1PNO

Crystal structure of R. rubrum transhydrogenase domain III bound to NADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

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This is version 1.3 of the entry. See complete history


Literature

Conformational Change in the NADP(H) Binding Domain of Transhydrogenase Defines Four States

Sundaresan, V.Yamaguchi, M.Chartron, J.Stout, C.D.

(2003) Biochemistry 42: 12143-12153

  • DOI: https://doi.org/10.1021/bi035006q
  • Primary Citation of Related Structures:  
    1PNO, 1PNQ

  • PubMed Abstract: 

    Proton-translocating transhydrogenase (TH) couples direct and stereospecific hydride transfer between NAD(H) and NADP(H), bound to soluble domains dI and dIII, respectively, to proton translocation across a membrane bound domain, dII. The reaction occurs with proton-gradient coupled conformational changes, which affect the energetics of substrate binding and interdomain interactions. The crystal structure of TH dIII from Rhodospirillum rubrum has been determined in the presence of NADPH (2.4 A) and NADP (2.1 A) (space group P6(1)22). Each structure has two molecules in the asymmetric unit, differing in the conformation of the NADP(H) binding loop D. In one molecule, loop D has an open conformation, with the B face of (dihydro)nicotinamide exposed to solvent. In the other molecule, loop D adopts a hitherto unobserved closed conformation, resulting in close interactions between NADP(H) and side chains of the highly conserved residues, betaSer405, betaPro406, and betaIle407. The conformational change shields the B face of (dihydro)nicotinamide from solvent, which would block hydride transfer in the intact enzyme. It also alters the environments of invariant residues betaHis346 and betaAsp393. However, there is little difference in either the open or the closed conformation upon change in oxidation state of nicotinamide, i.e., for NADP vs. NADPH. Consequently, the occurrence of two loop D conformations for both substrate oxidation states gives rise to four states: NADP-open, NADP-closed, NADPH-open, and NADPH-closed. Because these states are distinguished by protein conformation and by net charge they may be important in the proton translocating mechanism of intact TH.


  • Organizational Affiliation

    Department of Molecular Biology, 10550 North Torrey Pines Road, The Scripps Research Institute, La Jolla, California 92037, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P) transhydrogenase subunit beta
A, B
180Rhodospirillum rubrumMutation(s): 0 
Gene Names: PNTB OR NNTB
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
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.95α = 90
b = 117.95β = 90
c = 211.28γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
BEASTphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations