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: 101.86 kDa 
• Atom Count: 7082 
• Modelled Residue Count: 934 
• Deposited Residue Count: 942 
• Unique protein chains: 2

2OO5

Structure of transhydrogenase (dI.H2NADH)2(dIII.NADP+)1 asymmetric complex

• PDB DOI: 10.2210/pdb2OO5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodospirillum rubrum
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-01-25 Released: 2007-03-13 
• Deposition Author(s): Bhakta, T., Jackson, J.B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.275 
• R-Value Work: 0.219 
• R-Value Observed: 0.222 

Literature

Structures of the dI(2)dIII(1) Complex of Proton-Translocating Transhydrogenase with Bound, Inactive Analogues of NADH and NADPH Reveal Active Site Geometries

Bhakta, T., Whitehead, S.J., Snaith, J.S., Dafforn, T.R., Wilkie, J., Rajesh, S., White, S.A., Jackson, J.B.

(2007) Biochemistry 46: 3304-3318

• PubMed: 17323922 
• DOI: 10.1021/bi061843r
• Primary Citation of Related Structures:  
  2OO5, 2OOR


• PubMed Abstract: 
  

Transhydrogenase couples the redox reaction between NADH and NADP+ to proton translocation across a membrane. The enzyme comprises three components; dI binds NAD(H), dIII binds NADP(H), and dII spans the membrane. The 1,4,5,6-tetrahydro analogue of NADH (designated H2NADH) bound to isolated dI from Rhodospirillum rubrum transhydrogenase with similar affinity to the physiological nucleotide. Binding of either NADH or H2NADH led to closure of the dI mobile loop. The 1,4,5,6-tetrahydro analogue of NADPH (H2NADPH) bound very tightly to isolated R. rubrum dIII, but the rate constant for dissociation was greater than that for NADPH. The replacement of NADP+ on dIII either with H2NADPH or with NADPH caused a similar set of chemical shift alterations, signifying an equivalent conformational change. Despite similar binding properties to the natural nucleotides, neither H2NADH nor H2NADPH could serve as a hydride donor in transhydrogenation reactions. Mixtures of dI and dIII form dI2dIII1 complexes. The nucleotide charge distribution of complexes loaded either with H2NADH and NADP+ or with NAD+ and H2NADPH should more closely mimic the ground states for forward and reverse hydride transfer, respectively, than previously studied dead-end species. Crystal structures of such complexes at 2.6 and 2.3 A resolution are described. A transition state for hydride transfer between dihydronicotinamide and nicotinamide derivatives determined in ab initio quantum mechanical calculations resembles the organization of nucleotides in the transhydrogenase active site in the crystal structure. Molecular dynamics simulations of the enzyme indicate that the (dihydro)nicotinamide rings remain close to a ground state for hydride transfer throughout a 1.4 ns trajectory.

---

Organizational Affiliation: 

School of Biosciences, University of Birmingham, Edgbaston, UK.

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): 0  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	174	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	J [auth C]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
TXD	F [auth A], I [auth B]	1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H31 N7 O14 P2 GFDCQHGWOHYWLP-BFAIWXBASA-N
SO4	D [auth A], E [auth A], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.275 
• R-Value Work: 0.219 
• R-Value Observed: 0.222 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.199	α = 90
b = 101.025	β = 90
c = 131.721	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-01-25 
• Released Date: 2007-03-13 
Deposition Author(s): Bhakta, T., Jackson, J.B.

Revision History  

• Version 1.0: 2007-03-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance