4O93

Crystal structure of Thermus thermophilis transhydrogeanse domain II dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P) transhydrogenase subunit alpha 2
A, C
94Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_C1779
EC: 1.6.1.2 (PDB Primary Data), 7.1.1.1 (UniProt)
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P) transhydrogenase subunit beta
B, D
270Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_C1778
EC: 1.6.1.2 (PDB Primary Data), 7.1.1.1 (UniProt)
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
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.408α = 90
b = 86.92β = 94.55
c = 98.978γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
SHELXSphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2015-01-28
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations