1PTJ

Crystal structure analysis of the DI and DIII complex of transhydrogenase with a thio-nicotinamide nucleotide analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.234 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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, J.D.Quirk, P.G.Van Boxel, G.I.Rodrigues, D.J.White, S.A.Jackson, J.B.

(2003) J Biol Chem 278: 33208-33216

  • DOI: 10.1074/jbc.M303061200
  • Primary Citation of Related Structures:  
    1PT9, 1PTJ

  • PubMed Abstract: 
  • 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) ...

    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.


    Organizational Affiliation

    School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P) transhydrogenase subunit alpha part 1A, B381Rhodospirillum rubrumMutation(s): 0 
EC: 1.6.1.2 (PDB Primary Data), 7.1.1.1 (UniProt)
UniProt
Find proteins for Q2RSB2 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1))
Explore Q2RSB2 
Go to UniProtKB:  Q2RSB2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2RSB2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P) transhydrogenase subunit betaC174Rhodospirillum rubrumMutation(s): 0 
EC: 1.6.1.2 (PDB Primary Data), 7.1.1.1 (UniProt)
UniProt
Find proteins for Q2RSB4 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1))
Explore Q2RSB4 
Go to UniProtKB:  Q2RSB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2RSB4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
H [auth C]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
SND
Query on SND

Download Ideal Coordinates CCD File 
D [auth A]THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O13 P2 S
UQYPZLRUJKCREN-NNYOXOHSSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.089α = 90
b = 74.698β = 90
c = 205.014γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-07
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation