1ptj: Difference between revisions

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-{{Seed}}
-[[Image:1ptj.png|left|200px]]
-<!--
+==Crystal structure analysis of the DI and DIII complex of transhydrogenase with a thio-nicotinamide nucleotide analogue==
-The line below this paragraph, containing "STRUCTURE_1ptj", creates the "Structure Box" on the page.
+<StructureSection load='1ptj' size='340' side='right'caption='[[1ptj]], [[Resolution|resolution]] 2.61&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'>[[1ptj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PTJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PTJ FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.61&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SND:THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE'>SND</scene></td></tr>
-{{STRUCTURE_1ptj|  PDB=1ptj  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ptj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ptj OCA], [https://pdbe.org/1ptj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ptj RCSB], [https://www.ebi.ac.uk/pdbsum/1ptj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ptj ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PNTAA_RHORT PNTAA_RHORT] The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane.[UniProtKB:P07001]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pt/1ptj_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ptj ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Transhydrogenase couples the reduction of NADP+ by NADH to inward proton translocation across mitochondrial and bacterial membranes. The coupling reactions occur within the protein by long distance conformational changes. In intact transhydrogenase and in complexes formed from the isolated, nucleotide-binding components, thio-NADP(H) is a good analogue for NADP(H), but thio-NAD(H) is a poor analogue for NAD(H). Crystal structures of the nucleotide-binding components show that the twists of the 3-carbothiamide groups of thio-NADP+ and of thio-NAD+ (relative to the planes of the pyridine rings), which are defined by the dihedral, Xam, are altered relative to the twists of the 3-carboxamide groups of the physiological nucleotides. The finding that thio-NADP+ is a good substrate despite an increased Xam value shows that approach of the NADH prior to hydride transfer is not obstructed by the S atom in the analogue. That thio-NAD(H) is a poor substrate appears to be the result of failure in the conformational change that establishes the ground state for hydride transfer. This might be a consequence of restricted rotation of the 3-carbothiamide group during the conformational change.
-===Crystal structure analysis of the DI and DIII complex of transhydrogenase with a thio-nicotinamide nucleotide analogue===
+Interactions between transhydrogenase and thio-nicotinamide Analogues of NAD(H) and NADP(H) underline the importance of nucleotide conformational changes in coupling to proton translocation.,Singh A, Venning JD, Quirk PG, van Boxel GI, Rodrigues DJ, White SA, Jackson JB J Biol Chem. 2003 Aug 29;278(35):33208-16. Epub 2003 Jun 5. PMID:12791694<ref>PMID:12791694</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ptj" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12791694}}, adds the Publication Abstract to the page
+*[[NAD(P) transhydrogenase 3D structures|NAD(P) transhydrogenase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12791694 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12791694}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-PTJ is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PTJ OCA].
-==Reference==
-<ref group="xtra">PMID:12791694</ref><references group="xtra"/>
 [[Category: Rhodospirillum rubrum]]
-[[Category: Boxel, G I.van.]]
+[[Category: Jackson JB]]
-[[Category: Jackson, J B.]]
+[[Category: Quirk PG]]
-[[Category: Quirk, P G.]]
+[[Category: Rodrigues DJ]]
-[[Category: Rodrigues, D J.]]
+[[Category: Singh A]]
-[[Category: Singh, A.]]
+[[Category: Venning JD]]
-[[Category: Venning, J D.]]
+[[Category: White SA]]
-[[Category: White, S A.]]
+[[Category: Van Boxel GI]]
-[[Category: Mitochondria]]
-[[Category: Proton translocation]]
-[[Category: Thio-nicotinamide]]
-[[Category: Transhydrogenase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:50:22 2009''