Source 1primary paper2006Biochemistry
Toolkit/YcgF
YcgF
Also known as: Blrp, YcgF-Full
Taxonomy: Mechanism Branch / Component. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
YcgF (Blrp) is an Escherichia coli full-length blue-light sensing protein that contains an N-terminal FAD-binding BLUF domain and a C-terminal EAL domain. It functions as a BLUF-family photoreceptor in which the FAD chromophore undergoes light-responsive changes, and spectroscopy indicates coupling between the BLUF photochemistry and structural responses in the full-length protein.
Usefulness & Problems
Why this is useful
YcgF is useful as a native bacterial model for studying how a BLUF photoreceptor domain is integrated with a downstream output domain in a single polypeptide. It provides an experimentally characterized system for analyzing blue-light-triggered structural signaling from an FAD-binding sensor domain into a C-terminal EAL-containing region.
Problem solved
YcgF helps address the problem of how light sensing by a BLUF chromophore is transmitted to other parts of a multidomain protein. The available evidence specifically supports its use for dissecting domain-level coupling between an isolated BLUF module and the corresponding full-length photoreceptor.
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 bluf photoreceptorfad-based photochemistrylight-induced conformational changelight-induced conformational or structural changeTechniques
Structural CharacterizationTarget processes
recombinationsignalingInput: Light
Implementation Constraints
YcgF is a full-length Escherichia coli protein comprising an N-terminal FAD-binding BLUF domain and a C-terminal EAL domain, and domain dissection into a BLUF-only construct has been used for comparison. Its light responsiveness depends on the FAD chromophore, and the cited characterization relies on FTIR spectroscopy of the full-length protein and isolated BLUF domain.
Evidence in the supplied literature is narrow and primarily structural/spectroscopic rather than functional. The EAL domain is only described as predicted to have cyclic-di-GMP phosphodiesterase activity, so direct enzymatic output, signaling consequences, and application performance are not established here.
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
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
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
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
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
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
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.
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.
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.
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.
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.
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.
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 EAL domain of YcgF is predicted to have cyclic-di-GMP phosphodiesterase activity.
The EAL domain of YcgF is predicted to have cyclic-di-GMP phosphodiesterase activity.
The EAL domain of YcgF is predicted to have cyclic-di-GMP phosphodiesterase activity.
The EAL domain of YcgF is predicted to have cyclic-di-GMP phosphodiesterase activity.
The EAL domain of YcgF is predicted to have cyclic-di-GMP phosphodiesterase activity.
The EAL domain of YcgF is predicted to have cyclic-di-GMP phosphodiesterase activity.
The EAL domain of YcgF is predicted to have cyclic-di-GMP phosphodiesterase activity.
The EAL domain of YcgF is predicted to have cyclic-di-GMP phosphodiesterase activity.
The EAL domain of YcgF is predicted to have cyclic-di-GMP phosphodiesterase activity.
The EAL domain of YcgF is predicted to have cyclic-di-GMP phosphodiesterase activity.
The EAL domain of YcgF is predicted to have cyclic-di-GMP phosphodiesterase activity.
The EAL domain of YcgF is predicted to have cyclic-di-GMP phosphodiesterase activity.
The EAL domain of YcgF is predicted to have cyclic-di-GMP phosphodiesterase activity.
The EAL domain of YcgF is predicted to have cyclic-di-GMP phosphodiesterase activity.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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
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
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
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
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
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
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
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:
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
The domain architecture is directly supported: YcgF contains an N-terminal BLUF domain and a C-terminal EAL domain. FTIR band assignment showed that the FAD isoalloxazine C4=O stretching bands were induced at the same frequency and with the same intensity in full-length YcgF and the isolated BLUF domain, supporting clear spectroscopic readout of the BLUF photochemistry in both contexts.
Ranked Citations
- 1.