4a01: Difference between revisions

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-[[Image:4a01.png|left|200px]]
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+==Crystal Structure of the H-Translocating Pyrophosphatase==
-The line below this paragraph, containing "STRUCTURE_4a01", creates the "Structure Box" on the page.
+<StructureSection load='4a01' size='340' side='right'caption='[[4a01]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[4a01]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mung_bean Mung bean]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A01 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4A01 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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=DMU:DECYL-BETA-D-MALTOPYRANOSIDE'>DMU</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
--->
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </span></td></tr>
-{{STRUCTURE_4a01|  PDB=4a01  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4a01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4a01 OCA], [https://pdbe.org/4a01 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4a01 RCSB], [https://www.ebi.ac.uk/pdbsum/4a01 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4a01 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 ==
+H(+)-translocating pyrophosphatases (H(+)-PPases) are active proton transporters that establish a proton gradient across the endomembrane by means of pyrophosphate (PP(i)) hydrolysis. H(+)-PPases are found primarily as homodimers in the vacuolar membrane of plants and the plasma membrane of several protozoa and prokaryotes. The three-dimensional structure and detailed mechanisms underlying the enzymatic and proton translocation reactions of H(+)-PPases are unclear. Here we report the crystal structure of a Vigna radiata H(+)-PPase (VrH(+)-PPase) in complex with a non-hydrolysable substrate analogue, imidodiphosphate (IDP), at 2.35 A resolution. Each VrH(+)-PPase subunit consists of an integral membrane domain formed by 16 transmembrane helices. IDP is bound in the cytosolic region of each subunit and trapped by numerous charged residues and five Mg(2+) ions. A previously undescribed proton translocation pathway is formed by six core transmembrane helices. Proton pumping can be initialized by PP(i) hydrolysis, and H(+) is then transported into the vacuolar lumen through a pathway consisting of Arg 242, Asp 294, Lys 742 and Glu 301. We propose a working model of the mechanism for the coupling between proton pumping and PP(i) hydrolysis by H(+)-PPases.
-===Crystal Structure of the H-Translocating Pyrophosphatase===
+Crystal structure of a membrane-embedded H+-translocating pyrophosphatase.,Lin SM, Tsai JY, Hsiao CD, Huang YT, Chiu CL, Liu MH, Tung JY, Liu TH, Pan RL, Sun YJ Nature. 2012 Mar 28;484(7394):399-403. doi: 10.1038/nature10963. PMID:22456709<ref>PMID:22456709</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_22456709}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 4a01" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 22456709 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_22456709}}
-==About this Structure==
-[[4a01]] is a 2 chain structure of [[Inorganic pyrophosphatase]] with sequence from [http://en.wikipedia.org/wiki/Vigna_radiata Vigna radiata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A01 OCA].
 ==See Also==
-*[[Inorganic pyrophosphatase|Inorganic pyrophosphatase]]
+*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:022456709</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Inorganic diphosphatase]]
-[[Category: Vigna radiata]]
+[[Category: Large Structures]]
-[[Category: Chiu, C L.]]
+[[Category: Mung bean]]
-[[Category: Hsiao, C D.]]
+[[Category: Chiu, C L]]
-[[Category: Lin, S M.]]
+[[Category: Hsiao, C D]]
-[[Category: Pan, R L.]]
+[[Category: Lin, S M]]
-[[Category: Sun, Y J.]]
+[[Category: Pan, R L]]
-[[Category: Tsai, J Y.]]
+[[Category: Sun, Y J]]
+[[Category: Tsai, J Y]]
 [[Category: Hydrolase]]
 [[Category: Membrane protein]]
 [[Category: Proton pumping]]