PDBsum entry 5ajg

Fluorescent protein

PDB id: 5ajg

Contents

Protein chain

301 a.a.

Ligands

LBV

Waters ×263

PDB id:

5ajg

Name:

Fluorescent protein

Title:

Structure of infrared fluorescent protein ifp1.4 at 1.11 angstrom resolution

Structure:

Bacteriophytochrome. Chain: a. Fragment: residues 1-321. Synonym: infrared fluorescent protein ifp1.4, phytochrome-like protein. Engineered: yes. Mutation: yes

Source:

Deinococcus radiodurans. Organism_taxid: 1299. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.11Å R-factor: 0.147 R-free: 0.168

Authors:

C.Lafaye,X.Shu,A.Royant

Key ref:

M.Feliks et al. (2016). Structural Determinants of Improved Fluorescence in a Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins: Insights from Continuum Electrostatic Calculations and Molecular Dynamics Simulations. Biochemistry, 55, 4263-4274. PubMed id: 27471775 DOI: 10.1021/acs.biochem.6b00295

Date:

24-Feb-15 Release date: 09-Mar-16

Protein chain

Q9RZA4  (BPHY_DEIRA) -  Bacteriophytochrome from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 755 a.a.

Struc: 301 a.a.*

* PDB and UniProt seqs differ at 11 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.7.13.3 - histidine kinase.
• Reaction: ATP + protein L-histidine = ADP + protein N-phospho-L-histidine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/acs.biochem.6b00295

Biochemistry 55:4263-4274 (2016)

PubMed id: 27471775

Structural Determinants of Improved Fluorescence in a Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins: Insights from Continuum Electrostatic Calculations and Molecular Dynamics Simulations.

M.Feliks, C.Lafaye, X.Shu, A.Royant, M.Field.

ABSTRACT

Using X-ray crystallography, continuum electrostatic calculations, and molecular dynamics simulations, we have studied the structure, protonation behavior, and dynamics of the biliverdin chromophore and its molecular environment in a series of genetically engineered infrared fluorescent proteins (IFPs) based on the chromophore-binding domain of the Deinococcus radiodurans bacteriophytochrome. Our study suggests that the experimentally observed enhancement of fluorescent properties results from the improved rigidity and planarity of the biliverdin chromophore, in particular of the first two pyrrole rings neighboring the covalent linkage to the protein. We propose that the increases in the levels of both motion and bending of the chromophore out of planarity favor the decrease in fluorescence. The chromophore-binding pocket in some of the studied proteins, in particular the weakly fluorescent parent protein, is shown to be readily accessible to water molecules from the solvent. These waters entering the chromophore region form hydrogen bond networks that affect the otherwise planar conformation of the first three rings of the chromophore. On the basis of our simulations, the enhancement of fluorescence in IFPs can be achieved either by reducing the mobility of water molecules in the vicinity of the chromophore or by limiting the interactions of the nearby protein residues with the chromophore. Finally, simulations performed at both low and neutral pH values highlight differences in the dynamics of the chromophore and shed light on the mechanism of fluorescence loss at low pH.