Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-Å resolution

Daniel Yarbrough, Rebekka Wachter, Karen Kallio, Mikhail V. Matz, S. James Remington

Research output: Contribution to journalArticle

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Abstract

The crystal structure of DsRed, a red fluorescent protein from a corallimorpharian, has been determined at 2.0-Å resolution by multiple-wavelength anomalous dispersion and crystallographic refinement. Crystals of the selenomethionine-substituted protein have space group P21 and contain a tetramer with 222 noncrystallographic symmetry in the asymmetric unit. The refined model has satisfactory stereochemistry and a final crystallographic R factor of 0.162. The protein, which forms an obligatory tetramer in solution and in the crystal, is a squat rectangular prism comprising four protomers whose fold is extremely similar to that of the Aequorea victoria green fluorescent protein despite low (≈23%) amino acid sequence homology. The monomer consists of an 11-stranded β barrel with a coaxial helix. The chromophores, formed from the primary sequence -Gln-Tyr-Gly- (residues 66-68), are arranged in a ≈27 × 34-Å rectangular array in two approximately antiparallel pairs. The geometry at the α carbon of Gln-66 (refined without stereochemical restraints) is consistent with an sp2 hybridized center, in accord with the proposal that red fluorescence is because of an additional oxidation step that forms an acylimine extension to the chromophore [Gross, L. A., Baird, G. S., Hoffman, R. C., Baldridge, K. K. & Tsien, R. Y. (2000) Proc. Natl. Acad. Sci. USA 87, 11990-11995]. The carbonyl oxygen of Phe-65 is almost 90° out of the plane of the chromophore, consistent with theoretical calculations suggesting that this is the minimum energy conformation of this moiety despite the conjugation of this group with the rest of the chromophore.

Original languageEnglish (US)
Pages (from-to)462-467
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume98
Issue number2
DOIs
StatePublished - Jan 16 2001
Externally publishedYes

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Anthozoa
Selenomethionine
Amino Acid Sequence Homology
R Factors
Protein Subunits
Proteins
Carbon
Fluorescence
Oxygen
fluorescent protein 583
red fluorescent protein
Aequorea victoria green fluorescent protein

ASJC Scopus subject areas

  • Genetics
  • General

Cite this

Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-Å resolution. / Yarbrough, Daniel; Wachter, Rebekka; Kallio, Karen; Matz, Mikhail V.; Remington, S. James.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 98, No. 2, 16.01.2001, p. 462-467.

Research output: Contribution to journalArticle

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abstract = "The crystal structure of DsRed, a red fluorescent protein from a corallimorpharian, has been determined at 2.0-{\AA} resolution by multiple-wavelength anomalous dispersion and crystallographic refinement. Crystals of the selenomethionine-substituted protein have space group P21 and contain a tetramer with 222 noncrystallographic symmetry in the asymmetric unit. The refined model has satisfactory stereochemistry and a final crystallographic R factor of 0.162. The protein, which forms an obligatory tetramer in solution and in the crystal, is a squat rectangular prism comprising four protomers whose fold is extremely similar to that of the Aequorea victoria green fluorescent protein despite low (≈23{\%}) amino acid sequence homology. The monomer consists of an 11-stranded β barrel with a coaxial helix. The chromophores, formed from the primary sequence -Gln-Tyr-Gly- (residues 66-68), are arranged in a ≈27 × 34-{\AA} rectangular array in two approximately antiparallel pairs. The geometry at the α carbon of Gln-66 (refined without stereochemical restraints) is consistent with an sp2 hybridized center, in accord with the proposal that red fluorescence is because of an additional oxidation step that forms an acylimine extension to the chromophore [Gross, L. A., Baird, G. S., Hoffman, R. C., Baldridge, K. K. & Tsien, R. Y. (2000) Proc. Natl. Acad. Sci. USA 87, 11990-11995]. The carbonyl oxygen of Phe-65 is almost 90° out of the plane of the chromophore, consistent with theoretical calculations suggesting that this is the minimum energy conformation of this moiety despite the conjugation of this group with the rest of the chromophore.",
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