5gpj: Difference between revisions

Revision as of 06:49, 13 May 2020

Crystal Structure of Proton-Pumping Pyrophosphatase

Structural highlights

5gpj is a 4 chain structure with sequence from Mung bean. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	MG, PO4
Activity:	Inorganic diphosphatase, with EC number 3.6.1.1
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

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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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@@ Line 1: / Line 1: @@
 ==Crystal Structure of Proton-Pumping Pyrophosphatase==
-<StructureSection load='5gpj' size='340' side='right' caption='[[5gpj]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
+<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. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GPJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5gpj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mung_bean Mung bean]. 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 [http://proteopedia.org/fgij/fg.htm?mol=5GPJ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </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=5gpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gpj OCA], [http://pdbe.org/5gpj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gpj RCSB], [http://www.ebi.ac.uk/pdbsum/5gpj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gpj ProSAT]</span></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=5gpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gpj OCA], [http://pdbe.org/5gpj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gpj RCSB], [http://www.ebi.ac.uk/pdbsum/5gpj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gpj ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 24: / Line 24: @@
 </StructureSection>
 [[Category: Inorganic diphosphatase]]
+[[Category: Large Structures]]
+[[Category: Mung bean]]
 [[Category: Li, K M]]
 [[Category: Sun, Y J]]

5gpj: Difference between revisions

Revision as of 06:49, 13 May 2020

Crystal Structure of Proton-Pumping Pyrophosphatase

Structural highlights

Function

Publication Abstract from PubMed

References

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