1pnq

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(New page: 200px<br /><applet load="1pnq" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pnq, resolution 2.40&Aring;" /> '''Crystal structure of...)
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[[Image:1pnq.jpg|left|200px]]<br /><applet load="1pnq" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1pnq, resolution 2.40&Aring;" />
 
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'''Crystal structure of R. rubrum transhydrogenase domain III bound to NADPH'''<br />
 
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==Overview==
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==Crystal structure of R. rubrum transhydrogenase domain III bound to NADPH==
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Proton-translocating transhydrogenase (TH) couples direct and, stereospecific hydride transfer between NAD(H) and NADP(H), bound to, soluble domains dI and dIII, respectively, to proton translocation across, a membrane bound domain, dII. The reaction occurs with proton-gradient, coupled conformational changes, which affect the energetics of substrate, binding and interdomain interactions. The crystal structure of TH dIII, from Rhodospirillum rubrum has been determined in the presence of NADPH, (2.4 A) and NADP (2.1 A) (space group P6(1)22). Each structure has two, molecules in the asymmetric unit, differing in the conformation of the, NADP(H) binding loop D. In one molecule, loop D has an open conformation, with the B face of (dihydro)nicotinamide exposed to solvent. In the other, molecule, loop D adopts a hitherto unobserved closed conformation, resulting in close interactions between NADP(H) and side chains of the, highly conserved residues, betaSer405, betaPro406, and betaIle407. The, conformational change shields the B face of (dihydro)nicotinamide from, solvent, which would block hydride transfer in the intact enzyme. It also, alters the environments of invariant residues betaHis346 and betaAsp393., However, there is little difference in either the open or the closed, conformation upon change in oxidation state of nicotinamide, i.e., for, NADP vs. NADPH. Consequently, the occurrence of two loop D conformations, for both substrate oxidation states gives rise to four states: NADP-open, NADP-closed, NADPH-open, and NADPH-closed. Because these states are, distinguished by protein conformation and by net charge they may be, important in the proton translocating mechanism of intact TH.
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<StructureSection load='1pnq' size='340' side='right'caption='[[1pnq]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1pnq]] is a 2 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=1PNQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PNQ FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pnq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pnq OCA], [https://pdbe.org/1pnq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pnq RCSB], [https://www.ebi.ac.uk/pdbsum/1pnq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pnq ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PNTB_RHORT PNTB_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]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pn/1pnq_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1pnq ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1PNQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum] with NDP as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/NAD(P)(+)_transhydrogenase_(AB-specific) NAD(P)(+) transhydrogenase (AB-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.1.2 1.6.1.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PNQ OCA].
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*[[NAD(P) transhydrogenase 3D structures|NAD(P) transhydrogenase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Conformational change in the NADP(H) binding domain of transhydrogenase defines four states., Sundaresan V, Yamaguchi M, Chartron J, Stout CD, Biochemistry. 2003 Oct 28;42(42):12143-53. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14567675 14567675]
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[[Category: Large Structures]]
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[[Category: NAD(P)(+) transhydrogenase (AB-specific)]]
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[[Category: Rhodospirillum rubrum]]
[[Category: Rhodospirillum rubrum]]
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[[Category: Single protein]]
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[[Category: Chartron J]]
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[[Category: Chartron, J.]]
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[[Category: Stout CD]]
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[[Category: Stout, C.D.]]
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[[Category: Sundaresan V]]
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[[Category: Sundaresan, V.]]
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[[Category: Yamaguchi M]]
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[[Category: Yamaguchi, M.]]
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[[Category: NDP]]
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[[Category: nadph]]
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[[Category: nucleotide binding fold]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:57:16 2007''
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Current revision

Crystal structure of R. rubrum transhydrogenase domain III bound to NADPH

PDB ID 1pnq

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