Met repressor sandbox (Beasley): Difference between revisions
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[[Image: | [[Image:1cma.jpg|left|200px|thumb|''E. coli'' met repressor-operator complex, [[1cma]]]] | ||
{{STRUCTURE_1cma| PDB=1cma | SCENE= }} | {{STRUCTURE_1cma| PDB=1cma | SCENE= }} | ||
===''E. coli'' met repressor=== | ===''E. coli'' met repressor=== | ||
The <scene name=' | The <scene name='Met_repressor_sandbox_(Beasley)/Just_the_met_repressor/1'>met repressor</scene> regulates the transcription genes involved in the biosythesis of methionine in ''E. coli'', and is the product of the metJ gene <ref name="Voet">Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. p. 578-579. Print.</ref> Methionine is an important amino acid that acts as the initiator of protein synthesis (as N-formyl methionine) and of protein elongation. It is also the precursor of spermidine, a polyamine involved in cellular metabolism.<ref name="Phillips,S">PMID 8735275</ref> The met repressor is a dimer of identical 104 amino acid subunits, and is capable of repressing or depressing target genes within 30 minutes of a change of methionine concentration.<ref name="Augustus">PMID 19289840</ref> Each subunit contains a flexible loop (residues 12-20) leading into a β-strand that pairs with the related strand of the other subunit to form a two stranded antiparallel β-sheet or β-ribbon.<ref name="Phillips,S" /> The rest of the met repressor subunit consists of three α helices: A (30-45), B (52-66), and C (86-94) linked by different sized loops.<ref name="Phillips,S" /> | ||
==Key structural features of the met repressor== | ==Key structural features of the met repressor== | ||
The met operators in ''E. coli'' consist of tandem repeats of eight base pair sequences, AGACGTCT, known as 'met | The met operators in ''E. coli'' consist of tandem repeats of eight base pair sequences, AGACGTCT, with each sequence known as a <scene name='Met_repressor_sandbox_(Beasley)/Met_box/1'>'met box'</scene>. <ref name="Phillips,S" /> These met boxes vary in length from 16-40 base pairs, corresponding to two to five met boxes. The consensus sequence is highly symmetrical, with centers of inverted repeats at the center of each met box and at the junctions between them. The <scene name='Met_repressor_sandbox_(Beasley)/Just_dna/2'>self complementary 19-base oligonucleotide</scene>, that the met repressor binds to in the ''E. coli'' met repressor-operator complex at the top of the page, has the sequence 5'-TT '''AGACGTCT''' '''AGACGTCT''' A-3' which contains two tandem consensus met boxes (the met boxes are in bold).<ref name="Phillips">PMID 1406951</ref> One of the products of the methionine biosynthetic pathway is <scene name='Met_repressor_sandbox_(Beasley)/Sam/7'>S-adenosylmethionine (SAM)</scene> and it acts as a corepressor. The met repressor has to bind two molecules of SAM non-cooperatively because the free repressor dimer (aporepressor) has a low affinity for DNA.<ref name="Phillips" /> Three-dimensional structures of the met repressor have been reported in the presence and absence of SAM.<ref name="Phillips" /> The SAM binding does not significantly change the structure of the protein, but it greatly increases the affinity for the operator on DNA. <ref name="Phillips,S" /> Sam binds to the face of the repressor dimer, away from the DNA, with interaction between the met repressor and SAM coming from the positively charged sulfur atoms of the SAM lying at the carboxy termini of the repressor's B helices. <ref name="Phillips" /> From the SAM scene, it can be seen that the sulfur of SAM binds to each Alanine 64 of the repressor dimer. | ||
The following image represents SAM: | |||
[[Image:SAM.png]] | [[Image:SAM.png]] | ||