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| | ==HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN D0 (HNRNP D0 RBD1), NMR== | | ==HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN D0 (HNRNP D0 RBD1), NMR== |
| - | <StructureSection load='1hd0' size='340' side='right'caption='[[1hd0]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''> | + | <StructureSection load='1hd0' size='340' side='right'caption='[[1hd0]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1hd0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HD0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1HD0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1hd0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HD0 FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1hd1|1hd1]]</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='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=1hd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hd0 OCA], [http://pdbe.org/1hd0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1hd0 RCSB], [http://www.ebi.ac.uk/pdbsum/1hd0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1hd0 ProSAT]</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=1hd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hd0 OCA], [https://pdbe.org/1hd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hd0 RCSB], [https://www.ebi.ac.uk/pdbsum/1hd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hd0 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/HNRPD_HUMAN HNRPD_HUMAN]] Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto-oncogenes and cytokine mRNAs. Also binds to double- and single-stranded DNA sequences in a specific manner and functions a transcription factor. Each of the RNA-binding domains specifically can bind solely to a single-stranded non-monotonous 5'-UUAG-3' sequence and also weaker to the single-stranded 5'-TTAGGG-3' telomeric DNA repeat. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'-TTAGGG-3' repeats. Binding of RRM1 to DNA inhibits the formation of DNA quadruplex structure which may play a role in telomere elongation. May be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain.<ref>PMID:11051545</ref> <ref>PMID:10080887</ref> | + | [https://www.uniprot.org/uniprot/HNRPD_HUMAN HNRPD_HUMAN] Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto-oncogenes and cytokine mRNAs. Also binds to double- and single-stranded DNA sequences in a specific manner and functions a transcription factor. Each of the RNA-binding domains specifically can bind solely to a single-stranded non-monotonous 5'-UUAG-3' sequence and also weaker to the single-stranded 5'-TTAGGG-3' telomeric DNA repeat. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'-TTAGGG-3' repeats. Binding of RRM1 to DNA inhibits the formation of DNA quadruplex structure which may play a role in telomere elongation. May be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain.<ref>PMID:11051545</ref> <ref>PMID:10080887</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Nucleoprotein|Nucleoprotein]] | + | *[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ishikawa, F]] | + | [[Category: Ishikawa F]] |
| - | [[Category: Katahira, M]] | + | [[Category: Katahira M]] |
| - | [[Category: Kohno, T]] | + | [[Category: Kohno T]] |
| - | [[Category: Kurihara, Y]] | + | [[Category: Kurihara Y]] |
| - | [[Category: Matsuda, G]] | + | [[Category: Matsuda G]] |
| - | [[Category: Nagata, T]] | + | [[Category: Nagata T]] |
| - | [[Category: Saeki, J]] | + | [[Category: Saeki J]] |
| - | [[Category: Uesugi, S]] | + | [[Category: Uesugi S]] |
| - | [[Category: Yanagida, Y]] | + | [[Category: Yanagida Y]] |
| - | [[Category: Rna binding protein]]
| + | |
| - | [[Category: Rna-binding domain]]
| + | |
| Structural highlights
Function
HNRPD_HUMAN Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto-oncogenes and cytokine mRNAs. Also binds to double- and single-stranded DNA sequences in a specific manner and functions a transcription factor. Each of the RNA-binding domains specifically can bind solely to a single-stranded non-monotonous 5'-UUAG-3' sequence and also weaker to the single-stranded 5'-TTAGGG-3' telomeric DNA repeat. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'-TTAGGG-3' repeats. Binding of RRM1 to DNA inhibits the formation of DNA quadruplex structure which may play a role in telomere elongation. May be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain.[1] [2]
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
Heterogeneous nuclear ribonucleoprotein (hnRNP) D0 has two ribonucleoprotein (RNP)-type RNA-binding domains (RBDs), each of which can bind solely to the UUAG sequence specifically. The structure of the N-terminal RBD (RBD1) determined by NMR is presented here. It folds into a compact alphabeta structure comprising a four-stranded antiparallel beta-sheet packed against two alpha-helices, which is characteristic of the RNP-type RBDs. Special structural features of RBD1 include N-capping boxes for both alpha-helices, a beta-bulge in the second beta-strand, and an additional short antiparallel beta-sheet coupled with a beta-turn-like structure in a loop. Two hydrogen bonds which restrict the positions of loops were identified. Backbone resonance assignments for RBD1 complexed with r(UUAGGG) revealed that the overall folding is maintained in the complex. The candidate residues involved in the interactions with RNA were identified by chemical shift perturbation analysis. They are located in the central and peripheral regions of the RNA-binding surface composed of the four-stranded beta-sheet, loops, and the C-terminal region. It is suggested that non-specific interactions with RNA are performed by the residues in the central region of the RNA-binding surface, while specific interactions are performed by those in the peripheral regions. It was also found that RBD1 has the ability to inhibit the formation of the quadruplex structure.
Structure and interactions with RNA of the N-terminal UUAG-specific RNA-binding domain of hnRNP D0.,Nagata T, Kurihara Y, Matsuda G, Saeki J, Kohno T, Yanagida Y, Ishikawa F, Uesugi S, Katahira M J Mol Biol. 1999 Mar 26;287(2):221-37. PMID:10080887[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Grosset C, Chen CY, Xu N, Sonenberg N, Jacquemin-Sablon H, Shyu AB. A mechanism for translationally coupled mRNA turnover: interaction between the poly(A) tail and a c-fos RNA coding determinant via a protein complex. Cell. 2000 Sep 29;103(1):29-40. PMID:11051545
- ↑ Nagata T, Kurihara Y, Matsuda G, Saeki J, Kohno T, Yanagida Y, Ishikawa F, Uesugi S, Katahira M. Structure and interactions with RNA of the N-terminal UUAG-specific RNA-binding domain of hnRNP D0. J Mol Biol. 1999 Mar 26;287(2):221-37. PMID:10080887
- ↑ Nagata T, Kurihara Y, Matsuda G, Saeki J, Kohno T, Yanagida Y, Ishikawa F, Uesugi S, Katahira M. Structure and interactions with RNA of the N-terminal UUAG-specific RNA-binding domain of hnRNP D0. J Mol Biol. 1999 Mar 26;287(2):221-37. PMID:10080887
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