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PDBsum entry 1f8g

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1f8g
Jmol
Contents
Protein chains
382 a.a. *
Ligands
NAD ×4
Waters ×1459
* Residue conservation analysis
PDB id:
1f8g
Name: Oxidoreductase
Title: The x-ray structure of nicotinamide nucleotide transhydrogenase from rhodospirillum rubrum complexed with NAD+
Structure: Nicotinamide nucleotide transhydrogenase. Chain: a, b, c, d. Engineered: yes
Source: Rhodospirillum rubrum. Organism_taxid: 1085. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.00Å     R-factor:   0.210     R-free:   0.260
Authors: P.A.Buckley,J.Baz Jackson,T.Schneider,S.A.White,D.W.Rice, P.J.Baker
Key ref:
P.A.Buckley et al. (2000). Protein-protein recognition, hydride transfer and proton pumping in the transhydrogenase complex. Structure, 8, 809-815. PubMed id: 10997900 DOI: 10.1016/S0969-2126(00)00171-4
Date:
30-Jun-00     Release date:   30-Jun-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q2RSB2  (PNTAA_RHORT) -  NAD(P) transhydrogenase subunit alpha part 1
Seq:
Struc:
384 a.a.
382 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.6.1.2  - NAD(P)(+) transhydrogenase (Re/Si-specific).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NADPH + NAD+ = NADP+ + NADH
NADPH
+
NAD(+)
Bound ligand (Het Group name = NAD)
corresponds exactly
= NADP(+)
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     nucleotide binding     10 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(00)00171-4 Structure 8:809-815 (2000)
PubMed id: 10997900  
 
 
Protein-protein recognition, hydride transfer and proton pumping in the transhydrogenase complex.
P.A.Buckley, J.Baz Jackson, T.Schneider, S.A.White, D.W.Rice, P.J.Baker.
 
