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1wtb

From Proteopedia

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Current revision

Complex structure of the C-terminal RNA-binding domain of hnRNP D (AUF1) with telomere DNA

Structural highlights

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

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 D, also known as AUF1, has two DNA/RNA-binding domains, each of which can specifically bind to single-stranded d(TTAGGG)n, the human telomeric repeat. Here, the structure of the C-terminal-binding domain (BD2) complexed with single-stranded d(TTAGGG) determined by NMR is presented. The structure has revealed that each residue of the d(TAG) segment is recognized by BD2 in a base-specific manner. The interactions deduced from the structure have been confirmed by gel retardation experiments with mutant BD2 and DNA. It is known that single-stranded DNA with the telomeric repeat tends to form a quadruplex and that the quadruplex has an inhibitory effect on telomere elongation by telomerase. This time it is revealed that BD2 unfolds the quadruplex of such DNA upon binding. Moreover, the effect of BD2 on the elongation by telomerase was examined in vitro. These results suggest the possible involvement of heterogeneous nuclear ribonucleoprotein D in maintenance of the telomere 3'-overhang either through protection of a single-stranded DNA or destabilization of the potentially deleterious quadruplex structure for the elongation by telomerase.

Structure of hnRNP D complexed with single-stranded telomere DNA and unfolding of the quadruplex by heterogeneous nuclear ribonucleoprotein D.,Enokizono Y, Konishi Y, Nagata K, Ouhashi K, Uesugi S, Ishikawa F, Katahira M J Biol Chem. 2005 May 13;280(19):18862-70. Epub 2005 Feb 24. PMID:15734733^[3]

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

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
↑ Enokizono Y, Konishi Y, Nagata K, Ouhashi K, Uesugi S, Ishikawa F, Katahira M. Structure of hnRNP D complexed with single-stranded telomere DNA and unfolding of the quadruplex by heterogeneous nuclear ribonucleoprotein D. J Biol Chem. 2005 May 13;280(19):18862-70. Epub 2005 Feb 24. PMID:15734733 doi:http://dx.doi.org/10.1074/jbc.M411822200

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/1wtb"

@@ Line 1: / Line 1: @@
 ==Complex structure of the C-terminal RNA-binding domain of hnRNP D (AUF1) with telomere DNA==
-<StructureSection load='1wtb' size='340' side='right' caption='[[1wtb]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='1wtb' size='340' side='right'caption='[[1wtb]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1wtb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WTB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WTB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1wtb]] is a 2 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=1WTB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WTB FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1iqt|1iqt]], [[1hd0|1hd0]], [[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=1wtb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wtb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wtb RCSB], [http://www.ebi.ac.uk/pdbsum/1wtb PDBsum]</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=1wtb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wtb OCA], [https://pdbe.org/1wtb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wtb RCSB], [https://www.ebi.ac.uk/pdbsum/1wtb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wtb ProSAT]</span></td></tr>
 </table>
 == 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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wt/1wtb_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wt/1wtb_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1wtb ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1wtb" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Nucleoprotein|Nucleoprotein]]
+*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
 == References ==
 <references/>
@@ Line 34: / Line 36: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Enokizono, Y]]
+[[Category: Large Structures]]
-[[Category: Ishikawa, F]]
+[[Category: Enokizono Y]]
-[[Category: Katahira, M]]
+[[Category: Ishikawa F]]
-[[Category: Konishi, Y]]
+[[Category: Katahira M]]
-[[Category: Nagata, K]]
+[[Category: Konishi Y]]
-[[Category: Ouhashi, K]]
+[[Category: Nagata K]]
-[[Category: Uesugi, S]]
+[[Category: Ouhashi K]]
-[[Category: Auf1]]
+[[Category: Uesugi S]]
-[[Category: Complex]]
-[[Category: Dna-binding domain]]
-[[Category: Hnrnp d]]
-[[Category: Rna-binding domain]]
-[[Category: Rrm]]
-[[Category: Structural genomic]]
-[[Category: Telomere]]
-[[Category: Transcription-dna complex]]

1wtb

From Proteopedia

Current revision

Complex structure of the C-terminal RNA-binding domain of hnRNP D (AUF1) with telomere DNA

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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