Poly(A) Polymerase: Difference between revisions

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New page: left|200px<br /><applet load="2q66" size="450" color="white" frame="true" align="right" spinBox="true" caption="2q66, resolution 1.800Å" /> '''Structure of Yeast ...
 
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[[Image:2q66.gif|left|200px]]<br /><applet load="2q66" size="450" color="white" frame="true" align="right" spinBox="true"
<StructureSection load='' size='350' side='right' caption='Structure of Yeast Poly(A) Polymerase with ATP, Mg+2 ion (green) and oligo(A) (PDB entry [[2q66]])' scene='Proteopedia:Main_page_develop/2q66_initial/3'>
caption="2q66, resolution 1.800&Aring;" />
[[Image:2q66.png|left|170px]]
'''Structure of Yeast Poly(A) Polymerase with ATP and oligo(A)'''<br />


==Overview==
__TOC__
We report the 1.8 A structure of yeast poly(A) polymerase (PAP) trapped in, complex with ATP and a five residue poly(A) by mutation of the, catalytically required aspartic acid 154 to alanine. The enzyme has, undergone significant domain movement and reveals a closed conformation, with extensive interactions between the substrates and all three, polymerase domains. Both substrates and 31 buried water molecules are, enclosed within a central cavity that is open at both ends. Four PAP, mutants were subjected to detailed kinetic analysis, and studies of the, adenylyltransfer (forward), pyrophosphorolysis (reverse), and, nucleotidyltransfer reaction utilizing CTP for the mutants are presented., The results support a model in which binding of both poly(A) and the, correct nucleotide, MgATP, induces a conformational change, resulting in, formation of a stable, closed enzyme state. Thermodynamic considerations, of the data are discussed as they pertain to domain closure, substrate, specificity, and catalytic strategies utilized by PAP.
==Function==


==About this Structure==
[[Poly(A) Polymerase]] (polynucleotide adenylytransferase, [[EC Number|EC]] 2.7.7.19) is the enzyme responsible for adding a polyadenine tail to the 3' end of a nascent pre-mRNA transcript. Its substrates are ATP and RNA. The poly(A) tail that poly-A polymerase adds to the 3' end of the pre-mRNA transcript is important for nuclear export, translation and stability of the mRNA.
2Q66 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with MG, ATP and EDO as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase Polynucleotide adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.19 2.7.7.19] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2Q66 OCA].
*'''Star-PAP''' selects mRNA targets for polyadenylation<ref>PMID:34576144</ref>.
 
==Determinants of ATP Recognition==
Poly(A) Polymerase binds specifically to ATP and adds it at the end of a messenger RNA chain. This structure contains an oligo(A) polynucleotide with five nucleotides, an ATP molecule, and a magnesium ion. The enzyme is an inactive mutant with the catalytic aspartate 154 changed to alanine. Poly(A) polymerase normally has a second magnesium ion, but that second magnesium ion is absent from this structure due to the inactivating mutation D154A. In the <scene name='2q66/2q66_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 ATP. The magnesium is coordinated by <scene name='2q66/2q66_asp/2'>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='2q66/2q66_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='2q66/2q66_asn/1'>ASN 226</scene> may form a [[hydrogen bond]] to adenine in the active enzyme, but the distance is a bit too long in this mutant structure. Instead of forming specific hydrogen bonds with the enzyme, most of the hydrogen-bonding groups in the base, sugar and phosphate interact with a shell of <scene name='Goodsell_Sandbox/2q66_water/2'>buried water molecules</scene>. Discrimination between ATP and GTP is achieved through a close steric contact between the <scene name='2q66/2q66_c2/2'>adenine C2 (in white) and the sidechains of THR 304 and MET310 (shown in cyan)</scene>. Guanine bases have an extra amino group at this position that would be too bulky to fit against these amino acids.
 
