PDBsum entry 1bfp

Luminescence

PDB id

1bfp

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Contents

			Protein chain

					227 a.a. *

			Waters ×82

* Residue conservation analysis

PDB id:

1bfp

Links

Name:

Luminescence

Title:

Blue variant of green fluorescent protein

Structure:

Blue fluorescent protein. Chain: a. Synonym: blue-emission variant. Engineered: yes. Mutation: yes

Source:

Aequorea victoria. Organism_taxid: 6100. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: the n-terminal his-tag has been removed

Resolution:

2.10Å

R-factor:

0.181

Authors:

R.M.Wachter,S.J.Remington

Key ref:

R.M.Wachter et al. (1997). Crystal structure and photodynamic behavior of the blue emission variant Y66H/Y145F of green fluorescent protein. Biochemistry, 36, 9759-9765. PubMed id: 9245407 DOI: 10.1021/bi970563w

Date:

09-Apr-97

Release date:

07-Jul-97

PROCHECK

	Headers

	References

Protein chain

P42212 (GFP_AEQVI) - Green fluorescent protein from Aequorea victoria

Seq: Struc:					238 a.a. 227 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1021/bi970563w	Biochemistry 36:9759-9765 (1997)
PubMed id: 9245407

Crystal structure and photodynamic behavior of the blue emission variant Y66H/Y145F of green fluorescent protein.
R.M.Wachter, B.A.King, R.Heim, K.Kallio, R.Y.Tsien, S.G.Boxer, S.J.Remington.

ABSTRACT

The crystal structure of a blue emission variant (Y66H/Y145F) of the Aequorea victoria green fluorescent protein has been determined by molecular replacement and the model refined. The crystallographic R-factor is 18.1% for all data from 20 to 2.1 A, and the model geometry is excellent. The chromophore is non-native and is autocatalytically generated from the internal tripeptide Ser65-His66-Gly67. The final electron density maps indicate that the formation of the chromophore is complete, including 1,2 dehydration of His66 as indicated by the planarity of the chromophore. The chromophore is in the cis conformation, with no evidence for any substantial fraction of the trans configuration or uncyclized apoprotein, and is well-shielded from bulk solvent by the folded protein. These characteristics indicate that the machinery for production of the chromophore from a buried tripeptide unit is not only intact but also highly efficient in spite of a major change in chromophore chemical structure. Nevertheless, there are significant rearrangements in the hydrogen bond configuration around the chromophore as compared to wild-type, indicating flexibility of the active site. pH titration of the intact protein and the chromopeptide (pKa1 = 4.9 +/- 0.1, pKa2 = 12.0 +/- 0.1) suggests that the predominant form of the chromophore in the intact protein is electrically neutral. In contrast to the wild-type protein [Chattoraj, M., King, B. A., Bublitz, G. U., & Boxer, S. G. (1996) Proc. Natl. Acad. Sci. U.S.A., 8362-8367], femtosecond fluorescence up-conversion spectroscopy of the intact protein and a partially deuterated form strongly suggests that excited-state proton transfer is not coupled to fluorescence emission.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21335090

A.Royant, and M.Noirclerc-Savoye (2011).
Stabilizing role of glutamic acid 222 in the structure of Enhanced Green Fluorescent Protein.

J Struct Biol, 174, 385-390.

PDB code:

2y0g

19067572

C.M.Megley, L.A.Dickson, S.L.Maddalo, G.J.Chandler, and M.Zimmer (2009).
Photophysics and dihedral freedom of the chromophore in yellow, blue, and green fluorescent protein.

J Phys Chem B, 113, 302-308.

19771336

S.R.Meech (2009).
Excited state reactions in fluorescent proteins.

Chem Soc Rev, 38, 2922-2934.

18427834

J.Urra, M.Sandoval, I.Cornejo, L.F.Barros, F.V.Sepúlveda, and L.P.Cid (2008).
A genetically encoded ratiometric sensor to measure extracellular pH in microdomains bounded by basolateral membranes of epithelial cells.

Pflugers Arch, 457, 233-242.

18690664

V.Krasnenko, A.H.Tkaczyk, E.R.Tkaczyk, and K.Mauring (2008).
Physicochemical properties of blue fluorescent protein determined via molecular dynamics simulation.

Biopolymers, 89, 1136-1143.

17434942

D.Arosio, G.Garau, F.Ricci, L.Marchetti, R.Bizzarri, R.Nifosì, and F.Beltram (2007).
Spectroscopic and structural study of proton and halide ion cooperative binding to gfp.

Biophys J, 93, 232-244.

PDB codes:

2h6v 2o24 2o29 2o2b

17721879

J.Y.Hasegawa, K.Fujimoto, B.Swerts, T.Miyahara, and H.Nakatsuji (2007).
Excited states of GFP chromophore and active site studied by the SAC-CI method: effect of protein-environment and mutations.

J Comput Chem, 28, 2443-2452.

17721596

N.M.Webber, and S.R.Meech (2007).
Electronic spectroscopy and solvatochromism in the chromophore of GFP and the Y66F mutant.

Photochem Photobiol Sci, 6, 976-981.

17600852

R.Nifosí, P.Amat, and V.Tozzini (2007).
Variation of spectral, structural, and vibrational properties within the intrinsically fluorescent proteins family: a density functional study.

J Comput Chem, 28, 2366-2377.

16387641

J.Duebel, S.Haverkamp, W.Schleich, G.Feng, G.J.Augustine, T.Kuner, and T.Euler (2006).
Two-photon imaging reveals somatodendritic chloride gradient in retinal ON-type bipolar cells expressing the biosensor Clomeleon.

Neuron, 49, 81-94.

