6l8k

From Proteopedia

(Difference between revisions)

Current revision

Structure of URT1 in complex with UTP

Structural highlights

6l8k is a 1 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.999Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

URT1_ARATH UTP:RNA uridylyltransferase with a marked preference for uridine polymerization and a distributive activity for the first added nucleotides (PubMed:23748567, PubMed:25928405). Uridylates oligo(A)-tailed mRNAs to prevent 3' to 5' ribonucleotytic attacks (PubMed:23748567). Can prevent the 3' trimming of mRNAs still engaged on polysomes (PubMed:23748567). Acts synergistically with HESO1 in unmethylated miRNA uridylation, leading to their degradation (PubMed:25928341). URT1 and HESO1 prefer substrates with different 3' end nucleotides and act cooperatively to tail different forms of the same miRNAs (PubMed:25928405). URT1 and HESO1 act sequentially, with URT1 mono-uridylating the miRNAs followed by their further uridylation by HESO1 (PubMed:25928405). Has no effect on uridylation of heterochromatic siRNAs (PubMed:25928341). Able to act on AGO1-bound miRNAs and the uridylated species stay associated with AGO1 (PubMed:25928405).^[1] ^[2] ^[3]

Publication Abstract from PubMed

3' uridylation is an essential modification associated with coding and noncoding RNA degradation in eukaryotes. In Arabidopsis, HESO1 was first identified as the major nucleotidyl transferase that uridylates most unmethylated miRNAs, and URT1 was later reported to play a redundant but important role in miRNA uridylation when HESO1 is absent. Two enzymes work sequentially and collaboratively to tail different forms of the same miRNAs in vivo. For mRNA, however, URT1 becomes the main enzyme to uridylate the majority of mRNA and repairs their deadenylated ends to restore the binding site for Poly(A) Binding Protein (PABP). HESO1, on the other hand, targets mostly the mRNAs with very short oligo(A) tails and fails in fulfilling the same task. To understand the structural basis these two functional homologues possess for their different substrate preferences and catalytic behaviors, we first determined the crystal structures of URT1 in the absence and presence of UTP. Our structures, together with functional assay and sequence analysis, indicated that URT1 has a conserved UTP-recognition mechanism analogue to the terminal uridylyl transferases from other species whereas HESO1 may evolve separately to recognize UTP in a different way. Moreover, URT1 N552 may be an important residue in interacting with 3' nucleotide of RNA substrate. The URT1 structure we determined represents the first structure of uridylyl transferase from plants, shedding light on the mechanisms of URT1/HESO1-dependent RNA metabolism.

Crystal structure of Arabidopsis terminal uridylyl transferase URT1.,Zhu L, Hu Q, Cheng L, Jiang Y, Lv M, Liu Y, Li F, Shi Y, Gong Q Biochem Biophys Res Commun. 2020 Jan 30. pii: S0006-291X(20)30207-2. doi:, 10.1016/j.bbrc.2020.01.124. PMID:32008746^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sement FM, Ferrier E, Zuber H, Merret R, Alioua M, Deragon JM, Bousquet-Antonelli C, Lange H, Gagliardi D. Uridylation prevents 3' trimming of oligoadenylated mRNAs. Nucleic Acids Res. 2013 Aug;41(14):7115-27. doi: 10.1093/nar/gkt465. Epub 2013, Jun 6. PMID:23748567 doi:http://dx.doi.org/10.1093/nar/gkt465
↑ Wang X, Zhang S, Dou Y, Zhang C, Chen X, Yu B, Ren G. Synergistic and independent actions of multiple terminal nucleotidyl transferases in the 3' tailing of small RNAs in Arabidopsis. PLoS Genet. 2015 Apr 30;11(4):e1005091. doi: 10.1371/journal.pgen.1005091., eCollection 2015 Apr. PMID:25928341 doi:http://dx.doi.org/10.1371/journal.pgen.1005091
↑ Tu B, Liu L, Xu C, Zhai J, Li S, Lopez MA, Zhao Y, Yu Y, Ramachandran V, Ren G, Yu B, Li S, Meyers BC, Mo B, Chen X. Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis. PLoS Genet. 2015 Apr 30;11(4):e1005119. doi: 10.1371/journal.pgen.1005119., eCollection 2015 Apr. PMID:25928405 doi:http://dx.doi.org/10.1371/journal.pgen.1005119
↑ Zhu L, Hu Q, Cheng L, Jiang Y, Lv M, Liu Y, Li F, Shi Y, Gong Q. Crystal structure of Arabidopsis terminal uridylyl transferase URT1. Biochem Biophys Res Commun. 2020 Jan 30. pii: S0006-291X(20)30207-2. doi:, 10.1016/j.bbrc.2020.01.124. PMID:32008746 doi:http://dx.doi.org/10.1016/j.bbrc.2020.01.124

