2H6V | pdb_00002h6v

Spectroscopic and structural study of the heterotropic linkage between halide and proton ion binding to GFP proteins- E2(GFP) APO FORM

PDB DOI: https://doi.org/10.2210/pdb2H6V/pdb

Classification: LUMINESCENT PROTEIN
Organism(s): Aequorea victoria
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-06-01 Released: 2007-05-15
Deposition Author(s): Garau, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.187 (Depositor), 0.193 (DCC)
R-Value Work:
0.159 (Depositor), 0.168 (DCC)
R-Value Observed:
0.160 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Spectroscopic and Structural Study of Proton and Halide Ion Cooperative Binding to GFP

Arosio, D., Garau, G., Ricci, F., Marchetti, L., Bizzarri, R., Nifosi, R., Beltram, F.

(2007) Biophys J 93: 232-244

PubMed: 17434942 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1529/biophysj.106.102319
Primary Citation Related Structures:
2H6V, 2O24, 2O29, 2O2B

PubMed Abstract:
This study reports the influence of halogens on fluorescence properties of the Aequorea victoria Green Fluorescent Protein variant S65T/T203Y (E(2)GFP). Halide binding forms a specific nonfluorescent complex generating a substantial drop of the fluorescence via static quenching. Spectroscopic analysis under different solution conditions reveals high halogen affinity, which is strongly dependent on the pH. This evidences the presence in E(2)GFP of interacting binding sites for halide ions and for protons. Thermodynamic link and cooperative interaction are assessed demonstrating that binding of one halide ion is associated with the binding of one proton in a cooperative fashion with the formation, in the pH range 4.5-10, of a single fully protonated E(2)GFP.halogen complex. To resolve the structural determinants of E(2)GFP sensitivity to halogens, high-resolution crystallographic structures were obtained for the halide-free and I(-), Br(-), and Cl(-) bound E(2)GFP. Remarkably the first high-resolution (1.4 A) crystallographic structure of a chloride-bound GFP is reported. The chloride ion occupies a specific and unique binding pocket in direct contact (3.4 A) with the chromophore imidazolidinone aromatic ring. Unanticipated flexibility, strongly modulated by halide ion interactions, is observed in the region surrounding the chromophore. Furthermore molecular dynamics simulations identified E222 residue (along with the chromophore Y66 residue) being in the protonated state when E(2)GFP.halogen complex is formed. The impact of these results on high-sensitivity biosensor design will be discussed.

Organizational Affiliation

Scuola Normale Superiore, National Enterprise for nanoScience and nanoTechnology-Consiglio Nazionale delle Ricerche-Instituto Nazionale di Fisica della Materia, Pisa, Italy. d.arosio@sns.it

Macromolecule Content

Total Structure Weight: 27.54 kDa
Atom Count: 2,148
Modeled Residue Count: 234
Deposited Residue Count: 242
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	242	Aequorea victoria	Mutation(s): 4 Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42212
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]