Source 1primary paper2006Biochemistry
Toolkit/YcgF BLUF domain
YcgF BLUF domain
Also known as: BLUF domain, YcgF-BLUF
Taxonomy: Mechanism Branch / Component. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
The YcgF BLUF domain is the N-terminal FAD-binding blue-light sensor from Escherichia coli YcgF. In isolation, it forms a light-induced signaling state with flavin FTIR and UV-visible properties, and dark-state recovery kinetics, that match those of full-length YcgF.
Usefulness & Problems
Why this is useful
This domain is useful as a minimal blue-light sensing module for studying BLUF photochemistry independently of the C-terminal EAL region. The evidence indicates that it preserves core flavin-centered signaling-state formation while separating those events from additional full-length protein structural responses.
Problem solved
It helps dissect which light-induced changes in YcgF arise from the BLUF photoreceptor core versus from other regions of the full-length protein. Specifically, comparison of isolated YcgF-BLUF with full-length YcgF revealed that many protein IR bands seen in the full-length construct are absent from the isolated domain.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Component: A low-level protein part used inside a larger architecture that realizes a mechanism.
Mechanisms
blue-light sensing by a flavin-binding bluf photoreceptor domainblue-light sensing by an fad-binding bluf photoreceptor domaininterdomain allosteric structural coupling from the n-terminal bluf domain to the c-terminal eal domainlight-induced signaling-state formationTechniques
Structural CharacterizationTarget processes
recombinationsignalingInput: Light
Implementation Constraints
The domain is derived from the N-terminus of Escherichia coli YcgF, a protein composed of an N-terminal BLUF domain and a C-terminal EAL domain. Characterization in the cited work used isolated-domain preparation and comparison to full-length YcgF by light-induced FTIR difference spectroscopy and flavin UV-visible absorption measurements, with FAD as the chromophore.
The isolated BLUF domain lacked most IR bands induced in full-length YcgF, indicating that it does not capture the broader light-triggered structural changes present in the intact protein. Evidence here is limited to spectroscopic characterization and does not establish downstream functional outputs or performance in engineered applications.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
The C4=O stretching bands of the FAD isoalloxazine ring were induced at the same frequency and with the same band intensity in YcgF-Full and YcgF-BLUF spectra.
the bands for the C4=O stretching of a FAD isoalloxazine ring were induced at the same frequency with the same band intensity in the spectra for YcgF-Full and YcgF-BLUF
Escherichia coli YcgF is a BLUF protein composed of an N-terminal BLUF domain and a C-terminal EAL domain.
The Escherichia coli YcgF protein is a BLUF protein consisting of the N-terminal FAD-binding hold (BLUF domain) and the C-terminal EAL domain.
The light-induced FTIR difference spectrum of full-length YcgF was markedly different from that of the isolated YcgF BLUF domain, and the BLUF-domain spectrum lacked most IR bands induced in the full-length protein.
The light-induced FTIR difference spectrum of YcgF-Full, however, was markedly different from that of YcgF-BLUF. The spectrum of YcgF-BLUF lacked most of the IR bands that were induced in the YcgF-Full spectrum.
YcgF-Full and YcgF-BLUF showed identical dark-state flavin UV-visible absorption spectra and identical kinetics of relaxation from the light-induced signaling state to the dark state.
YcgF-Full and YcgF-BLUF showed identical UV-visible absorption spectra of flavin in the dark state and a light-induced absorption red shift for the signaling state, which relaxed to the dark state showing identical kinetics.
The full-length-specific protein bands are discussed as being predominantly attributable to structural changes in the C-terminal EAL domain triggered by light excitation of the N-terminal BLUF domain.
The possibility that full-length-specific protein bands are predominantly ascribed to structural changes of the C-terminal EAL domain in the signaling state as a consequence of light excitation of the N-terminal BLUF domain is discussed.
At medium-low temperatures, the YcgF-Full FTIR spectrum resembled the YcgF-BLUF spectrum because protein bands were selectively suppressed.
the YcgF-Full spectrum resembled that of the YcgF-BLUF when illuminated at medium-low temperatures because of the selective suppression of protein bands
Approval Evidence
1 source6 linked approval claimsfirst-pass slug ycgf-bluf-domain
Light-induced structural changes for the signaling state formation were studied using the light-induced Fourier transform infrared (FTIR) difference spectroscopy of both the full-length YcgF protein (YcgF-Full) and its BLUF domain (YcgF-BLUF).
Source:
band assignmentsupports
The C4=O stretching bands of the FAD isoalloxazine ring were induced at the same frequency and with the same band intensity in YcgF-Full and YcgF-BLUF spectra.
the bands for the C4=O stretching of a FAD isoalloxazine ring were induced at the same frequency with the same band intensity in the spectra for YcgF-Full and YcgF-BLUF
Source:
compositionsupports
Escherichia coli YcgF is a BLUF protein composed of an N-terminal BLUF domain and a C-terminal EAL domain.
The Escherichia coli YcgF protein is a BLUF protein consisting of the N-terminal FAD-binding hold (BLUF domain) and the C-terminal EAL domain.
Source:
spectral differencesupports
The light-induced FTIR difference spectrum of full-length YcgF was markedly different from that of the isolated YcgF BLUF domain, and the BLUF-domain spectrum lacked most IR bands induced in the full-length protein.
The light-induced FTIR difference spectrum of YcgF-Full, however, was markedly different from that of YcgF-BLUF. The spectrum of YcgF-BLUF lacked most of the IR bands that were induced in the YcgF-Full spectrum.
Source:
spectral similaritysupports
YcgF-Full and YcgF-BLUF showed identical dark-state flavin UV-visible absorption spectra and identical kinetics of relaxation from the light-induced signaling state to the dark state.
YcgF-Full and YcgF-BLUF showed identical UV-visible absorption spectra of flavin in the dark state and a light-induced absorption red shift for the signaling state, which relaxed to the dark state showing identical kinetics.
Source:
structural interpretationneutral
The full-length-specific protein bands are discussed as being predominantly attributable to structural changes in the C-terminal EAL domain triggered by light excitation of the N-terminal BLUF domain.
The possibility that full-length-specific protein bands are predominantly ascribed to structural changes of the C-terminal EAL domain in the signaling state as a consequence of light excitation of the N-terminal BLUF domain is discussed.
Source:
temperature effectsupports
At medium-low temperatures, the YcgF-Full FTIR spectrum resembled the YcgF-BLUF spectrum because protein bands were selectively suppressed.
the YcgF-Full spectrum resembled that of the YcgF-BLUF when illuminated at medium-low temperatures because of the selective suppression of protein bands
Source:
Comparisons
Source-backed strengths
YcgF-BLUF showed identical dark-state flavin UV-visible absorption spectra and identical relaxation kinetics from the light-induced signaling state to the dark state relative to full-length YcgF. The FAD isoalloxazine C4=O stretching bands were induced at the same frequency and intensity in the isolated domain and full-length protein, supporting faithful retention of the core flavin photoreaction.
Ranked Citations
- 1.