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6l8k"

Categories: Arabidopsis thaliana | Large Structures | Lingru Z

@@ Line 3: / Line 3: @@
 <StructureSection load='6l8k' size='340' side='right'caption='[[6l8k]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6l8k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6L8K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6l8k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L8K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6L8K FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</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]] 2.999&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">URT1, At2g45620, F17K2.15 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_uridylyltransferase RNA uridylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.52 2.7.7.52] </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=6l8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l8k OCA], [https://pdbe.org/6l8k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6l8k RCSB], [https://www.ebi.ac.uk/pdbsum/6l8k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6l8k 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=6l8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l8k OCA], [http://pdbe.org/6l8k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6l8k RCSB], [http://www.ebi.ac.uk/pdbsum/6l8k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6l8k ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/URT1_ARATH URT1_ARATH]] UTP:RNA uridylyltransferase with a marked preference for uridine polymerization and a distributive activity for the first added nucleotides (PubMed:23748567, PubMed:25928405). Uridylates oligo(A)-tailed mRNAs to prevent 3' to 5' ribonucleotytic attacks (PubMed:23748567). Can prevent the 3' trimming of mRNAs still engaged on polysomes (PubMed:23748567). Acts synergistically with HESO1 in unmethylated miRNA uridylation, leading to their degradation (PubMed:25928341). URT1 and HESO1 prefer substrates with different 3' end nucleotides and act cooperatively to tail different forms of the same miRNAs (PubMed:25928405). URT1 and HESO1 act sequentially, with URT1 mono-uridylating the miRNAs followed by their further uridylation by HESO1 (PubMed:25928405). Has no effect on uridylation of heterochromatic siRNAs (PubMed:25928341). Able to act on AGO1-bound miRNAs and the uridylated species stay associated with AGO1 (PubMed:25928405).<ref>PMID:23748567</ref> <ref>PMID:25928341</ref> <ref>PMID:25928405</ref>
+[https://www.uniprot.org/uniprot/URT1_ARATH URT1_ARATH] UTP:RNA uridylyltransferase with a marked preference for uridine polymerization and a distributive activity for the first added nucleotides (PubMed:23748567, PubMed:25928405). Uridylates oligo(A)-tailed mRNAs to prevent 3' to 5' ribonucleotytic attacks (PubMed:23748567). Can prevent the 3' trimming of mRNAs still engaged on polysomes (PubMed:23748567). Acts synergistically with HESO1 in unmethylated miRNA uridylation, leading to their degradation (PubMed:25928341). URT1 and HESO1 prefer substrates with different 3' end nucleotides and act cooperatively to tail different forms of the same miRNAs (PubMed:25928405). URT1 and HESO1 act sequentially, with URT1 mono-uridylating the miRNAs followed by their further uridylation by HESO1 (PubMed:25928405). Has no effect on uridylation of heterochromatic siRNAs (PubMed:25928341). Able to act on AGO1-bound miRNAs and the uridylated species stay associated with AGO1 (PubMed:25928405).<ref>PMID:23748567</ref> <ref>PMID:25928341</ref> <ref>PMID:25928405</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 19: @@
 </div>
 <div class="pdbe-citations 6l8k" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[RNA uridylyltransferase|RNA uridylyltransferase]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: RNA uridylyltransferase]]
+[[Category: Lingru Z]]
-[[Category: Lingru, Z]]
-[[Category: Complex]]
-[[Category: Transferase]]
-[[Category: Uridylyltransferase]]

6l8k

From Proteopedia

Current revision

Structure of URT1 in complex with UTP

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox