4O9U

Mechanism of transhydrogenase coupling proton translocation and hydride transfer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.93 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

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This is version 1.2 of the entry. See complete history


Literature

Structural biology. Division of labor in transhydrogenase by alternating proton translocation and hydride transfer.

Leung, J.H.Schurig-Briccio, L.A.Yamaguchi, M.Moeller, A.Speir, J.A.Gennis, R.B.Stout, C.D.

(2015) Science 347: 178-181

  • DOI: https://doi.org/10.1126/science.1260451
  • Primary Citation of Related Structures:  
    4O93, 4O9P, 4O9T, 4O9U

  • PubMed Abstract: 

    NADPH/NADP(+) (the reduced form of NADP(+)/nicotinamide adenine dinucleotide phosphate) homeostasis is critical for countering oxidative stress in cells. Nicotinamide nucleotide transhydrogenase (TH), a membrane enzyme present in both bacteria and mitochondria, couples the proton motive force to the generation of NADPH. We present the 2.8 Å crystal structure of the transmembrane proton channel domain of TH from Thermus thermophilus and the 6.9 Å crystal structure of the entire enzyme (holo-TH). The membrane domain crystallized as a symmetric dimer, with each protomer containing a putative proton channel. The holo-TH is a highly asymmetric dimer with the NADP(H)-binding domain (dIII) in two different orientations. This unusual arrangement suggests a catalytic mechanism in which the two copies of dIII alternatively function in proton translocation and hydride transfer.


  • Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P) transhydrogenase subunit alpha 2
A, C
100Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_C1779
EC: 1.6.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q72GR9 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72GR9 
Go to UniProtKB:  Q72GR9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72GR9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P) transhydrogenase subunit beta
B, D
450Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_C1778
EC: 1.6.1.2
Membrane Entity: Yes 
UniProt
Find proteins for Q72GS0 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72GS0 
Go to UniProtKB:  Q72GS0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72GS0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NAD/NADP transhydrogenase alpha subunit 1
E, F
384Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_C1780
UniProt
Find proteins for Q72GR8 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72GR8 
Go to UniProtKB:  Q72GR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72GR8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.93 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.331α = 90
b = 160.59β = 128.36
c = 139.624γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-03-13
    Changes: Source and taxonomy