2rok

From Proteopedia

(Difference between revisions)

Current revision

Solution structure of the cap-binding domain of PARN complexed with the cap analog

Structural highlights

2rok is a 1 chain structure with sequence from Mus musculus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

PARN_MOUSE 3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development. Interacts with both the 3'-end poly(A) tail and the 5'-end cap structure during degradation, the interaction with the cap structure being required for an efficient degradation of poly(A) tails. Involved in nonsense-mediated mRNA decay, a critical process of selective degradation of mRNAs that contain premature stop codons. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly via its interaction with KHSRP. Probably mediates the removal of poly(A) tails of AREs mRNAs, which constitutes the first step of destabilization (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The degradation of the poly(A) tail is crucial for posttranscriptional gene regulation and for quality control of mRNA. Poly(A)-specific ribonuclease (PARN) is one of the major mammalian 3' specific exo-ribonucleases involved in the degradation of the mRNA poly(A) tail, and it is also involved in the regulation of translation in early embryonic development. The interaction between PARN and the m(7)GpppG cap of mRNA plays a key role in stimulating the rate of deadenylation. Here we report the solution structures of the cap-binding domain of mouse PARN with and without the m(7)GpppG cap analog. The structure of the cap-binding domain adopts the RNA recognition motif (RRM) with a characteristic alpha-helical extension at its C-terminus, which covers the beta-sheet surface (hereafter referred to as PARN RRM). In the complex structure of PARN RRM with the cap analog, the base of the N(7)-methyl guanosine (m(7)G) of the cap analog stacks with the solvent-exposed aromatic side chain of the distinctive tryptophan residue 468, located at the C-terminal end of the second beta-strand. These unique structural features in PARN RRM reveal a novel cap-binding mode, which is distinct from the nucleotide recognition mode of the canonical RRM domains.

The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition.,Nagata T, Suzuki S, Endo R, Shirouzu M, Terada T, Inoue M, Kigawa T, Kobayashi N, Guntert P, Tanaka A, Hayashizaki Y, Muto Y, Yokoyama S Nucleic Acids Res. 2008 Aug;36(14):4754-67. Epub 2008 Jul 19. PMID:18641416^[1]

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

References

↑ Nagata T, Suzuki S, Endo R, Shirouzu M, Terada T, Inoue M, Kigawa T, Kobayashi N, Guntert P, Tanaka A, Hayashizaki Y, Muto Y, Yokoyama S. The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition. Nucleic Acids Res. 2008 Aug;36(14):4754-67. Epub 2008 Jul 19. PMID:18641416 doi:10.1093/nar/gkn458

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2rok"

@@ Line 1: / Line 1: @@
 ==Solution structure of the cap-binding domain of PARN complexed with the cap analog==
-<StructureSection load='2rok' size='340' side='right'caption='[[2rok]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2rok' size='340' side='right'caption='[[2rok]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2rok]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ROK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ROK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2rok]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ROK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ROK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1whv|1whv]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Parn ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.4 3.1.13.4] </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=2rok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rok OCA], [https://pdbe.org/2rok PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rok RCSB], [https://www.ebi.ac.uk/pdbsum/2rok PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rok ProSAT], [https://www.topsan.org/Proteins/RSGI/2rok TOPSAN]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PARN_MOUSE PARN_MOUSE] 3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails. Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development. Interacts with both the 3'-end poly(A) tail and the 5'-end cap structure during degradation, the interaction with the cap structure being required for an efficient degradation of poly(A) tails. Involved in nonsense-mediated mRNA decay, a critical process of selective degradation of mRNAs that contain premature stop codons. Also involved in degradation of inherently unstable mRNAs that contain AU-rich elements (AREs) in their 3'-UTR, possibly via its interaction with KHSRP. Probably mediates the removal of poly(A) tails of AREs mRNAs, which constitutes the first step of destabilization (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 37: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Lk3 transgenic mice]]
+[[Category: Mus musculus]]
-[[Category: Endo, R]]
+[[Category: Endo R]]
-[[Category: Guntert, P]]
+[[Category: Guntert P]]
-[[Category: Hayashizaki, Y]]
+[[Category: Hayashizaki Y]]
-[[Category: Inoue, M]]
+[[Category: Inoue M]]
-[[Category: Kigawa, T]]
+[[Category: Kigawa T]]
-[[Category: Muto, Y]]
+[[Category: Muto Y]]
-[[Category: Nagata, T]]
+[[Category: Nagata T]]
-[[Category: Structural genomic]]
+[[Category: Shirouzu M]]
-[[Category: Shirouzu, M]]
+[[Category: Suzuki S]]
-[[Category: Suzuki, S]]
+[[Category: Terada T]]
-[[Category: Terada, T]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S]]
-[[Category: Cap]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Rbd]]
-[[Category: Rna binding protein]]
-[[Category: Rrm]]
-[[Category: Rsgi]]

2rok

From Proteopedia

Current revision

Solution structure of the cap-binding domain of PARN complexed with the cap analog

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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