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| | ==Crystal structure of human mitochondrial poly(A) polymerase (PAPD1)== | | ==Crystal structure of human mitochondrial poly(A) polymerase (PAPD1)== |
| - | <StructureSection load='3pq1' size='340' side='right' caption='[[3pq1]], [[Resolution|resolution]] 3.10Å' scene=''> | + | <StructureSection load='3pq1' size='340' side='right'caption='[[3pq1]], [[Resolution|resolution]] 3.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3pq1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PQ1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3pq1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PQ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PQ1 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MTPAP, PAPD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pq1 OCA], [https://pdbe.org/3pq1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pq1 RCSB], [https://www.ebi.ac.uk/pdbsum/3pq1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pq1 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3pq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pq1 RCSB], [http://www.ebi.ac.uk/pdbsum/3pq1 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Disease == | | == Disease == |
| - | [[http://www.uniprot.org/uniprot/PAPD1_HUMAN PAPD1_HUMAN]] Autosomal recessive spastic ataxia - optic atrophy - dysarthria. The disease is caused by mutations affecting the gene represented in this entry. MTPAP mutations result in a defect of mitochondrial mRNA maturation. Affected individuals exhibit a drastic decrease in poly(A) tail length of mitochondrial mRNA transcripts, including COX1 and RNA14 (PubMed:20970105).<ref>PMID:20970105</ref> | + | [https://www.uniprot.org/uniprot/PAPD1_HUMAN PAPD1_HUMAN] Autosomal recessive spastic ataxia - optic atrophy - dysarthria. The disease is caused by mutations affecting the gene represented in this entry. MTPAP mutations result in a defect of mitochondrial mRNA maturation. Affected individuals exhibit a drastic decrease in poly(A) tail length of mitochondrial mRNA transcripts, including COX1 and RNA14 (PubMed:20970105).<ref>PMID:20970105</ref> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PAPD1_HUMAN PAPD1_HUMAN]] Polymerase that creates the 3' poly(A) tail of mitochondrial transcripts. Can use all four nucleotides, but has higher activity with ATP and UTP (in vitro). Plays a role in replication-dependent histone mRNA degradation. May be involved in the terminal uridylation of mature histone mRNAs before their degradation is initiated. Might be responsible for the creation of some UAA stop codons which are not encoded in mtDNA.<ref>PMID:15547249</ref> <ref>PMID:15769737</ref> <ref>PMID:18172165</ref> <ref>PMID:20970105</ref> <ref>PMID:21292163</ref> | + | [https://www.uniprot.org/uniprot/PAPD1_HUMAN PAPD1_HUMAN] Polymerase that creates the 3' poly(A) tail of mitochondrial transcripts. Can use all four nucleotides, but has higher activity with ATP and UTP (in vitro). Plays a role in replication-dependent histone mRNA degradation. May be involved in the terminal uridylation of mature histone mRNAs before their degradation is initiated. Might be responsible for the creation of some UAA stop codons which are not encoded in mtDNA.<ref>PMID:15547249</ref> <ref>PMID:15769737</ref> <ref>PMID:18172165</ref> <ref>PMID:20970105</ref> <ref>PMID:21292163</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3pq1" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[RNA polymerase|RNA polymerase]] | + | *[[Poly(A) RNA polymerase|Poly(A) RNA polymerase]] |
| | + | *[[Poly(A) polymerase 3D structures|Poly(A) polymerase 3D structures]] |
| | *[[RNA uridylyltransferase|RNA uridylyltransferase]] | | *[[RNA uridylyltransferase|RNA uridylyltransferase]] |
| | == References == | | == References == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Homo sapiens]] | | [[Category: Homo sapiens]] |
| - | [[Category: Polynucleotide adenylyltransferase]] | + | [[Category: Large Structures]] |
| - | [[Category: Bai, Y]] | + | [[Category: Bai Y]] |
| - | [[Category: Chang, J H]] | + | [[Category: Chang JH]] |
| - | [[Category: Srivastava, S K]] | + | [[Category: Srivastava SK]] |
| - | [[Category: Tong, L]] | + | [[Category: Tong L]] |
| - | [[Category: Mitochondria]]
| + | |
| - | [[Category: Nucleotidyl transferase]]
| + | |
| - | [[Category: Rnp-type rna binding domain]]
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| - | [[Category: Transferase]]
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| Structural highlights
Disease
PAPD1_HUMAN Autosomal recessive spastic ataxia - optic atrophy - dysarthria. The disease is caused by mutations affecting the gene represented in this entry. MTPAP mutations result in a defect of mitochondrial mRNA maturation. Affected individuals exhibit a drastic decrease in poly(A) tail length of mitochondrial mRNA transcripts, including COX1 and RNA14 (PubMed:20970105).[1]
Function
PAPD1_HUMAN Polymerase that creates the 3' poly(A) tail of mitochondrial transcripts. Can use all four nucleotides, but has higher activity with ATP and UTP (in vitro). Plays a role in replication-dependent histone mRNA degradation. May be involved in the terminal uridylation of mature histone mRNAs before their degradation is initiated. Might be responsible for the creation of some UAA stop codons which are not encoded in mtDNA.[2] [3] [4] [5] [6]
Publication Abstract from PubMed
Poly(A) polymerases (PAPs) are found in most living organisms and have important roles in RNA function and metabolism. Here, we report the crystal structure of human PAPD1, a noncanonical PAP that can polyadenylate RNAs in the mitochondria (also known as mtPAP) and oligouridylate histone mRNAs (TUTase1). The overall structure of the palm and fingers domains is similar to that in the canonical PAPs. The active site is located at the interface between the two domains, with a large pocket that can accommodate the substrates. The structure reveals the presence of a previously unrecognized domain in the N-terminal region of PAPD1, with a backbone fold that is similar to that of RNP-type RNA binding domains. This domain (named the RL domain), together with a beta-arm insertion in the palm domain, contributes to dimerization of PAPD1. Surprisingly, our mutagenesis and biochemical studies show that dimerization is required for the catalytic activity of PAPD1.
Structural basis for dimerization and activity of human PAPD1, a noncanonical poly(A) polymerase.,Bai Y, Srivastava SK, Chang JH, Manley JL, Tong L Mol Cell. 2011 Feb 4;41(3):311-20. PMID:21292163[7]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Crosby AH, Patel H, Chioza BA, Proukakis C, Gurtz K, Patton MA, Sharifi R, Harlalka G, Simpson MA, Dick K, Reed JA, Al-Memar A, Chrzanowska-Lightowlers ZM, Cross HE, Lightowlers RN. Defective mitochondrial mRNA maturation is associated with spastic ataxia. Am J Hum Genet. 2010 Nov 12;87(5):655-60. doi: 10.1016/j.ajhg.2010.09.013. Epub, 2010 Oct 21. PMID:20970105 doi:http://dx.doi.org/10.1016/j.ajhg.2010.09.013
- ↑ Tomecki R, Dmochowska A, Gewartowski K, Dziembowski A, Stepien PP. Identification of a novel human nuclear-encoded mitochondrial poly(A) polymerase. Nucleic Acids Res. 2004 Nov 16;32(20):6001-14. Print 2004. PMID:15547249 doi:http://dx.doi.org/32/20/6001
- ↑ Nagaike T, Suzuki T, Katoh T, Ueda T. Human mitochondrial mRNAs are stabilized with polyadenylation regulated by mitochondria-specific poly(A) polymerase and polynucleotide phosphorylase. J Biol Chem. 2005 May 20;280(20):19721-7. Epub 2005 Mar 14. PMID:15769737 doi:http://dx.doi.org/10.1074/jbc.M500804200
- ↑ Mullen TE, Marzluff WF. Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'. Genes Dev. 2008 Jan 1;22(1):50-65. doi: 10.1101/gad.1622708. PMID:18172165 doi:10.1101/gad.1622708
- ↑ Crosby AH, Patel H, Chioza BA, Proukakis C, Gurtz K, Patton MA, Sharifi R, Harlalka G, Simpson MA, Dick K, Reed JA, Al-Memar A, Chrzanowska-Lightowlers ZM, Cross HE, Lightowlers RN. Defective mitochondrial mRNA maturation is associated with spastic ataxia. Am J Hum Genet. 2010 Nov 12;87(5):655-60. doi: 10.1016/j.ajhg.2010.09.013. Epub, 2010 Oct 21. PMID:20970105 doi:http://dx.doi.org/10.1016/j.ajhg.2010.09.013
- ↑ Bai Y, Srivastava SK, Chang JH, Manley JL, Tong L. Structural basis for dimerization and activity of human PAPD1, a noncanonical poly(A) polymerase. Mol Cell. 2011 Feb 4;41(3):311-20. PMID:21292163 doi:10.1016/j.molcel.2011.01.013
- ↑ Bai Y, Srivastava SK, Chang JH, Manley JL, Tong L. Structural basis for dimerization and activity of human PAPD1, a noncanonical poly(A) polymerase. Mol Cell. 2011 Feb 4;41(3):311-20. PMID:21292163 doi:10.1016/j.molcel.2011.01.013
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