 
<blockquote>
This section complements the article on [http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb106_1.html Poly(A) Polymerase] in the
[http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] Series. See also [[Teaching Scenes, Tutorials, and Educators' Pages]].
</blockquote>
 
==3D structures of poly(A) polymerase==
 
[[Poly(A) polymerase 3D structures]]
 
</StructureSection>
 
Note: the regulatory subunit of Vaccinia virus Poly(A) polymerase is called '''VP39''' and the catalytic subunit name is '''VP55'''
 
==Additional Resources==
For additional information, see: [[Translation]] <br/>
For additional examples of transferases, see: [[Transferase]]
 
*PDB entry [[2q66]]


==Reference==
==Reference==
Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis., Balbo PB, Bohm A, Structure. 2007 Sep;15(9):1117-31. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17850751 17850751]
Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis., Balbo PB, Bohm A, Structure. 2007 Sep;15(9):1117-31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17850751 17850751]
<references/>
[[Category:Topic Page]]
[[Category: Polynucleotide adenylyltransferase]]
[[Category: Polynucleotide adenylyltransferase]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Balbo, P.]]
[[Category: Balbo, P.]]
[[Category: Bohm, A.]]
[[Category: Bohm, A.]]
[[Category: ATP]]
[[Category: Protein rna complex atp polymerase complex]]
[[Category: EDO]]
[[Category: Transferase/rna complex]]
[[Category: MG]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: protein rna complex atp polymerase complex]]
[[Category: transferase/rna complex]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:49:20 2007''

Latest revision as of 10:18, 22 July 2024

Function

Poly(A) Polymerase (polynucleotide adenylytransferase, EC 2.7.7.19) is the enzyme responsible for adding a polyadenine tail to the 3' end of a nascent pre-mRNA transcript. Its substrates are ATP and RNA. The poly(A) tail that poly-A polymerase adds to the 3' end of the pre-mRNA transcript is important for nuclear export, translation and stability of the mRNA.

  • Star-PAP selects mRNA targets for polyadenylation[1].

Determinants of ATP Recognition

Poly(A) Polymerase binds specifically to ATP and adds it at the end of a messenger RNA chain. This structure contains an oligo(A) polynucleotide with five nucleotides, an ATP molecule, and a magnesium ion. The enzyme is an inactive mutant with the catalytic aspartate 154 changed to alanine. Poly(A) polymerase normally has a second magnesium ion, but that second magnesium ion is absent from this structure due to the inactivating mutation D154A. In the , 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 ATP. The magnesium is coordinated by , and the magnesium coordinates with the phosphates of ATP, positioning the nucleotide in the active site. The adenine base is sandwiched between the . Surprisingly, there are very few contacts with the hydrogen-bonding groups in the adenine base. may form a hydrogen bond to adenine in the active enzyme, but the distance is a bit too long in this mutant structure. Instead of forming specific hydrogen bonds with the enzyme, most of the hydrogen-bonding groups in the base, sugar and phosphate interact with a shell of . Discrimination between ATP and GTP is achieved through a close steric contact between the . Guanine bases have an extra amino group at this position that would be too bulky to fit against these amino acids.


This section complements the article on Poly(A) Polymerase in the Molecule of the Month Series. See also Teaching Scenes, Tutorials, and Educators' Pages.

3D structures of poly(A) polymerase

Poly(A) polymerase 3D structures


Structure of Yeast Poly(A) Polymerase with ATP, Mg+2 ion (green) and oligo(A) (PDB entry 2q66)

Drag the structure with the mouse to rotate

Note: the regulatory subunit of Vaccinia virus Poly(A) polymerase is called VP39 and the catalytic subunit name is VP55

Additional ResourcesAdditional Resources

For additional information, see: Translation
For additional examples of transferases, see: Transferase

ReferenceReference

Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis., Balbo PB, Bohm A, Structure. 2007 Sep;15(9):1117-31. PMID:17850751

  1. ↑ Koshre GR, Shaji F, Mohanan NK, Mohan N, Ali J, Laishram RS. Star-PAP RNA Binding Landscape Reveals Novel Role of Star-PAP in mRNA Metabolism That Requires RBM10-RNA Association. Int J Mol Sci. 2021 Sep 15;22(18):9980. PMID:34576144 doi:10.3390/ijms22189980

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OCA, David S. Goodsell, Eric Martz, Eran Hodis, Jaime Prilusky, David Canner, Michal Harel, Alexander Berchansky, Joel L. Sussman
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