Crystal structure of cryptochrome 3 from Arabidopsis thaliana and its implications for photolyase activity

Yihua Huang, Richard Baxter, Barbara S. Smith, Carrie L. Partch, Christopher L. Colbert, Johann Deisenhofer

Research output: Contribution to journalArticle

85 Citations (Scopus)

Abstract

Cryptochromes use near-UV/blue light to regulate a variety of growth and adaptive process. Recent biochemical studies demonstrate that the Cryptochrome-Drosophila, Arabidopsis, Synechocystis, Human (Cry-DASH) subfamily of cryptochromes have photolyase activity exclusively for single-stranded cyclobutane pyrimidine dimer (CPD)-containing DNA substrate [Selby C, Sancar A (2006) Proc Natl Acad Sci USA 103:17696-17700]. The crystal structure of cryptochrome 3 from Arabidopsis thaliana (At-Cry3), a member of the Cry-DASH proteins, at 2.1 Å resolution, reveals that both the light-harvesting cofactor 5,10-methenyl-tetrahydrofolylpolyglutamate (MTHF) and the catalytic cofactor flavin adenine dinucleotide (FAD) are noncovalently bound to the protein. The residues responsible for binding of MTHF in At-Cry3 are not conserved in Escherichia coli photolyase but are strongly conserved in the Cry-DASH subfamily of cryptochromes. The distance and orientation between MTHF and flavin adenine dinucleotide in At-Cry3 is similar to that of E. coli photolyase, in conjunction with the presence of electron transfer chain, suggesting the conservation of redox activity in At-Cry3. Two amino acid substitutions and the penetration of three charged side chains into the CPD-binding cavity in At-Cry3 alter the hydrophobic environment that is accommodating the hydrophobic sugar ring and thymine base moieties in class I CPD photolyases. These changes most likely make CPD binding less energetically favorable and, hence, insufficient to compete with pairing and stacking interactions between the CPD and the duplex DNA substrate. Thus, Cry-DASH subfamily proteins may be unable to stabilize CPD flipped out from the duplex DNA substrate but may be able to preserve the DNA repair activity toward single-stranded CPD-containing DNA substrate.

Original languageEnglish (US)
Pages (from-to)17701-17706
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume103
Issue number47
DOIs
StatePublished - Nov 21 2006

Fingerprint

Cryptochromes
Deoxyribodipyrimidine Photo-Lyase
Pyrimidine Dimers
Arabidopsis
Synechocystis
Drosophila
Flavin-Adenine Dinucleotide
DNA
Escherichia coli
Thymine
Amino Acid Substitution
Ultraviolet Rays
DNA Repair
Oxidation-Reduction
Proteins
Electrons
Light

Keywords

  • Cryptochrome-DASH
  • DNA repair
  • Light-harvesting cofactor

ASJC Scopus subject areas

  • Genetics
  • General

Cite this

Crystal structure of cryptochrome 3 from Arabidopsis thaliana and its implications for photolyase activity. / Huang, Yihua; Baxter, Richard; Smith, Barbara S.; Partch, Carrie L.; Colbert, Christopher L.; Deisenhofer, Johann.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 47, 21.11.2006, p. 17701-17706.

Research output: Contribution to journalArticle

Huang, Yihua ; Baxter, Richard ; Smith, Barbara S. ; Partch, Carrie L. ; Colbert, Christopher L. ; Deisenhofer, Johann. / Crystal structure of cryptochrome 3 from Arabidopsis thaliana and its implications for photolyase activity. In: Proceedings of the National Academy of Sciences of the United States of America. 2006 ; Vol. 103, No. 47. pp. 17701-17706.
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