Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 104.18 kDa 
• Atom Count: 6758 
• Modelled Residue Count: 896 
• Deposited Residue Count: 971 
• Unique protein chains: 2

2FRD

Structure of Transhydrogenase (dI.S138A.NADH)2(dIII.NADPH)1 asymmetric complex

• PDB DOI: 10.2210/pdb2FRD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodospirillum rubrum
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-01-19 Released: 2006-02-28 
• Deposition Author(s): Brondijk, T.H., van Boxel, G.I., Mather, O.C., Quirk, P.G., White, S.A., Jackson, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.272 
• R-Value Work: 0.213 
• R-Value Observed: 0.219 

Literature

The Role of Invariant Amino Acid Residues at the Hydride Transfer Site of Proton-translocating Transhydrogenase.

Brondijk, T.H., van Boxel, G.I., Mather, O.C., Quirk, P.G., White, S.A., Jackson, J.B.

(2006) J Biol Chem 281: 13345-13354

• PubMed: 16533815 
• DOI: 10.1074/jbc.M513230200
• Primary Citation of Related Structures:  
  2FR8, 2FRD, 2FSV


• PubMed Abstract: 
  

Transhydrogenase couples proton translocation across a membrane to hydride transfer between NADH and NADP+. Previous x-ray structures of complexes of the nucleotide-binding components of transhydrogenase ("dI2dIII1" complexes) indicate that the dihydronicotinamide ring of NADH can move from a distal position relative to the nicotinamide ring of NADP+ to a proximal position. The movement might be responsible for gating hydride transfer during proton translocation. We have mutated three invariant amino acids, Arg-127, Asp-135, and Ser-138, in the NAD(H)-binding site of Rhodospirillum rubrum transhydrogenase. In each mutant, turnover by the intact enzyme is strongly inhibited. Stopped-flow experiments using dI2dIII1 complexes show that inhibition results from a block in the steps associated with hydride transfer. Mutation of Asp-135 and Ser-138 had no effect on the binding affinity of either NAD+ or NADH, but mutation of Arg-127 led to much weaker binding of NADH and slightly weaker binding of NAD+. X-ray structures of dI2dIII1 complexes carrying the mutations showed that their effects were restricted to the locality of the bound NAD(H). The results are consistent with the suggestion that in wild-type protein movement of the Arg-127 side chain, and its hydrogen bonding to Asp-135 and Ser-138, stabilizes the dihydronicotinamide of NADH in the proximal position for hydride transfer.

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Organizational Affiliation: 

School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P) transhydrogenase subunit alpha part 1	A, B	384	Rhodospirillum rubrum	Mutation(s): 1  Gene Names: pntAA, nntA1 EC: 1.6.1.2 (PDB Primary Data), 7.1.1.1 (UniProt)
UniProt
Find proteins for Q2RSB2 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RSB2  Go to UniProtKB:  Q2RSB2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P) transhydrogenase subunit beta	C	203	Rhodospirillum rubrum	Mutation(s): 0  Gene Names: pntB, nntB EC: 1.6.1.2 (PDB Primary Data), 7.1.1.1 (UniProt)
UniProt
Find proteins for P0C188 (Rhodospirillum rubrum) Explore P0C188  Go to UniProtKB:  P0C188

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	F [auth C]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
NAI	D [auth A], E [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NAD	PDBBind:  2FRD	Kd: 2.90e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.272 
• R-Value Work: 0.213 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.3	α = 90
b = 74.11	β = 90
c = 205.22	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-01-19 
• Released Date: 2006-02-28 
Deposition Author(s): Brondijk, T.H., van Boxel, G.I., Mather, O.C., Quirk, P.G., White, S.A., Jackson, J.B.

Revision History  

• Version 1.0: 2006-02-28
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2013-11-20
  Changes: Non-polymer description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations