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NF-Y Transcription Factor Sandbox
From Proteopedia
Overview
A transcription factor (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins through translation. NF-Y is a transcription factor involved in histone post-translational modifications (PTMs) [1]. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome [2]. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA[2].
Protein StructureTemplate:STRUCTURE 4awl The NF-Y transcription factor consists of , , and subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer[3]. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal , interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)[1]. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)[1]. that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)[1](Hydrophobic Polar). The NF-Y heterotrimer is also stabilized by the segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA[1].
Protein FunctionThese PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications [2]. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters[1]. NF-Y is regulated by redox mechanisms[4]. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: , , and ; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation[4]. DNA InteractionNF-Y interacts with DNA in several ways; one particular way is by using the C terminal of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the box and causes the minor groove to widen at the CCAAT box[1]. Van der Waals and provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA[1](Hydrophobic Polar). References
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