NF-Y Transcription Factor Sandbox

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<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
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== Overview ==
== Overview ==
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== Protein Structure ==
== Protein Structure ==
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The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> 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<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, 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)<ref name="mainarticle" />. 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)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> 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)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> 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<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, 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)<ref name="mainarticle" />. 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)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> 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)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
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===DNA Interaction===
===DNA Interaction===
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NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> 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<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> 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<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}).
{{Template:ColorKey_Polar}}).

Revision as of 05:28, 7 November 2013

Structure of Variola Topoisomerase 1B with DNA (PDB entry 3igc)

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Proteopedia Page Contributors and Editors (what is this?)

Michele White, Alyssa Wall

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