  ABSTRACT  
 
BACKGROUND: Membrane-bound ion pumps are involved in metabolic regulation, osmoregulation, cell signalling, nerve transmission and energy transduction. How the ion electrochemical gradient interacts with the scalar chemistry and how the catalytic machinery is gated to ensure high coupling efficiency are fundamental to the mechanism of action of such pumps. Transhydrogenase is a conformationally coupled proton pump linking a proton gradient to the redox reaction between NAD(H) and NADP(H). The enzyme has three components; dI binds NAD(H), dII spans the membrane and dIII binds NADP(H). RESULTS: The first crystal structure of a transhydrogenase dI component (from Rhodospirillum rubrum) has been determined at 2.0 A resolution. The monomer comprises two domains. Both are involved in dimer formation, and one has a Rossmann fold that binds NAD+ in a novel mode. The two domains can adopt different conformations. In the most closed conformation, the nicotinamide ring is expelled from the cleft between the two domains and is exposed on the outside of the protein. In this conformation it is possible to dock the structure of dI/NAD+ with that of a dIII/NADP+ complex to provide the first insights into the molecular basis of the hydride-transfer step. CONCLUSIONS: Analysis of the model of the dI/dIII complex identifies residues potentially involved in dI/dIII interaction and shows how domain motion in dI results in a shift in position of the nicotinamide ring of NAD+. We propose that this movement is responsible for switching between the forbidden and allowed states for hydride transfer during proton pumping.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The dI component of transhydrogenase. (a) A stereo representation of the Ca backbone of a single subunit. (b) A cartoon of the dI dimer, viewed down the twofold axis, showing the NAD^+ (magenta ball and sticks) bound to each subunit. (c) The final (2F[o]-F[c]) electron density map, contoured at 0.7 s, around the NAD^+ bound to the most closed subunit D.
 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 809-815) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19210777 H.Li, H.Zhang, M.Zheng, J.Luo, L.Kang, X.Liu, X.Wang, and H.Jiang (2009).
An effective docking strategy for virtual screening based on multi-objective optimization algorithm.
  BMC Bioinformatics, 10, 58.  
18972197 A.Pedersen, G.B.Karlsson, and J.Rydström (2008).
Proton-translocating transhydrogenase: an update of unsolved and controversial issues.
  J Bioenerg Biomembr, 40, 463-473.  
17911104 U.M.Obiozo, T.H.Brondijk, A.J.White, G.van Boxel, T.R.Dafforn, S.A.White, and J.B.Jackson (2007).
Substitution of tyrosine 146 in the dI component of proton-translocating transhydrogenase leads to reversible dissociation of the active dimer into inactive monomers.
  J Biol Chem, 282, 36434-36443.  
16533815 T.H.Brondijk, G.I.van Boxel, O.C.Mather, P.G.Quirk, S.A.White, and J.B.Jackson (2006).
The role of invariant amino acid residues at the hydride transfer site of proton-translocating transhydrogenase.
  J Biol Chem, 281, 13345-13354.
PDB codes: 2fr8 2frd 2fsv
15039572 C.Oswald, T.Johansson, S.Törnroth, M.Okvist, and U.Krengel (2004).
Crystallization and preliminary crystallographic analysis of the NAD(H)-binding domain of Escherichia coli transhydrogenase.
  Acta Crystallogr D Biol Crystallogr, 60, 743-745.  
12791694 A.Singh, J.D.Venning, P.G.Quirk, G.I.van Boxel, D.J.Rodrigues, S.A.White, and J.B.Jackson (2003).
Interactions between transhydrogenase and thio-nicotinamide Analogues of NAD(H) and NADP(H) underline the importance of nucleotide conformational changes in coupling to proton translocation.
  J Biol Chem, 278, 33208-33216.
PDB codes: 1pt9 1ptj
14573954 F.Dall'Antonia, P.J.Baker, and T.R.Schneider (2003).
Optimization of selenium substructures as obtained from SHELXD.
  Acta Crystallogr D Biol Crystallogr, 59, 1987-1994.  
12972415 J.Broos, E.Gabellieri, G.I.van Boxel, J.B.Jackson, and G.B.Strambini (2003).
Tryptophan phosphorescence spectroscopy reveals that a domain in the NAD(H)-binding component (dI) of transhydrogenase from Rhodospirillum rubrum has an extremely rigid and conformationally homogeneous protein core.
  J Biol Chem, 278, 47578-47584.  
12952962 M.Yamaguchi, and C.D.Stout (2003).
Essential glycine in the proton channel of Escherichia coli transhydrogenase.
  J Biol Chem, 278, 45333-45339.  
12839984 S.Ricagno, S.Jonsson, N.Richards, and Y.Lindqvist (2003).
Formyl-CoA transferase encloses the CoA binding site at the interface of an interlocked dimer.
  EMBO J, 22, 3210-3219.
PDB codes: 1p5h 1p5r
14567675 V.Sundaresan, M.Yamaguchi, J.Chartron, and C.D.Stout (2003).
Conformational change in the NADP(H) binding domain of transhydrogenase defines four states.
  Biochemistry, 42, 12143-12153.
PDB codes: 1pno 1pnq
12004068 C.J.Weston, J.D.Venning, and J.B.Jackson (2002).
The membrane-peripheral subunits of transhydrogenase from Entamoeba histolytica are functional only when dimerized.
  J Biol Chem, 277, 26163-26170.  
12230562 C.Johansson, A.Pedersen, B.G.Karlsson, and J.Rydström (2002).
Redox-sensitive loops D and E regulate NADP(H) binding in domain III and domain I-domain III interactions in proton-translocating Escherichia coli transhydrogenase.
  Eur J Biochem, 269, 4505-4515.  
11976492 M.Roth, P.Carpentier, O.Kaïkati, J.Joly, P.Charrault, M.Pirocchi, R.Kahn, E.Fanchon, L.Jacquamet, F.Borel, A.Bertoni, P.Israel-Gouy, and J.L.Ferrer (2002).
FIP: a highly automated beamline for multiwavelength anomalous diffraction experiments.
  Acta Crystallogr D Biol Crystallogr, 58, 805-814.  
12087099 M.Yamaguchi, C.D.Stout, and Y.Hatefi (2002).
The proton channel of the energy-transducing nicotinamide nucleotide transhydrogenase of Escherichia coli.
  J Biol Chem, 277, 33670-33675.  
12351820 T.R.Schneider, and G.M.Sheldrick (2002).
Substructure solution with SHELXD.
  Acta Crystallogr D Biol Crystallogr, 58, 1772-1779.  
11231296 D.J.Rodrigues, J.D.Venning, P.G.Quirk, and J.B.Jackson (2001).
A change in ionization of the NADP(H)-binding component (dIII) of proton-translocating transhydrogenase regulates both hydride transfer and nucleotide release.
  Eur J Biochem, 268, 1430-1438.  
11250201 N.P.Cotton, S.A.White, S.J.Peake, S.McSweeney, and J.B.Jackson (2001).
The crystal structure of an asymmetric complex of the two nucleotide binding components of proton-translocating transhydrogenase.
  Structure, 9, 165-176.
PDB code: 1hzz
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.