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 1.1 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: 10.1126/science.1260451
  • Primary Citation of Related Structures:  
    4O9P, 4O9T, 4O9U, 4O93

  • 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 ...

    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. dave@scripps.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P) transhydrogenase subunit alpha 2A, C94Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_C1779
EC: 1.6.1.2 (PDB Primary Data), 7.1.1.1 (UniProt)
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Transhydrogenases		Protein: 
Nicotinamide nucleotide transhydrogenase (TH) proton channel domain, pH 8.5
Find proteins for Q72GR9 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore Q72GR9 
Go to UniProtKB:  Q72GR9
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P) transhydrogenase subunit betaB, D270Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_C1778
EC: 1.6.1.2 (PDB Primary Data), 7.1.1.1 (UniProt)
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Transhydrogenases		Protein: 
Nicotinamide nucleotide transhydrogenase (TH) proton channel domain, pH 8.5
Find proteins for Q72GS0 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore Q72GS0 
Go to UniProtKB:  Q72GS0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG
Download Ideal Coordinates CCD File 
 E [auth A], F [auth C]MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N		 Ligand Interaction
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

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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