2ZO7

Crystal Structure of a Kusabira-Cyan Mutant (KCY-R1), a Cyan/Green-Emitting GFP-Like Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of a new cyan fluorescent protein and its hue-shifted variants

Kikuchi, A.Fukumura, E.Karasawa, S.Shiro, Y.Miyawaki, A.

(2009) Biochemistry 48: 5276-5283

  • DOI: 10.1021/bi801658p
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Green fluorescent protein (GFP) based techniques are well established in molecular biology; however, the detailed mechanism for the fine-tuning of fluorescent colors remains unclear. Here, we report the cloning and crystal structure of a new cyan-emi ...

    Green fluorescent protein (GFP) based techniques are well established in molecular biology; however, the detailed mechanism for the fine-tuning of fluorescent colors remains unclear. Here, we report the cloning and crystal structure of a new cyan-emitting GFP-like protein, KCy. We also developed a mutant protein with a high folding efficiency (KCy-G4219: lambda(abs) = 453 nm; lambda(em) = 486 nm). X-ray diffraction analysis revealed that the KCy chromophore is formed from an internal Ser62-Tyr63-Gly64 tripeptide. The serine residue at the first position of the chromophore-forming tripeptide has a short polar chain (-OH) that forms a noncovalent interaction with the His38 imidazole at a distance of 2.96 A. Substitution of His38 in KCy-G4219 with Gln (KCy-R1) or Leu residues resulted in a slight but significant red shift of the emission peak maximum from 486 to 492 or 496 nm, respectively. The crystal structure of KCy-R1 determined at a resolution of 1.58 A showed that the noncovalent interaction between Ser62-OH and the substituted Gln38 occurred over a longer distance (3.07 A) than that observed in the wild-type KCy. Such an interaction is absent in the Leu mutant, suggesting that this interaction is one of the key factors responsible for fine-tuning the emission peak maxima, which are affected by chromophore polarization. Moreover, the structural comparison suggests that an additional water molecule buried in the space between the Ala158 residue and the chromophore phenolate is also responsible for the chromophore polarization.


    Organizational Affiliation

    Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo, Hyogo 679-5148, Japan. kikuchi@spring8.or.jp



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYAN/GREEN-EMITTING GFP-LIKE PROTEIN, KUSABIRA-CYAN MUTANT (KCY-R1)
A
222Lithophyllon concinnaMutation(s): 0 
Protein Feature View
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GYS
Query on GYS
AL-PEPTIDE LINKINGC14 H15 N3 O5SER,TYR,GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.689α = 90
b = 45.016β = 94.98
c = 51.158γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-05-02
    Changes: Other