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PDBsum entry 1zgo
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protein Protein-protein interface(s) links
Luminescent protein PDB id
1zgo

 

 

 

 

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Contents
Protein chains
218 a.a. *
Waters ×535
* Residue conservation analysis
PDB id:
1zgo
Name: Luminescent protein
Title: High resolution crystal structure of the discosoma red fluorescent protein (dsred)
Structure: Red fluorescent protein drfp583. Chain: a, b, c, d. Synonym: dsred. Engineered: yes
Source: Discosoma sp.. Organism_taxid: 86600. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
1.40Å     R-factor:   0.163     R-free:   0.206
Authors: J.L.Tubbs,J.A.Tainer,E.D.Getzoff
Key ref:
J.L.Tubbs et al. (2005). Crystallographic structures of Discosoma red fluorescent protein with immature and mature chromophores: linking peptide bond trans-cis isomerization and acylimine formation in chromophore maturation. Biochemistry, 44, 9833-9840. PubMed id: 16026155 DOI: 10.1021/bi0472907
Date:
21-Apr-05     Release date:   02-Aug-05    
PROCHECK
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 Headers
 References

Protein chains
Q9U6Y8  (RFP_DISSP) -  Red fluorescent protein drFP583 from Discosoma sp.
Seq:
Struc: 		225 a.a.
218 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
DOI no: 10.1021/bi0472907 Biochemistry 44:9833-9840 (2005)
PubMed id: 16026155  
 
 
Crystallographic structures of Discosoma red fluorescent protein with immature and mature chromophores: linking peptide bond trans-cis isomerization and acylimine formation in chromophore maturation.
J.L.Tubbs, J.A.Tainer, E.D.Getzoff.
 
