9C5D image
Deposition Date 2024-06-06
Release Date 2024-10-09
Last Version Date 2024-10-30
Entry Detail
PDB ID:
9C5D
Keywords:
Title:
E. coli peptidyl-prolyl cis-trans isomerase containing (2S,3S)-4-Fluorovaline
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.30 Å
R-Value Free:
0.18
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Peptidyl-prolyl cis-trans isomerase B
Gene (Uniprot):ppiB
Chain IDs:A, B, C, D
Chain Length:170
Number of Molecules:4
Biological Source:Escherichia coli
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
A1AVU A VAL modified residue
Primary Citation
1.3 angstrom Crystal Structure of E. coli Peptidyl-Prolyl Isomerase B with Uniform Substitution of Valine by (2 S ,3 S )-4-Fluorovaline Reveals Structure Conservation and Multiple Staggered Rotamers of CH 2 F Groups.
Biochemistry 63 2602 2608 (2024)
PMID: 39316701 DOI: 10.1021/acs.biochem.4c00345

Abstact

(2S,3S)-4-Fluorovaline (FVal) is an analogue of valine, where a single CH3 group is substituted by a CH2F group. In the absence of valine, E. coli valyl-tRNA synthetase uses FVal as a substitute, enabling the production of proteins uniformly labeled with FVal. Here, we describe the production and analysis of E. coli peptidyl-prolyl isomerase B where all 16 valine residues have been replaced by FVal synthesized with a 13C-labeled CH2F group. Although the melting temperature is lower by about 11 °C relative to the wild-type protein, the three-dimensional protein structure is almost completely conserved, as shown by X-ray crystallography. The CH2F groups invariably populate staggered rotamers. Most CH2F groups populate two different rotamers. The increased space requirement of fluorine versus hydrogen does not prohibit rotamers that position fluorine next to a backbone carbonyl carbon. 19F NMR spectra show a signal dispersion over 25 ppm. The most high-field shifted 19F resonances correlate with large 3JHF coupling constants, confirming the impact of the γ-gauche effect on the signal dispersion. The present work is the second experimental verification of the effect and extends its validity to fluorovaline. The abundance of valine in proteins and structural conservation with FVal renders this valine analogue attractive for probing proteins by 19F NMR spectroscopy.

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Primary Citation of related structures