17115054

M.A.Mena, T.P.Treynor, S.L.Mayo, and P.S.Daugherty (2006).
Blue fluorescent proteins with enhanced brightness and photostability from a structurally targeted library.

Nat Biotechnol, 24, 1569-1571.

16441351

R.Dixit, R.Cyr, and S.Gilroy (2006).
Using intrinsically fluorescent proteins for plant cell imaging.

Plant J, 45, 599-615.

16613487

S.L.Maddalo, and M.Zimmer (2006).
The role of the protein matrix in green fluorescent protein fluorescence.

Photochem Photobiol, 82, 367-372.

15937281

A.M.Saxena, J.B.Udgaonkar, and G.Krishnamoorthy (2005).
Protein dynamics control proton transfer from bulk solvent to protein interior: a case study with a green fluorescent protein.

Protein Sci, 14, 1787-1799.

16092146

D.Xie, and J.Zeng (2005).
Electronic excitations of green fluorescent proteins: protonation states of chromophore model compound in solutions.

J Comput Chem, 26, 1487-1496.

15888441

J.A.Sniegowski, J.W.Lappe, H.N.Patel, H.A.Huffman, and R.M.Wachter (2005).
Base catalysis of chromophore formation in Arg96 and Glu222 variants of green fluorescent protein.

J Biol Chem, 280, 26248-26255.

15884066

S.Bonsma, R.Purchase, S.Jezowski, J.Gallus, F.Könz, and S.Völker (2005).
Green and red fluorescent proteins: photo- and thermally induced dynamics probed by site-selective spectroscopy and hole burning.

Chemphyschem, 6, 838-849.

15390267

R.Arai, W.Wriggers, Y.Nishikawa, T.Nagamune, and T.Fujisawa (2004).
Conformations of variably linked chimeric proteins evaluated by synchrotron X-ray small-angle scattering.

Proteins, 57, 829-838.

12944297

A.Follenius-Wund, M.Bourotte, M.Schmitt, F.Iyice, H.Lami, J.J.Bourguignon, J.Haiech, and C.Pigault (2003).
Fluorescent derivatives of the GFP chromophore give a new insight into the GFP fluorescence process.

Biophys J, 85, 1839-1850.

12868107

A.K.Das, J.Y.Hasegawa, T.Miyahara, M.Ehara, and H.Nakatsuji (2003).
Electronic excitations of the green fluorescent protein chromophore in its protonation states: SAC/SAC-CI study.

J Comput Chem, 24, 1421-1431.

11209050

D.Yarbrough, R.M.Wachter, K.Kallio, M.V.Matz, and S.J.Remington (2001).
Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-A resolution.

Proc Natl Acad Sci U S A, 98, 462-467.

PDB code:

1g7k

10757992

A.F.Bell, X.He, R.M.Wachter, and P.J.Tonge (2000).
Probing the ground state structure of the green fluorescent protein chromophore using Raman spectroscopy.

Biochemistry, 39, 4423-4431.

11056031

R.Battistutta, A.Negro, and G.Zanotti (2000).
Crystal structure and refolding properties of the mutant F99S/M153T/V163A of the green fluorescent protein.

Proteins, 41, 429-437.

PDB code:

1b9c

10716703

T.M.Creemers, A.J.Lock, V.Subramaniam, T.M.Jovin, and S.Völker (2000).
Photophysics and optical switching in green fluorescent protein mutants.

Proc Natl Acad Sci U S A, 97, 2974-2978.

10512807

C.Scharnagl, R.Raupp-Kossmann, and S.F.Fischer (1999).
Molecular basis for pH sensitivity and proton transfer in green fluorescent protein: protonation and conformational substates from electrostatic calculations.

Biophys J, 77, 1839-1857.

10216152

M.H.Vos, and J.L.Martin (1999).
Femtosecond processes in proteins.

Biochim Biophys Acta, 1411, 1.

10508593

R.M.Wachter, and S.J.Remington (1999).
Sensitivity of the yellow variant of green fluorescent protein to halides and nitrate.

Curr Biol, 9, R628-R629.

10339561

W.Weber, V.Helms, J.A.McCammon, and P.W.Langhoff (1999).
Shedding light on the dark and weakly fluorescent states of green fluorescent proteins.

Proc Natl Acad Sci U S A, 96, 6177-6182.

9618493

J.Llopis, J.M.McCaffery, A.Miyawaki, M.G.Farquhar, and R.Y.Tsien (1998).
Measurement of cytosolic, mitochondrial, and Golgi pH in single living cells with green fluorescent proteins.

Proc Natl Acad Sci U S A, 95, 6803-6808.

9782051

R.M.Wachter, M.A.Elsliger, K.Kallio, G.T.Hanson, and S.J.Remington (1998).
Structural basis of spectral shifts in the yellow-emission variants of green fluorescent protein.

Structure, 6, 1267-1277.

PDB codes:

1yfp 2yfp

9759496

R.Y.Tsien (1998).
The green fluorescent protein.

Annu Rev Biochem, 67, 509-544.

9891783

T.Wilson, and J.W.Hastings (1998).
Bioluminescence.

Annu Rev Cell Dev Biol, 14, 197-230.

9811841

U.Haupts, S.Maiti, P.Schwille, and W.W.Webb (1998).
Dynamics of fluorescence fluctuations in green fluorescent protein observed by fluorescence correlation spectroscopy.

Proc Natl Acad Sci U S A, 95, 13573-13578.

9335045

T.Misteli, and D.L.Spector (1997).
Applications of the green fluorescent protein in cell biology and biotechnology.

Nat Biotechnol, 15, 961-964.

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 code is shown on the right.