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1u2d

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Structre of transhydrogenaes (dI.NADH)2(dIII.NADPH)1 asymmetric complex

Structural highlights

1u2d is a 3 chain structure with sequence from Rhodospirillum rubrum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Transhydrogenase couples the redox (hydride-transfer) reaction between NAD(H) and NADP(H) to proton translocation across a membrane. The redox reaction is catalyzed at the interface between two components (dI and dIII) which protrude from the membrane. A complex formed from recombinant dI and dIII (the dI(2)dIII(1) complex) from Rhodospirillum rubrum transhydrogenase catalyzes fast single-turnover hydride transfer between bound nucleotides. In this report we describe three new crystal structures of the dI(2)dIII(1) complex in different nucleotide-bound forms. The structures reveal an asymmetry in nucleotide binding that complements results from solution studies and supports the notion that intact transhydrogenase functions by an alternating site mechanism. In one structure, the redox site is occupied by NADH (on dI) and NADPH (on dIII). The dihydronicotinamide rings take up positions which may approximate to the ground state for hydride transfer: the redox-active C4(N) atoms are separated by only 3.6 A, and the perceived reaction stereochemistry matches that observed experimentally. The NADH conformation is different in the two dI polypeptides of this form of the dI(2)dIII(1) complex. Comparisons between a number of X-ray structures show that a conformational change in the NADH is driven by relative movement of the two domains which comprise dI. It is suggested that an equivalent conformational change in the intact enzyme is important in gating the hydride-transfer reaction. The observed nucleotide conformational change in the dI(2)dIII(1) complex is accompanied by rearrangements in the orientation of local amino acid side chains which may be responsible for sealing the site from the solvent and polarizing hydride transfer.

Active-site conformational changes associated with hydride transfer in proton-translocating transhydrogenase.,Mather OC, Singh A, van Boxel GI, White SA, Jackson JB Biochemistry. 2004 Aug 31;43(34):10952-64. PMID:15323555^[1]

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

References

↑ Mather OC, Singh A, van Boxel GI, White SA, Jackson JB. Active-site conformational changes associated with hydride transfer in proton-translocating transhydrogenase. Biochemistry. 2004 Aug 31;43(34):10952-64. PMID:15323555 doi:10.1021/bi0497594

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1u2d"

@@ Line 1: / Line 1: @@
 ==Structre of transhydrogenaes (dI.NADH)2(dIII.NADPH)1 asymmetric complex==
-<StructureSection load='1u2d' size='340' side='right' caption='[[1u2d]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='1u2d' size='340' side='right'caption='[[1u2d]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1u2d]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"dicrospirillum_rubrum"_enderlein_1925 "dicrospirillum rubrum" enderlein 1925]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U2D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1u2d]] 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=1U2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U2D FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1hzz|1hzz]], [[1nm5|1nm5]], [[1ptj|1ptj]], [[1u28|1u28]], [[1u2g|1u2g]], [[1u31|1u31]]</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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pntAA, nntA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 "Dicrospirillum rubrum" Enderlein 1925]), pntB, nntB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1085 "Dicrospirillum rubrum" Enderlein 1925])</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=1u2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u2d OCA], [https://pdbe.org/1u2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u2d RCSB], [https://www.ebi.ac.uk/pdbsum/1u2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u2d ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(P)(+)_transhydrogenase_(Re/Si-specific) NAD(P)(+) transhydrogenase (Re/Si-specific)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.1.2 1.6.1.2] </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=1u2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u2d OCA], [http://pdbe.org/1u2d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u2d RCSB], [http://www.ebi.ac.uk/pdbsum/1u2d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u2d ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PNTAA_RHORU PNTAA_RHORU]] The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity). [[http://www.uniprot.org/uniprot/PNTB_RHORU PNTB_RHORU]] The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity).
+[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]]
@@ Line 34: / Line 32: @@
 ==See Also==
 *[[NAD(P) transhydrogenase|NAD(P) transhydrogenase]]
+*[[NAD(P) transhydrogenase 3D structures|NAD(P) transhydrogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Dicrospirillum rubrum enderlein 1925]]
+[[Category: Large Structures]]
-[[Category: Boxel, G I.van]]
+[[Category: Rhodospirillum rubrum]]
-[[Category: Jackson, J B]]
+[[Category: Jackson JB]]
-[[Category: Mather, O C]]
+[[Category: Mather OC]]
-[[Category: Singh, A]]
+[[Category: Singh A]]
-[[Category: White, S A]]
+[[Category: White SA]]
-[[Category: Nad+]]
+[[Category: Van Boxel GI]]
-[[Category: Nadp+]]
-[[Category: Oxidoreductase]]

1u2d

From Proteopedia

Current revision

Structre of transhydrogenaes (dI.NADH)2(dIII.NADPH)1 asymmetric complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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