The nicotinamide dinucleotide binding motif: a comparison of nucleotide binding proteins

@article{Bellamacina1996TheND,
  title={The nicotinamide dinucleotide binding motif: a comparison of nucleotide binding proteins},
  author={Cornelia R Bellamacina},
  journal={The FASEB Journal},
  year={1996},
  volume={10},
  pages={1257 - 1269}
}
  • C. Bellamacina
  • Published 1 September 1996
  • Biology, Chemistry
  • The FASEB Journal
Classical nicotinamide adenine dinucleotide (NAD+) binding proteins contain a βαβαβ unit. By comparing 14 such proteins, it is observed that an additional β strand associates with this unit to form the “core” topology, the minimum structure necessary to bind cofactor. Although the overall topologies of the cofactor binding domains of nicotinamide binding proteins vary, they all contain at least the core topology. The first 30‐35 amino acids of the core topology, called the “fingerprint” region… 

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References

SHOWING 1-10 OF 53 REFERENCES

Atomic structure of ferredoxin-NADP+ reductase: prototype for a structurally novel flavoenzyme family.

TLDR
Conclusive evidence is presented that the ferredoxin reductase structure is a prototype for the nicotinamide dinucleotide and FAD binding domains of the enzymes NADPH-cytochrome P450 reduct enzyme, NAD PH-sulfite reductases, NADH-cy tochrome b5 reductasing enzymes, and NADh-nitrate reduCTase.

Crystallographic investigations of nicotinamide adenine dinucleotide binding to horse liver alcohol dehydrogenase.

TLDR
The binding of NAD to liver alcohol dehydrogenase has been studied in four different ternary complexes by using crystallographic methods, and the overall conformation of the NAD molecule is similar to that observed for other dehydrogenases, but differs in details.

Crystal structure of rat liver dihydropteridine reductase.

TLDR
The structure of a binary complex of dihydropteridine reductase with its cofactor, NADH, has been solved and refined to a final R factor of 15.4% by using 2.3 A diffraction data.

On the three-dimensional structure and catalytic mechanism of triose phosphate isomerase.

  • T. AlberD. Banner I. Wilson
  • Chemistry
    Philosophical transactions of the Royal Society of London. Series B, Biological sciences
  • 1981
TLDR
Crystallographic studies of the binding of DHAP to both the chicken and the yeast enzymes reveal a common mode of binding and suggest a mechanisms for catalysis involving polarization of the substrate carbonyl group.

Binding of nucleotides by proteins

The NADPH binding site on beef liver catalase.

  • I. FitaM. Rossmann
  • Biology, Chemistry
    Proceedings of the National Academy of Sciences of the United States of America
  • 1985
TLDR
In contrast to nearly all other known structures of protein-bound NADP, NAD, and FAD, the NADP molecule of beef liver catalase is folded into a right-handed helix and bound, in part, in the vicinity of the carboxyl end of two alpha-helices.
...