Goodsell Sandbox: Difference between revisions
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{{STRUCTURE_2q66 | PDB=2q66 | SCENE=Goodsell_Sandbox/ | {{STRUCTURE_2q66 | PDB=2q66 | SCENE=Goodsell_Sandbox/2q66_summary/1 }} | ||
ATP Recognition | ATP Recognition | ||
Poly(A) polymerase binds specifically to ATP and adds it the end of a messenger RNA chain. This structure contains a oligo(A) polynucleotide with five nucleotides, an ATP molecule, and a magnesium ion. The protein is a mutant that changes the catalytic aspartate 154 to alanine. In the <scene name='Goodsell_Sandbox/2q66_summary/1'>summary picture</scene>, the enzyme is in blue backbone representation, the RNA chain is in yellow, the ATP is in red, the magnesium is in green, and ALA154 is in magenta. Several mechanisms are used to achieve the specificity for adenosine nucleotides. The magnesium is coordinated by <scene name='Goodsell_Sandbox/2q66_asp/3'>ASP100 and ASP102</scene>, and the magnesium coordinates with the phosphates of ATP, positioning the nucleotide in the active site. The adenine base is sandwiched between the <scene name='Goodsell_Sandbox/2q66_stacking/2'>terminal base of the RNA (in yellow) and VAL234 (in cyan)</scene>. Surprisingly, there are very few contacts with the hydrogen-bonding groups in the adenine base. <scene name='Goodsell_Sandbox/2q66_asn/1'>ASN 236</scene> may form a hydrogen bond to adenine in the active enzyme, but the distance it a bit too long in this mutant structure. Instead, most of the hydrogen-bonding groups in the base, sugar and phosphate interact with a shell of <scene name='Goodsell_Sandbox/2q66_water/2'>water molecules</scene>. Discrimination between ATP and GTP is achieved through a close steric contact between the <scene name='Goodsell_Sandbox/ | Poly(A) polymerase binds specifically to ATP and adds it the end of a messenger RNA chain. This structure contains a oligo(A) polynucleotide with five nucleotides, an ATP molecule, and a magnesium ion. The protein is a mutant that changes the catalytic aspartate 154 to alanine. In the <scene name='Goodsell_Sandbox/2q66_summary/1'>summary picture</scene>, the enzyme is in blue backbone representation, the RNA chain is in yellow, the ATP is in red, the magnesium is in green, and ALA154 is in magenta. Several mechanisms are used to achieve the specificity for adenosine nucleotides. The magnesium is coordinated by <scene name='Goodsell_Sandbox/2q66_asp/3'>ASP100 and ASP102</scene>, and the magnesium coordinates with the phosphates of ATP, positioning the nucleotide in the active site. The adenine base is sandwiched between the <scene name='Goodsell_Sandbox/2q66_stacking/2'>terminal base of the RNA (in yellow) and VAL234 (in cyan)</scene>. Surprisingly, there are very few contacts with the hydrogen-bonding groups in the adenine base. <scene name='Goodsell_Sandbox/2q66_asn/1'>ASN 236</scene> may form a hydrogen bond to adenine in the active enzyme, but the distance it a bit too long in this mutant structure. Instead, most of the hydrogen-bonding groups in the base, sugar and phosphate interact with a shell of <scene name='Goodsell_Sandbox/2q66_water/2'>water molecules</scene>. Discrimination between ATP and GTP is achieved through a close steric contact between the <scene name='Goodsell_Sandbox/2q66_c2/2'>adenine C2 and THR 304 and MET310 (shown in cyan)</scene>. Guanine bases have an extra amino group at this position, and would be too bulky to fit against these amino acids. | ||
Revision as of 22:31, 11 September 2008
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| 2q66, resolution 1.80Å (default scene) | |||||||||||||
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| Ligands: | ATP, EDO, MG | ||||||||||||
| Gene: | PAP1 (Saccharomyces cerevisiae) | ||||||||||||
| Activity: | Polynucleotide adenylyltransferase, with EC number 2.7.7.19 | ||||||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
ATP Recognition
Poly(A) polymerase binds specifically to ATP and adds it the end of a messenger RNA chain. This structure contains a oligo(A) polynucleotide with five nucleotides, an ATP molecule, and a magnesium ion. The protein is a mutant that changes the catalytic aspartate 154 to alanine. In the summary picture, the enzyme is in blue backbone representation, the RNA chain is in yellow, the ATP is in red, the magnesium is in green, and ALA154 is in magenta. Several mechanisms are used to achieve the specificity for adenosine nucleotides. The magnesium is coordinated by ASP100 and ASP102, and the magnesium coordinates with the phosphates of ATP, positioning the nucleotide in the active site. The adenine base is sandwiched between the terminal base of the RNA (in yellow) and VAL234 (in cyan). Surprisingly, there are very few contacts with the hydrogen-bonding groups in the adenine base. ASN 236 may form a hydrogen bond to adenine in the active enzyme, but the distance it a bit too long in this mutant structure. Instead, most of the hydrogen-bonding groups in the base, sugar and phosphate interact with a shell of water molecules. Discrimination between ATP and GTP is achieved through a close steric contact between the adenine C2 and THR 304 and MET310 (shown in cyan). Guanine bases have an extra amino group at this position, and would be too bulky to fit against these amino acids.
