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5lzq

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Current revision

Crystal structure of Thermotoga maritima sodium pumping membrane integral pyrophosphatase in complex with imidodiphosphate and magnesium, and with bound sodium ion

Structural highlights

5lzq is a 2 chain structure with sequence from Thermotoga maritima MSB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.495Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HPPA_THEMA Sodium pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for Na(+) movement across the membrane.[HAMAP-Rule:MF_01129]^[1] ^[2] ^[3]

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^[4]

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

References

↑ Perez-Castineira JR, Lopez-Marques RL, Losada M, Serrano A. A thermostable K(+)-stimulated vacuolar-type pyrophosphatase from the hyperthermophilic bacterium Thermotoga maritima. FEBS Lett. 2001 May 4;496(1):6-11. PMID:11343697
↑ Malinen AM, Belogurov GA, Baykov AA, Lahti R. Na+-pyrophosphatase: a novel primary sodium pump. Biochemistry. 2007 Jul 31;46(30):8872-8. Epub 2007 Jul 3. PMID:17605473 doi:http://dx.doi.org/10.1021/bi700564b
↑ Kellosalo J, Kajander T, Kogan K, Pokharel K, Goldman A. The structure and catalytic cycle of a sodium-pumping pyrophosphatase. Science. 2012 Jul 27;337(6093):473-6. PMID:22837527 doi:10.1126/science.1222505
↑ 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:http://dx.doi.org/10.1038/ncomms13596

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5lzq"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Thermotoga maritima sodium pumping membrane integral pyrophosphatase in complex with imidodiphosphate and magnesium, and with bound sodium ion==
-<StructureSection load='5lzq' size='340' side='right' caption='[[5lzq]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
+<StructureSection load='5lzq' size='340' side='right'caption='[[5lzq]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5lzq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LZQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LZQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5lzq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LZQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LZQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PN:IMIDODIPHOSPHORIC+ACID'>2PN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 3.495&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PN:IMIDODIPHOSPHORIC+ACID'>2PN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=5lzq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lzq OCA], [http://pdbe.org/5lzq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lzq RCSB], [http://www.ebi.ac.uk/pdbsum/5lzq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lzq 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=5lzq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lzq OCA], [https://pdbe.org/5lzq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lzq RCSB], [https://www.ebi.ac.uk/pdbsum/5lzq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lzq ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/HPPA_THEMA HPPA_THEMA]] Sodium pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for Na(+) movement across the membrane.[HAMAP-Rule:MF_01129]<ref>PMID:11343697</ref> <ref>PMID:17605473</ref> <ref>PMID:22837527</ref>
+[https://www.uniprot.org/uniprot/HPPA_THEMA HPPA_THEMA] Sodium pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for Na(+) movement across the membrane.[HAMAP-Rule:MF_01129]<ref>PMID:11343697</ref> <ref>PMID:17605473</ref> <ref>PMID:22837527</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Inorganic diphosphatase]]
+[[Category: Large Structures]]
-[[Category: Goldman, A]]
+[[Category: Thermotoga maritima MSB8]]
-[[Category: Kajander, T]]
+[[Category: Goldman A]]
-[[Category: Kellosalo, J]]
+[[Category: Kajander T]]
-[[Category: Wilkinson, C]]
+[[Category: Kellosalo J]]
-[[Category: Imidodiphosphate]]
+[[Category: Wilkinson C]]
-[[Category: Pyrophosphatase]]
-[[Category: Transport protein]]

5lzq

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Current revision

Crystal structure of Thermotoga maritima sodium pumping membrane integral pyrophosphatase in complex with imidodiphosphate and magnesium, and with bound sodium ion

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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