  ABSTRACT  
 
The mature self-synthesizing p-hydroxybenzylideneimidazolinone-like fluorophores of Discosoma red fluorescent protein (DsRed) and Aequorea victoria green fluorescent protein (GFP) are extensively studied as powerful biological markers. Yet, the spontaneous formation of these fluorophores by cyclization, oxidation, and dehydration reactions of tripeptides within their protein environment remains incompletely understood. The mature DsRed fluorophore (Gln 66, Tyr 67, and Gly 68) differs from the GFP fluorophore by an acylimine that results in Gln 66 Calpha planar geometry and by a Phe 65-Gln 66 cis peptide bond. DsRed green-to-red maturation includes a green-fluorescing immature chromophore and requires a chromophore peptide bond trans-cis isomerization that is slow and incomplete. To clarify the unique structural chemistry for the individual immature "green" and mature "red" chromophores of DsRed, we report here the determination and analysis of crystal structures for the wild-type protein (1.4 A resolution), the entirely green DsRed K70M mutant protein (1.9 A resolution), and the DsRed designed mutant Q66M (1.9 A resolution), which shows increased red chromophore relative to the wild-type DsRed. Whereas the mature, red-fluorescing chromophore has the expected cis peptide bond and a sp(2)-hybridized Gln 66 Calpha with planar geometry, the crystal structure of the immature green-fluorescing chromophore of DsRed, presented here for the first time, reveals a trans peptide bond and a sp(3)-hybridized Gln 66 Calpha with tetrahedral geometry. These results characterize a GFP-like immature green DsRed chromophore structure, reveal distinct mature and immature chromophore environments, and furthermore provide evidence for the coupling of acylimine formation with trans-cis isomerization.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23396808 S.Classen, G.L.Hura, J.M.Holton, R.P.Rambo, I.Rodic, P.J.McGuire, K.Dyer, M.Hammel, G.Meigs, K.A.Frankel, and J.A.Tainer (2013).
Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source.
  J Appl Crystallogr, 46, 1.  
20635430 C.Blum, A.J.Meixner, and V.Subramaniam (2011).
Dark proteins disturb multichromophore coupling in tetrameric fluorescent proteins.
  J Biophotonics, 4, 114-121.  
20394363 F.V.Subach, G.H.Patterson, M.Renz, J.Lippincott-Schwartz, and V.V.Verkhusha (2010).
Bright monomeric photoactivatable red fluorescent protein for two-color super-resolution sptPALM of live cells.
  J Am Chem Soc, 132, 6481-6491.  
21134271 I.Zaitoun, C.S.Erickson, K.Schell, and M.L.Epstein (2010).
Use of RNAlater in fluorescence-activated cell sorting (FACS) reduces the fluorescence from GFP but not from DsRed.
  BMC Res Notes, 3, 328.  
18854990 C.Blum, and V.Subramaniam (2009).
Single-molecule spectroscopy of fluorescent proteins.
  Anal Bioanal Chem, 393, 527-541.  
19934036 F.V.Subach, V.N.Malashkevich, W.D.Zencheck, H.Xiao, G.S.Filonov, S.C.Almo, and V.V.Verkhusha (2009).
Photoactivation mechanism of PAmCherry based on crystal structures of the protein in the dark and fluorescent states.
  Proc Natl Acad Sci U S A, 106, 21097-21102.
PDB codes: 3kcs 3kct
19737938 S.Pletnev, N.G.Gurskaya, N.V.Pletneva, K.A.Lukyanov, D.M.Chudakov, V.I.Martynov, V.O.Popov, M.V.Kovalchuk, A.Wlodawer, Z.Dauter, and V.Pletnev (2009).
Structural basis for phototoxicity of the genetically encoded photosensitizer KillerRed.
  J Biol Chem, 284, 32028-32039.
PDB codes: 3gb3 3gl4
19606312 W.Yan, D.Xie, and J.Zeng (2009).
The 559-to-600 nm shift observed in red fluorescent protein eqFP611 is attributed to cis-trans isomerization of the chromophore in an anionic protein pocket.
  Phys Chem Chem Phys, 11, 6042-6050.  
19165727 X.Shu, L.Wang, L.Colip, K.Kallio, and S.J.Remington (2009).
Unique interactions between the chromophore and glutamate 16 lead to far-red emission in a red fluorescent protein.
  Protein Sci, 18, 460-466.  
18991554 E.E.Khrameeva, V.L.Drutsa, E.P.Vrzheshch, D.V.Dmitrienko, and P.V.Vrzheshch (2008).
Mutants of monomeric red fluorescent protein mRFP1 at residue 66: structure modeling by molecular dynamics and search for correlations with spectral properties.
  Biochemistry (Mosc), 73, 1085-1095.  
18682399 S.Pletnev, D.Shcherbo, D.M.Chudakov, N.Pletneva, E.M.Merzlyak, A.Wlodawer, Z.Dauter, and V.Pletnev (2008).
A crystallographic study of bright far-red fluorescent protein mKate reveals pH-induced cis-trans isomerization of the chromophore.
  J Biol Chem, 283, 28980-28987.
PDB codes: 3bx9 3bxa 3bxb 3bxc
17881826 N.Pletneva, V.Pletnev, T.Tikhonova, A.A.Pakhomov, V.Popov, V.I.Martynov, A.Wlodawer, Z.Dauter, and S.Pletnev (2007).
Refined crystal structures of red and green fluorescent proteins from the button polyp Zoanthus.
  Acta Crystallogr D Biol Crystallogr, 63, 1082-1093.
PDB codes: 2icr 2ojk 2pxs 2pxw
17886433 N.V.Pletneva, S.V.Pletnev, D.M.Chudakov, T.V.Tikhonova, V.O.Popov, V.I.Martynov, A.Wlodawer, Z.Dauter, and V.Z.Pletnev (2007).
[Three-dimensional structure of yellow fluorescent protein zYFP538 from Zoanthus sp. at the resolution 1.8 angstrom]
  Bioorg Khim, 33, 421-430.
PDB code: 2ogr
17125463 D.V.Dmitrienko, E.P.Vrzheshch, V.L.Drutsa, and P.V.Vrzheshch (2006).
Red fluorescent protein DsRed: parametrization of its chromophore as an amino acid residue for computer modeling in the OPLS-AA force field.
  Biochemistry (Mosc), 71, 1133-1152.  
16223340 R.M.Wachter (2006).
The family of GFP-like proteins: structure, function, photophysics and biosensor applications. Introduction and perspective.
  Photochem Photobiol, 82, 339-344.  
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.

 

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