties of vacuolar membrane proton-translocating inorganic pyrophosphatase from mung bean. J Biol Chem. 1989 Nov 25;264(33):20068-73. PMID:2555340
↑ Nakanishi Y, Maeshima M. Molecular cloning of vacuolar H(+)-pyrophosphatase and its developmental expression in growing hypocotyl of mung bean. Plant Physiol. 1998 Feb;116(2):589-97. PMID:9489011
↑ Li KM, Wilkinson C, Kellosalo J, Tsai JY, Kajander T, Jeuken LJ, Sun YJ, Goldman A. Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism. Nat Commun. 2016 Dec 6;7:13596. doi: 10.1038/ncomms13596. PMID:27922000 doi:https://dx.doi.org/10.1038/ncomms13596

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Yang SJ, Jiang SS, Kuo SY, Hung SH, Tam MF, Pan RL. Localization of a carboxylic residue possibly involved in the inhibition of vacuolar H+-pyrophosphatase by N, N'-dicyclohexylcarbodi-imide. Biochem J. 1999 Sep 15;342 Pt 3:641-6. PMID:10477275

[2] Lin SM, Tsai JY, Hsiao CD, Huang YT, Chiu CL, Liu MH, Tung JY, Liu TH, Pan RL, Sun YJ. Crystal structure of a membrane-embedded H+-translocating pyrophosphatase. Nature. 2012 Mar 28;484(7394):399-403. doi: 10.1038/nature10963. PMID:22456709 doi:10.1038/nature10963

[3] Maeshima M, Yoshida S. Purification and properties of vacuolar membrane proton-translocating inorganic pyrophosphatase from mung bean. J Biol Chem. 1989 Nov 25;264(33):20068-73. PMID:2555340

[4] Nakanishi Y, Maeshima M. Molecular cloning of vacuolar H(+)-pyrophosphatase and its developmental expression in growing hypocotyl of mung bean. Plant Physiol. 1998 Feb;116(2):589-97. PMID:9489011

[5] Li KM, Wilkinson C, Kellosalo J, Tsai JY, Kajander T, Jeuken LJ, Sun YJ, Goldman A. Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism. Nat Commun. 2016 Dec 6;7:13596. doi: 10.1038/ncomms13596. PMID:27922000 doi:https://dx.doi.org/10.1038/ncomms13596

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[2]

[3]

[4]

[5]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5gpj is ON HOLD
+==Crystal Structure of Proton-Pumping Pyrophosphatase==
+<StructureSection load='5gpj' size='340' side='right'caption='[[5gpj]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5gpj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Vigna_radiata_var._radiata Vigna radiata var. radiata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GPJ FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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'>[https://proteopedia.org/fgij/fg.htm?mol=5gpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gpj OCA], [https://pdbe.org/5gpj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gpj RCSB], [https://www.ebi.ac.uk/pdbsum/5gpj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gpj ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AVP_VIGRR AVP_VIGRR] Proton-translocating inorganic pyrophosphatase that contributes to the transtonoplast (from cytosol to vacuole lumen) H(+)-electrochemical potential difference. It establishes a proton gradient of similar and often greater magnitude than the H(+)-ATPase on the same membrane.<ref>PMID:10477275</ref> <ref>PMID:22456709</ref> <ref>PMID:2555340</ref> <ref>PMID:9489011</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Membrane-bound pyrophosphatases (M-PPases), which couple proton/sodium ion transport to pyrophosphate synthesis/hydrolysis, are important in abiotic stress resistance and in the infectivity of protozoan parasites. Here, three M-PPase structures in different catalytic states show that closure of the substrate-binding pocket by helices 5-6 affects helix 13 in the dimer interface and causes helix 12 to move down. This springs a 'molecular mousetrap', repositioning a conserved aspartate and activating the nucleophilic water. Corkscrew motion at helices 6 and 16 rearranges the key ionic gate residues and leads to ion pumping. The pumped ion is above the ion gate in one of the ion-bound structures, but below it in the other. Electrometric measurements show a single-turnover event with a non-hydrolysable inhibitor, supporting our model that ion pumping precedes hydrolysis. We propose a complete catalytic cycle for both proton and sodium-pumping M-PPases, and one that also explains the basis for ion specificity.
-Authors:
+Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism.,Li KM, Wilkinson C, Kellosalo J, Tsai JY, Kajander T, Jeuken LJ, Sun YJ, Goldman A Nat Commun. 2016 Dec 6;7:13596. doi: 10.1038/ncomms13596. PMID:27922000<ref>PMID:27922000</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5gpj" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Vigna radiata var. radiata]]
+[[Category: Li KM]]
+[[Category: Sun YJ]]
+[[Category: Tsai JY]]

5gpj: Difference between revisions

Latest revision as of 11:38, 2 August 2023

Crystal Structure of Proton-Pumping Pyrophosphatase

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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