2OOR

Structure of transhydrogenase (dI.NAD+)2(dIII.H2NADPH)1 asymmetric complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structures of the dI(2)dIII(1) Complex of Proton-Translocating Transhydrogenase with Bound, Inactive Analogues of NADH and NADPH Reveal Active Site Geometries

Bhakta, T.Whitehead, S.J.Snaith, J.S.Dafforn, T.R.Wilkie, J.Rajesh, S.White, S.A.Jackson, J.B.

(2007) Biochemistry 46: 3304-3318

  • DOI: 10.1021/bi061843r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Transhydrogenase couples the redox reaction between NADH and NADP+ to proton translocation across a membrane. The enzyme comprises three components; dI binds NAD(H), dIII binds NADP(H), and dII spans the membrane. The 1,4,5,6-tetrahydro analogue of N ...

    Transhydrogenase couples the redox reaction between NADH and NADP+ to proton translocation across a membrane. The enzyme comprises three components; dI binds NAD(H), dIII binds NADP(H), and dII spans the membrane. The 1,4,5,6-tetrahydro analogue of NADH (designated H2NADH) bound to isolated dI from Rhodospirillum rubrum transhydrogenase with similar affinity to the physiological nucleotide. Binding of either NADH or H2NADH led to closure of the dI mobile loop. The 1,4,5,6-tetrahydro analogue of NADPH (H2NADPH) bound very tightly to isolated R. rubrum dIII, but the rate constant for dissociation was greater than that for NADPH. The replacement of NADP+ on dIII either with H2NADPH or with NADPH caused a similar set of chemical shift alterations, signifying an equivalent conformational change. Despite similar binding properties to the natural nucleotides, neither H2NADH nor H2NADPH could serve as a hydride donor in transhydrogenation reactions. Mixtures of dI and dIII form dI2dIII1 complexes. The nucleotide charge distribution of complexes loaded either with H2NADH and NADP+ or with NAD+ and H2NADPH should more closely mimic the ground states for forward and reverse hydride transfer, respectively, than previously studied dead-end species. Crystal structures of such complexes at 2.6 and 2.3 A resolution are described. A transition state for hydride transfer between dihydronicotinamide and nicotinamide derivatives determined in ab initio quantum mechanical calculations resembles the organization of nucleotides in the transhydrogenase active site in the crystal structure. Molecular dynamics simulations of the enzyme indicate that the (dihydro)nicotinamide rings remain close to a ground state for hydride transfer throughout a 1.4 ns trajectory.


    Organizational Affiliation

    School of Biosciences, University of Birmingham, Edgbaston, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD(P) transhydrogenase subunit alpha part 1
A, B
384Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1)Mutation(s): 0 
Gene Names: pntAA (nntA1)
EC: 1.6.1.2
Find proteins for Q2RSB2 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1))
Go to UniProtKB:  Q2RSB2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NAD(P) transhydrogenase subunit beta
C
174Rhodospirillum rubrumMutation(s): 0 
Gene Names: pntB (nntB)
EC: 1.6.1.2
Find proteins for P0C188 (Rhodospirillum rubrum)
Go to UniProtKB:  P0C188
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
TXP
Query on TXP

Download SDF File 
Download CCD File 
C
1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE
C21 H32 N7 O17 P3
MGWIKFWDIJJFDG-ILTSWSAWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NADKd: 300000 nM BINDINGMOAD
TXPKd: 27000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.247 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.194α = 90.00
b = 74.451β = 90.00
c = 204.844γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2018-01-24
    Type: Structure summary